Background The finger lime (Citrus australasica), one of six Australian endemic citrus species sh... more Background The finger lime (Citrus australasica), one of six Australian endemic citrus species shows a high natural phenotypic diversity and novel characteristics. The wide variation and unique horticultural features have made this lime an attractive candidate for domestication. Currently no haplotype resolved genome is available for this species. Here we present a high quality, haplotype-resolved reference genome for this species using PacBio HiFi and Hi-C sequencing. Results Hifiasm assembly and SALSA scaffolding resulted in a collapsed genome size of 344.2 Mb and 321.1 Mb and 323.2 Mb size for the two haplotypes. The nine pseudochromosomes of the collapsed genome had an N50 of 35.2 Mb, 99.1% genome assembly completeness and 98.9% gene annotation completeness (BUSCO). A total of 41,304 genes were predicted in the nuclear genome. Comparison with C. australis revealed that 13,661 genes in pseudochromosomes were unique in C. australasica. These were mainly involved in plant-pathogen interactions, stress response, cellular metabolic and developmental processes, and signal transduction. The two genomes showed a syntenic arrangement at the chromosome level with large structural rearrangements in some chromosomes. Genetic variation among five C. australasica cultivars was analysed. Genes related to defense, synthesis of volatile compounds and red/yellow coloration were identified in the genome. A major expansion of genes encoding thylakoid curvature proteins was found in the C. australasica genome. Conclusions The genome of C. australasica present in this study is of high quality and contiguity. This genome helps deepen our understanding of citrus evolution and reveals disease resistance and quality related genes with potential to accelerate the genetic improvement of citrus.
bioRxiv (Cold Spring Harbor Laboratory), Dec 7, 2023
Macadamia, a genus native to Eastern Australia, comprises four species, Macadamia integrifolia, M... more Macadamia, a genus native to Eastern Australia, comprises four species, Macadamia integrifolia, M. tetraphylla, M. ternifolia, and M. jansenii. Macadamia was recently domesticated largely from a limited gene pool of Hawaiian germplasm and has become a commercially significant nut crop. Disease susceptibility and climate adaptability challenges, highlight the need for use of a wider range of genetic resources for macadamia production. High quality haploid resolved genome assemblies were generated using HiFiasm to allow comparison of the genomes of the four species. Assembly sizes ranged from 735 Mb to 795 Mb and N50 from 53.7 Mb to 56 Mb, indicating high assembly continuity with most of the chromosomes covered telomere to telomere. Repeat analysis revealed that approximately 1 61% of the genomes were repetitive sequence. The BUSCO completeness scores ranged from 1 95.0% to 98.9%, confirming good coverage of the genomes. Gene prediction identified 37198 1 to 40534 genes. The ks distribution plot of Macadamia and Telopea suggests Macadamia has 1 undergone a whole genome duplication event prior to divergence of the four species and that 1 Telopea genome was duplicated more recently. Synteny analysis revealed a high 1 conservation and similarity of the genome structure in all four species. Differences in the 1 content of genes of fatty acid and cyanogenic glycoside biosynthesis were found between the 1 species. An antimicrobial gene with a conserved cysteine motif was found in all four species.
bioRxiv (Cold Spring Harbor Laboratory), Dec 7, 2023
The rice reference genome (Oryza sativa ssp. japonica cv. Nipponbare) has been an important resou... more The rice reference genome (Oryza sativa ssp. japonica cv. Nipponbare) has been an important resource in plant science. We now report an improved and haplotype resolved genome sequence based upon more accurate sequencing technology. This improved assembly includes regions missing in earlier genomes sequences and the annotation of more than 3,000 new genes due to greater sequence accuracy. .
Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing.... more Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin mapping (Hi-C). We report here a telomere-to-telomere chromosome-level mango genome using only PacBio HiFi long reads. HiFi reads at high coverage (204X) resulted in the assembly of 17 chromosomes each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs with telomeres at one end and ribosomal repeats at the other end. Analysing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomereto-telomere. The assembled genome was 365 Mb with 100% completeness as assessed by BUSCO analysis. The haplotypes assembled demonstrated extensive structural differences. This approach may be useful for assembling telomere-to-telomere and haplotype-resolved genomes for many other plants. Main High-quality reference genomes and annotations are fundamental to characterize structural, and functional variations in genomes and to explore the mechanisms of important traits facilitating modern molecular breeding. As a result of the development and continued improvement of single-molecule long-read sequencing technologies, we can now assemble highly accurate telomere-totelomere (T2T) genomes. The era of de novo genome assembly began with Sanger sequencing, whereas the rst assembled eukaryotic genome was Saccharomyces cerevisiae in 1996[1]. Subsequently, genomes of many other species were assembled including rice[2], maize[3], Arabidopsis[4], and human[5]. Subsequent advances in next-generation sequencing have further improved the plant genome assemblies, while they still exhibited thousands of gaps within the pseudomolecules, primarily due to the high prevalence of repetitive sequences and limitations in read lengths (75-300bp)[6, 7] The continuous long-read (CLR) sequencing and nanopore sequencing developed by Paci c Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), respectively revolutionized genome analysis. They may generate long reads (> 10kb), spanning numerous repetitive elements within genomes. However, these technologies had comparatively higher error rates (5-20%). Enhancements in read accuracy of nanopore sequencing (up to 95-99%)[8] and the introduction of PacBio High Fidelity (HiFi) sequencing capable of generating 99.9% accurate long reads (15-25kb)[9] established these technologies as the gold standard for generating high-quality genomes. These new long-read sequencing technologies have resulted in enhanced quality and contiguity of assemblies for both model organisms and plants with complex genomes[10, 11]. However, the long-read data are often complemented with other techniques such as optical mapping, chromatin conformation capture (Hi-C), genetic maps, or hybrid approaches to scaffold and orient the contigs to reach chromosome-scale T2T genomes[12]. With the recent release of T2T assembly of human X chromosome[13], the rst T2T human genome was released, which used a combination of nanopore sequencing, HiFi sequencing, linked read sequencing from 10X Genomics, and optical mapping[14]. In recent years, T2T assembled genomes have been reported for various plant species, including rice[15], maize[6], banana[7, 16], kiwifruit[17], and watermelon[18] by using scaffolding methods to assembly contigs from long-read sequences to chromosome level. A recent banana genome used nanopore long reads plus Illumina short reads[7], while the other banana genome assembly has incorporated HiFi and nanopore reads along with Hi-C data[16]. T2T genome assemblies for rice[15] and watermelon[18] have used HiFi, nanopore reads and Hi-C data, whereas the maize genome[6] has used Illumina reads together with both long-read sequencing approaches.
The genus Mangifera (Anacardiaceae) includes 69 species of which Mangifera indica L. is the most ... more The genus Mangifera (Anacardiaceae) includes 69 species of which Mangifera indica L. is the most important and primarily cultivated species for commercial mango production. Although the species are classified based on morphological descriptors, molecular evidence has proposed the hybrid origin of two species suggesting the possibility that more of the species may be of hybrid origin. To analyze evolutionary relationships within the genus, 13 samples representing 11 Mangifera species were sequenced and whole chloroplast (Cp) genomes and 47 common single-copy nuclear gene sequences were assembled and used for phylogenetic analysis using concatenation and coalescence-based methods. The Cp genome size varied from 151,752 to 158,965 bp with M. caesia and M. laurina having the smallest and largest genomes, respectively. Genome annotation revealed 80 protein-coding genes, 31 tRNA and four rRNA genes across all the species. Comparative analysis of whole Cp genome sequence and nuclear gene-based phylogenies revealed topological conflicts suggesting chloroplast capture or cross hybridization. The Cp genomes of M. altissima, M. applanata, M. caloneura and M. lalijiwa were similar to those of M. indica (99.9% sequence similarity). Their close sequence relationship suggests a common ancestry and likely cross-hybridization between wild relatives and M. indica. This study provides improved knowledge of phylogenetic relationships in Mangifera, indicating extensive gene flow among the different species, suggesting that hybrids may be common within the genus.
This association study of Eucalyptus pilularis populations provides empirical evidence for the ro... more This association study of Eucalyptus pilularis populations provides empirical evidence for the role of Pectin Methylesterase (PME) in influencing solid wood characteristics of Eucalyptus. PME6 was primarily associated with the shrinkage and collapse of drying timber, which are phenotypic traits consistent with the role of pectin as a hydrophilic polysaccharide. PME7 was primarily associated with cellulose and pulp yield traits and had an inverse correlation with lignin content. Selection of specific alleles in these genes may be important for improving trees as sources of high-quality wood products. A heterozygote advantage was postulated for the PME7 loci and, in combination with haplotype blocks, may explain the absence of a homozygous class at all single-nucleotide polymorphisms investigated in this gene.
Magnolia grandiflora is an important medicinal, ornamental and horticultural plant species. The c... more Magnolia grandiflora is an important medicinal, ornamental and horticultural plant species. The chloroplast (cp) genome of M. grandiflora was sequenced using a 454 sequencing platform and the genome structure was compared with other related species. The complete cp genome of M. grandiflora was 159623 bp in length and contained a pair of inverted repeats (IR) of 26563 bp separated by large and small single copy (LSC, SSC) regions of 87757 and 18740 bp, respectively. A total of 129 genes were successfully annotated, 18 of which included introns. The identity, number and GC content of M. grandiflora cp genes were similar to those of other Magnoliaceae species genomes. Analysis revealed 218 simple sequence repeat (SSR) loci, most composed of A or T, contributing to a bias in base composition. The types and abundances of repeat units in Magnoliaceae species were relatively conserved and these loci will be useful for developing M. grandiflora cp genome vectors. In addition, results indicated that the cp genome size in Magnoliaceae species and the position of the IR border were closely related to the length of the ycf1 gene. Phylogenetic analyses based on 66 shared genes from 30 species using maximum parsimony (MP) and maximum likelihood (ML) methods provided strong support for the phylogenetic position of Magnolia. The availability of the complete cp genome sequence of M. grandiflora provides valuable information for breeding of desirable varieties, cp genetic engineering, developing useful molecular markers and phylogenetic analyses in Magnoliaceae.
Background: With high quantity and quality data production and low cost, next generation sequenci... more Background: With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. Results: The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution. Conclusions: Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology.
Salinity considerably lowers crop yield worldwide. Production of salt stress-tolerant species wil... more Salinity considerably lowers crop yield worldwide. Production of salt stress-tolerant species will be essential to maintain the food supply in the coming decades. Brassicas, including various members of the family Brassicaceae, are very necessary sources of human food. Importantly, the key crop species that are members of the Brassicaceae family are genetically diverse and therefore their response reaction and adaptation to salinity varies greatly. Canola (Brassica napus L.) is commonly grown for edible oils and other uses such as biodiesel fuel production. Although most types of canola are identified as salt-resistant, plant yield and development are reduced significantly by rising salinity levels. In saline situations, the plant's genome supports a range of physiological changes in some plant characteristics. Since the function of genes cannot indicate the exact condition of cells, proteomic approaches are emerged as methods to investigate the plant's responses to stresses in the molecular levels. Exploring the proteome complements research at the genome and transcriptome level and helps elucidate the mechanism of salt tolerance in plants. Proteins are reliable indicators of salinity responses, as they are directly involved in forming the new phenotype providing adaptation to salinity. In this chapter, we review the response of the rapeseed proteome to salinity stress.
IntroductionWheat is one of the most important staple crops worldwide, and an important source of... more IntroductionWheat is one of the most important staple crops worldwide, and an important source of human protein and mineral element intake. Continuously increasing stable production of wheat is critical for global food security under the challenge of population growth and limited resource input.ObjectiveSpike architecture determines the potential grain yield of wheat. However, the mechanisms of transcriptional regulation of spike architecture in wheat remain largely unknown, limiting further genetic improvement of wheat yield. In this study we explored the genetic basis of spike architecture in wheat.MethodsPopulation RNA-seq methods were used to identify the eQTLs and sQTLs associated with spike architecture and applied this to dissection of the genetic basis of gene expression and splicing controlling these complex yield-related traits.ResultsIn total, 4,143 expression quantitative trait loci (eQTLs) and 12,933 splice QTLs (sQTLs) were identified in wheat based on 178 RNA-seq samp...
Recently, a novel purple-pericarp super-sweetcorn line, ‘Tim1’ (A1A1.sh2sh2) is derived from the ... more Recently, a novel purple-pericarp super-sweetcorn line, ‘Tim1’ (A1A1.sh2sh2) is derived from the purple-pericarp maize ‘Costa Rica’ (A1Sh2.A1Sh2) and white shrunken2 (sh2) super-sweetcorn ‘Tims-white’ (a1sh2.a1sh2), however information regarding purple colour controlling anthocyanin biosynthesis genes and sweetcorn gene is lacking. Specific sequence differences in the CDS (coding DNA sequence) and promoter regions of the anthocyanin biosynthesis structural genes, anthocyanin1 (A1), purple aleurone1 (Pr1) and regulatory genes, purple plant1 (Pl1), plant colour1 (B1), coloured1 (R1), and the sweetcorn structural gene, shrunken2 (sh2) were investigated using the publicly available annotated yellow starchy maize, B73 (NAM5.0) as a reference genome. In the CDS region, the A1, Pl1 and R1 gene sequence differences of ‘Tim1’ and ‘Costa Rica’ were similar, as they control purple-pericarp pigmentation, however the B1 gene showed similarity between the ‘Tim1’ and ‘Tims-white’ lines, which may ...
The existence of purple-pericarp super-sweetcorn based on the most common supersweet mutation,shr... more The existence of purple-pericarp super-sweetcorn based on the most common supersweet mutation,shrunken2(sh2), has not been previously reported, partly due to its extremely tight genetic linkage to a non-functional anthocyanin biosynthesis gene,anthocyaninless1(a1). Generally, both aleurone- and pericarp-pigmented purple corn is starchy, the latter of which contains significantly higher anthocyanin compared to the former. The development of purple-pericarp super-sweetcorn is dependent on breaking thea1-sh2tight genetic linkage, which occurs at a very low frequency of <1 in 1000 meiotic crossovers. Here, to develop purple-pericarp super-sweetcorn, an initial cross between a male purple-pericarp maize (purple-round seed), ‘Costa Rica’ (A1Sh2.A1Sh2) and a female whiteshrunken2super-sweetcorn (white-shrunken seed), ‘Tims-white’ (a1sh2.a1sh2), was conducted. Subsequent self-pollination based on purple-pericarp-shrunken kernels identified a small frequency (0.08%) of initial heterozygou...
Domestication syndrome, i.e. seed shattering, seed dormancy and plant architecture have been sele... more Domestication syndrome, i.e. seed shattering, seed dormancy and plant architecture have been selected during the domestication of wild rice around 10,000 years ago. These traits evolved through a series of genomic modifications, including selection of nucleotide polymorphisms resulting from spontaneous mutations, recombination, and fixation of alleles and were incorporated into cultivated rice by hybridization or introgression. The Australian wild rice populations are geographically and genetically distinct and free from genetic exchange with cultivated rice unlike the wild populations in Asia. Furthermore, recent studies reveal they have numerous traits of value and unique alleles. Therefore, these populations seem to be suitable to use to investigate the genetic basis of domestication traits as well as other important traits. In this study, we aim to determine the origin and role of domestication loci using two Australian wild populations: Taxa A (like Oryza rufipogon) and Taxa B ...
Sugarcane is a crop of unequivocal importance which can meet requirements for food, feed fiber an... more Sugarcane is a crop of unequivocal importance which can meet requirements for food, feed fiber and fuel. This crop, with a large wealth of genetic resources and a rich breeding history, has only a very nascent genomic history with a monoploid genome sequence. Numerous efforts are underway to unravel the mysteries of this complex crop with advances in sequencing technologies. Efforts to capture the functional part of the genome using transcriptomic studies have long been a priority. R570, a French cultivar has been the most suitable material for many sugarcane genomics studies. In an attempt to utilize the revolutionary technology of long read sequencing, we have carried out isoform sequencing of this representative cultivar with a Pac Bio sequel I system. Recently we have compared sequel II data of the same cultivar from various vegetative and reproductive tissues. A greater sequencing depth may benefit the sugarcane fraternity with a more complete transcriptome and accurate gene an...
AimTo fill knowledge gaps regarding the distributions, ecogeographic niches and conservation stat... more AimTo fill knowledge gaps regarding the distributions, ecogeographic niches and conservation status of sorghum's wild relatives (Sorghum Moench).LocationThe study covered the potential native ranges of wild Sorghum taxa worldwide, including Australia, New Guinea, Asia, Africa and Central America.MethodsWe modelled the distributions of 23 wild Sorghum taxa, characterized their ecogeographic niches, assessed their conservation status both ex situ and in situ and performed preliminary threat assessments.ResultsThree taxa were categorized as “high priority” for further conservation based on their ex situ and in situ assessments, with a further 19 as “medium priority” and only one as “low priority”. The preliminary threat assessment indicated that 12 taxa may be Endangered, four Vulnerable and four Near Threatened. The taxa fill a wide range of climatic niches, both across and within taxa, including temperatures and precipitation.Main conclusionsTaxon richness hotspots, especially in...
Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which ... more Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts (Eucalyptus, Corymbia and Angophora; ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora, anchored into eleven chromosomes. Comparative analysis with Eucalyptus grandis reveals high synteny, although the two diverged approximately 60 million years ago and have different genome sizes (408 vs 641 Mb), with few large intra-chromosomal rearrangements. C. citriodora shares an ancient whole-genome duplication event with E. grandis but has undergone tandem gene family expansions related to terpene biosynthesis, innate pathogen resistance, and leaf wax formation, enab...
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. All studies published in MOLECULAR PLANT are embargoed until 3PM ET of the day they are published as corrected proofs on-line. Studies cannot be publicized as accepted manuscripts or uncorrected proofs.
Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conse... more Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. GeSeq was applied to species related to coffee, including 16 species of the Coffea and Psilanthus genera to reconstruct the ancestral chloroplast genomes and to evaluate their phylogenetic relationships. Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. Notably, the two main cultivated coffee species (i.e. Arabica and Robusta) did not group into the same clade and differ in their pattern of gene evolution. While Arabica coffee (Coffea arabica) belongs to the Coffea genus, Robusta coffee (Coffea canephora) is associated with the Psilanthus genus. A more extensive survey of related species is required to determine if this is a unique attribute of Robusta coffee or a more widespread feature of coffee tree species.
Background The finger lime (Citrus australasica), one of six Australian endemic citrus species sh... more Background The finger lime (Citrus australasica), one of six Australian endemic citrus species shows a high natural phenotypic diversity and novel characteristics. The wide variation and unique horticultural features have made this lime an attractive candidate for domestication. Currently no haplotype resolved genome is available for this species. Here we present a high quality, haplotype-resolved reference genome for this species using PacBio HiFi and Hi-C sequencing. Results Hifiasm assembly and SALSA scaffolding resulted in a collapsed genome size of 344.2 Mb and 321.1 Mb and 323.2 Mb size for the two haplotypes. The nine pseudochromosomes of the collapsed genome had an N50 of 35.2 Mb, 99.1% genome assembly completeness and 98.9% gene annotation completeness (BUSCO). A total of 41,304 genes were predicted in the nuclear genome. Comparison with C. australis revealed that 13,661 genes in pseudochromosomes were unique in C. australasica. These were mainly involved in plant-pathogen interactions, stress response, cellular metabolic and developmental processes, and signal transduction. The two genomes showed a syntenic arrangement at the chromosome level with large structural rearrangements in some chromosomes. Genetic variation among five C. australasica cultivars was analysed. Genes related to defense, synthesis of volatile compounds and red/yellow coloration were identified in the genome. A major expansion of genes encoding thylakoid curvature proteins was found in the C. australasica genome. Conclusions The genome of C. australasica present in this study is of high quality and contiguity. This genome helps deepen our understanding of citrus evolution and reveals disease resistance and quality related genes with potential to accelerate the genetic improvement of citrus.
bioRxiv (Cold Spring Harbor Laboratory), Dec 7, 2023
Macadamia, a genus native to Eastern Australia, comprises four species, Macadamia integrifolia, M... more Macadamia, a genus native to Eastern Australia, comprises four species, Macadamia integrifolia, M. tetraphylla, M. ternifolia, and M. jansenii. Macadamia was recently domesticated largely from a limited gene pool of Hawaiian germplasm and has become a commercially significant nut crop. Disease susceptibility and climate adaptability challenges, highlight the need for use of a wider range of genetic resources for macadamia production. High quality haploid resolved genome assemblies were generated using HiFiasm to allow comparison of the genomes of the four species. Assembly sizes ranged from 735 Mb to 795 Mb and N50 from 53.7 Mb to 56 Mb, indicating high assembly continuity with most of the chromosomes covered telomere to telomere. Repeat analysis revealed that approximately 1 61% of the genomes were repetitive sequence. The BUSCO completeness scores ranged from 1 95.0% to 98.9%, confirming good coverage of the genomes. Gene prediction identified 37198 1 to 40534 genes. The ks distribution plot of Macadamia and Telopea suggests Macadamia has 1 undergone a whole genome duplication event prior to divergence of the four species and that 1 Telopea genome was duplicated more recently. Synteny analysis revealed a high 1 conservation and similarity of the genome structure in all four species. Differences in the 1 content of genes of fatty acid and cyanogenic glycoside biosynthesis were found between the 1 species. An antimicrobial gene with a conserved cysteine motif was found in all four species.
bioRxiv (Cold Spring Harbor Laboratory), Dec 7, 2023
The rice reference genome (Oryza sativa ssp. japonica cv. Nipponbare) has been an important resou... more The rice reference genome (Oryza sativa ssp. japonica cv. Nipponbare) has been an important resource in plant science. We now report an improved and haplotype resolved genome sequence based upon more accurate sequencing technology. This improved assembly includes regions missing in earlier genomes sequences and the annotation of more than 3,000 new genes due to greater sequence accuracy. .
Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing.... more Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin mapping (Hi-C). We report here a telomere-to-telomere chromosome-level mango genome using only PacBio HiFi long reads. HiFi reads at high coverage (204X) resulted in the assembly of 17 chromosomes each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs with telomeres at one end and ribosomal repeats at the other end. Analysing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomereto-telomere. The assembled genome was 365 Mb with 100% completeness as assessed by BUSCO analysis. The haplotypes assembled demonstrated extensive structural differences. This approach may be useful for assembling telomere-to-telomere and haplotype-resolved genomes for many other plants. Main High-quality reference genomes and annotations are fundamental to characterize structural, and functional variations in genomes and to explore the mechanisms of important traits facilitating modern molecular breeding. As a result of the development and continued improvement of single-molecule long-read sequencing technologies, we can now assemble highly accurate telomere-totelomere (T2T) genomes. The era of de novo genome assembly began with Sanger sequencing, whereas the rst assembled eukaryotic genome was Saccharomyces cerevisiae in 1996[1]. Subsequently, genomes of many other species were assembled including rice[2], maize[3], Arabidopsis[4], and human[5]. Subsequent advances in next-generation sequencing have further improved the plant genome assemblies, while they still exhibited thousands of gaps within the pseudomolecules, primarily due to the high prevalence of repetitive sequences and limitations in read lengths (75-300bp)[6, 7] The continuous long-read (CLR) sequencing and nanopore sequencing developed by Paci c Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), respectively revolutionized genome analysis. They may generate long reads (> 10kb), spanning numerous repetitive elements within genomes. However, these technologies had comparatively higher error rates (5-20%). Enhancements in read accuracy of nanopore sequencing (up to 95-99%)[8] and the introduction of PacBio High Fidelity (HiFi) sequencing capable of generating 99.9% accurate long reads (15-25kb)[9] established these technologies as the gold standard for generating high-quality genomes. These new long-read sequencing technologies have resulted in enhanced quality and contiguity of assemblies for both model organisms and plants with complex genomes[10, 11]. However, the long-read data are often complemented with other techniques such as optical mapping, chromatin conformation capture (Hi-C), genetic maps, or hybrid approaches to scaffold and orient the contigs to reach chromosome-scale T2T genomes[12]. With the recent release of T2T assembly of human X chromosome[13], the rst T2T human genome was released, which used a combination of nanopore sequencing, HiFi sequencing, linked read sequencing from 10X Genomics, and optical mapping[14]. In recent years, T2T assembled genomes have been reported for various plant species, including rice[15], maize[6], banana[7, 16], kiwifruit[17], and watermelon[18] by using scaffolding methods to assembly contigs from long-read sequences to chromosome level. A recent banana genome used nanopore long reads plus Illumina short reads[7], while the other banana genome assembly has incorporated HiFi and nanopore reads along with Hi-C data[16]. T2T genome assemblies for rice[15] and watermelon[18] have used HiFi, nanopore reads and Hi-C data, whereas the maize genome[6] has used Illumina reads together with both long-read sequencing approaches.
The genus Mangifera (Anacardiaceae) includes 69 species of which Mangifera indica L. is the most ... more The genus Mangifera (Anacardiaceae) includes 69 species of which Mangifera indica L. is the most important and primarily cultivated species for commercial mango production. Although the species are classified based on morphological descriptors, molecular evidence has proposed the hybrid origin of two species suggesting the possibility that more of the species may be of hybrid origin. To analyze evolutionary relationships within the genus, 13 samples representing 11 Mangifera species were sequenced and whole chloroplast (Cp) genomes and 47 common single-copy nuclear gene sequences were assembled and used for phylogenetic analysis using concatenation and coalescence-based methods. The Cp genome size varied from 151,752 to 158,965 bp with M. caesia and M. laurina having the smallest and largest genomes, respectively. Genome annotation revealed 80 protein-coding genes, 31 tRNA and four rRNA genes across all the species. Comparative analysis of whole Cp genome sequence and nuclear gene-based phylogenies revealed topological conflicts suggesting chloroplast capture or cross hybridization. The Cp genomes of M. altissima, M. applanata, M. caloneura and M. lalijiwa were similar to those of M. indica (99.9% sequence similarity). Their close sequence relationship suggests a common ancestry and likely cross-hybridization between wild relatives and M. indica. This study provides improved knowledge of phylogenetic relationships in Mangifera, indicating extensive gene flow among the different species, suggesting that hybrids may be common within the genus.
This association study of Eucalyptus pilularis populations provides empirical evidence for the ro... more This association study of Eucalyptus pilularis populations provides empirical evidence for the role of Pectin Methylesterase (PME) in influencing solid wood characteristics of Eucalyptus. PME6 was primarily associated with the shrinkage and collapse of drying timber, which are phenotypic traits consistent with the role of pectin as a hydrophilic polysaccharide. PME7 was primarily associated with cellulose and pulp yield traits and had an inverse correlation with lignin content. Selection of specific alleles in these genes may be important for improving trees as sources of high-quality wood products. A heterozygote advantage was postulated for the PME7 loci and, in combination with haplotype blocks, may explain the absence of a homozygous class at all single-nucleotide polymorphisms investigated in this gene.
Magnolia grandiflora is an important medicinal, ornamental and horticultural plant species. The c... more Magnolia grandiflora is an important medicinal, ornamental and horticultural plant species. The chloroplast (cp) genome of M. grandiflora was sequenced using a 454 sequencing platform and the genome structure was compared with other related species. The complete cp genome of M. grandiflora was 159623 bp in length and contained a pair of inverted repeats (IR) of 26563 bp separated by large and small single copy (LSC, SSC) regions of 87757 and 18740 bp, respectively. A total of 129 genes were successfully annotated, 18 of which included introns. The identity, number and GC content of M. grandiflora cp genes were similar to those of other Magnoliaceae species genomes. Analysis revealed 218 simple sequence repeat (SSR) loci, most composed of A or T, contributing to a bias in base composition. The types and abundances of repeat units in Magnoliaceae species were relatively conserved and these loci will be useful for developing M. grandiflora cp genome vectors. In addition, results indicated that the cp genome size in Magnoliaceae species and the position of the IR border were closely related to the length of the ycf1 gene. Phylogenetic analyses based on 66 shared genes from 30 species using maximum parsimony (MP) and maximum likelihood (ML) methods provided strong support for the phylogenetic position of Magnolia. The availability of the complete cp genome sequence of M. grandiflora provides valuable information for breeding of desirable varieties, cp genetic engineering, developing useful molecular markers and phylogenetic analyses in Magnoliaceae.
Background: With high quantity and quality data production and low cost, next generation sequenci... more Background: With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. Results: The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution. Conclusions: Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology.
Salinity considerably lowers crop yield worldwide. Production of salt stress-tolerant species wil... more Salinity considerably lowers crop yield worldwide. Production of salt stress-tolerant species will be essential to maintain the food supply in the coming decades. Brassicas, including various members of the family Brassicaceae, are very necessary sources of human food. Importantly, the key crop species that are members of the Brassicaceae family are genetically diverse and therefore their response reaction and adaptation to salinity varies greatly. Canola (Brassica napus L.) is commonly grown for edible oils and other uses such as biodiesel fuel production. Although most types of canola are identified as salt-resistant, plant yield and development are reduced significantly by rising salinity levels. In saline situations, the plant's genome supports a range of physiological changes in some plant characteristics. Since the function of genes cannot indicate the exact condition of cells, proteomic approaches are emerged as methods to investigate the plant's responses to stresses in the molecular levels. Exploring the proteome complements research at the genome and transcriptome level and helps elucidate the mechanism of salt tolerance in plants. Proteins are reliable indicators of salinity responses, as they are directly involved in forming the new phenotype providing adaptation to salinity. In this chapter, we review the response of the rapeseed proteome to salinity stress.
IntroductionWheat is one of the most important staple crops worldwide, and an important source of... more IntroductionWheat is one of the most important staple crops worldwide, and an important source of human protein and mineral element intake. Continuously increasing stable production of wheat is critical for global food security under the challenge of population growth and limited resource input.ObjectiveSpike architecture determines the potential grain yield of wheat. However, the mechanisms of transcriptional regulation of spike architecture in wheat remain largely unknown, limiting further genetic improvement of wheat yield. In this study we explored the genetic basis of spike architecture in wheat.MethodsPopulation RNA-seq methods were used to identify the eQTLs and sQTLs associated with spike architecture and applied this to dissection of the genetic basis of gene expression and splicing controlling these complex yield-related traits.ResultsIn total, 4,143 expression quantitative trait loci (eQTLs) and 12,933 splice QTLs (sQTLs) were identified in wheat based on 178 RNA-seq samp...
Recently, a novel purple-pericarp super-sweetcorn line, ‘Tim1’ (A1A1.sh2sh2) is derived from the ... more Recently, a novel purple-pericarp super-sweetcorn line, ‘Tim1’ (A1A1.sh2sh2) is derived from the purple-pericarp maize ‘Costa Rica’ (A1Sh2.A1Sh2) and white shrunken2 (sh2) super-sweetcorn ‘Tims-white’ (a1sh2.a1sh2), however information regarding purple colour controlling anthocyanin biosynthesis genes and sweetcorn gene is lacking. Specific sequence differences in the CDS (coding DNA sequence) and promoter regions of the anthocyanin biosynthesis structural genes, anthocyanin1 (A1), purple aleurone1 (Pr1) and regulatory genes, purple plant1 (Pl1), plant colour1 (B1), coloured1 (R1), and the sweetcorn structural gene, shrunken2 (sh2) were investigated using the publicly available annotated yellow starchy maize, B73 (NAM5.0) as a reference genome. In the CDS region, the A1, Pl1 and R1 gene sequence differences of ‘Tim1’ and ‘Costa Rica’ were similar, as they control purple-pericarp pigmentation, however the B1 gene showed similarity between the ‘Tim1’ and ‘Tims-white’ lines, which may ...
The existence of purple-pericarp super-sweetcorn based on the most common supersweet mutation,shr... more The existence of purple-pericarp super-sweetcorn based on the most common supersweet mutation,shrunken2(sh2), has not been previously reported, partly due to its extremely tight genetic linkage to a non-functional anthocyanin biosynthesis gene,anthocyaninless1(a1). Generally, both aleurone- and pericarp-pigmented purple corn is starchy, the latter of which contains significantly higher anthocyanin compared to the former. The development of purple-pericarp super-sweetcorn is dependent on breaking thea1-sh2tight genetic linkage, which occurs at a very low frequency of <1 in 1000 meiotic crossovers. Here, to develop purple-pericarp super-sweetcorn, an initial cross between a male purple-pericarp maize (purple-round seed), ‘Costa Rica’ (A1Sh2.A1Sh2) and a female whiteshrunken2super-sweetcorn (white-shrunken seed), ‘Tims-white’ (a1sh2.a1sh2), was conducted. Subsequent self-pollination based on purple-pericarp-shrunken kernels identified a small frequency (0.08%) of initial heterozygou...
Domestication syndrome, i.e. seed shattering, seed dormancy and plant architecture have been sele... more Domestication syndrome, i.e. seed shattering, seed dormancy and plant architecture have been selected during the domestication of wild rice around 10,000 years ago. These traits evolved through a series of genomic modifications, including selection of nucleotide polymorphisms resulting from spontaneous mutations, recombination, and fixation of alleles and were incorporated into cultivated rice by hybridization or introgression. The Australian wild rice populations are geographically and genetically distinct and free from genetic exchange with cultivated rice unlike the wild populations in Asia. Furthermore, recent studies reveal they have numerous traits of value and unique alleles. Therefore, these populations seem to be suitable to use to investigate the genetic basis of domestication traits as well as other important traits. In this study, we aim to determine the origin and role of domestication loci using two Australian wild populations: Taxa A (like Oryza rufipogon) and Taxa B ...
Sugarcane is a crop of unequivocal importance which can meet requirements for food, feed fiber an... more Sugarcane is a crop of unequivocal importance which can meet requirements for food, feed fiber and fuel. This crop, with a large wealth of genetic resources and a rich breeding history, has only a very nascent genomic history with a monoploid genome sequence. Numerous efforts are underway to unravel the mysteries of this complex crop with advances in sequencing technologies. Efforts to capture the functional part of the genome using transcriptomic studies have long been a priority. R570, a French cultivar has been the most suitable material for many sugarcane genomics studies. In an attempt to utilize the revolutionary technology of long read sequencing, we have carried out isoform sequencing of this representative cultivar with a Pac Bio sequel I system. Recently we have compared sequel II data of the same cultivar from various vegetative and reproductive tissues. A greater sequencing depth may benefit the sugarcane fraternity with a more complete transcriptome and accurate gene an...
AimTo fill knowledge gaps regarding the distributions, ecogeographic niches and conservation stat... more AimTo fill knowledge gaps regarding the distributions, ecogeographic niches and conservation status of sorghum's wild relatives (Sorghum Moench).LocationThe study covered the potential native ranges of wild Sorghum taxa worldwide, including Australia, New Guinea, Asia, Africa and Central America.MethodsWe modelled the distributions of 23 wild Sorghum taxa, characterized their ecogeographic niches, assessed their conservation status both ex situ and in situ and performed preliminary threat assessments.ResultsThree taxa were categorized as “high priority” for further conservation based on their ex situ and in situ assessments, with a further 19 as “medium priority” and only one as “low priority”. The preliminary threat assessment indicated that 12 taxa may be Endangered, four Vulnerable and four Near Threatened. The taxa fill a wide range of climatic niches, both across and within taxa, including temperatures and precipitation.Main conclusionsTaxon richness hotspots, especially in...
Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which ... more Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts (Eucalyptus, Corymbia and Angophora; ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora, anchored into eleven chromosomes. Comparative analysis with Eucalyptus grandis reveals high synteny, although the two diverged approximately 60 million years ago and have different genome sizes (408 vs 641 Mb), with few large intra-chromosomal rearrangements. C. citriodora shares an ancient whole-genome duplication event with E. grandis but has undergone tandem gene family expansions related to terpene biosynthesis, innate pathogen resistance, and leaf wax formation, enab...
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. All studies published in MOLECULAR PLANT are embargoed until 3PM ET of the day they are published as corrected proofs on-line. Studies cannot be publicized as accepted manuscripts or uncorrected proofs.
Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conse... more Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. GeSeq was applied to species related to coffee, including 16 species of the Coffea and Psilanthus genera to reconstruct the ancestral chloroplast genomes and to evaluate their phylogenetic relationships. Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. Notably, the two main cultivated coffee species (i.e. Arabica and Robusta) did not group into the same clade and differ in their pattern of gene evolution. While Arabica coffee (Coffea arabica) belongs to the Coffea genus, Robusta coffee (Coffea canephora) is associated with the Psilanthus genus. A more extensive survey of related species is required to determine if this is a unique attribute of Robusta coffee or a more widespread feature of coffee tree species.
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