Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation.
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ABSTRACT:
SUBMITTER: Wang L
PROVIDER: S-EPMC8664484 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.
| S-EPMC7416625 | biostudies-literature
Project description:Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research. Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research. Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research.
2021-08-20 | GSE169198 | GEO
Project description:BACKGROUND: Many plants have large and complex genomes with an abundance of repeated sequences. Many plants are also polyploid. Both of these attributes typify the genome architecture in the tribe Triticeae, whose members include economically important wheat, rye and barley. Large genome sizes, an abundance of repeated sequences, and polyploidy present challenges to genome-wide SNP discovery using next-generation sequencing (NGS) of total genomic DNA by making alignment and clustering of short reads generated by the NGS platforms difficult, particularly in the absence of a reference genome sequence. RESULTS: An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions from repetitive sequences and sequences shared by paralogous genes. Multiple genome equivalents of shotgun reads of another genotype generated with SOLiD or Solexa are then mapped to the annotated Roche 454 reads to identify putative SNPs. A pipeline program package, AGSNP, was developed and used for genome-wide SNP discovery in Aegilops tauschii-the diploid source of the wheat D genome, and with a genome size of 4.02 Gb, of which 90% is repetitive sequences. Genomic DNA of Ae. tauschii accession AL8/78 was sequenced with the Roche 454 NGS platform. Genomic DNA and cDNA of Ae. tauschii accession AS75 was sequenced primarily with SOLiD, although some Solexa and Roche 454 genomic sequences were also generated. A total of 195,631 putative SNPs were discovered in gene sequences, 155,580 putative SNPs were discovered in uncharacterized single-copy regions, and another 145,907 putative SNPs were discovered in repeat junctions. These SNPs were dispersed across the entire Ae. tauschii genome. To assess the false positive SNP discovery rate, DNA containing putative SNPs was amplified by PCR from AL8/78 and AS75 and resequenced with the ABI 3730 xl. In a sample of 302 randomly selected putative SNPs, 84.0% in gene regions, 88.0% in repeat junctions, and 81.3% in uncharacterized regions were validated. CONCLUSION: An annotation-based genome-wide SNP discovery pipeline for NGS platforms was developed. The pipeline is suitable for SNP discovery in genomic libraries of complex genomes and does not require a reference genome sequence. The pipeline is applicable to all current NGS platforms, provided that at least one such platform generates relatively long reads. The pipeline package, AGSNP, and the discovered 497,118 Ae. tauschii SNPs can be accessed at (http://avena.pw.usda.gov/wheatD/agsnp.shtml).
| S-EPMC3041743 | biostudies-literature
Project description:Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete.
| S-EPMC3566107 | biostudies-literature
Project description:BackgroundThe common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics.ResultsHere we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 Gb size, with a contig N50 length of 6.37 Mb and a chromosomal scaffold N50 length of 143.91 Mb, representing the most contiguous and high-quality marmoset genome up to date. Approximately 90% of the assembled genome was represented in contigs longer than 1 Mb, with approximately 104-fold improvement in contiguity over the previously published marmoset genome. More than 98% of the gaps from the previously published genomes were filled successfully, which improved the mapping rates of genomic and transcriptomic data on to the assembled genome.ConclusionsAltogether the updated, high-quality common marmoset genome assembly provide improvements at various levels over the previous versions of the marmoset genome assemblies. This will allow researchers working on primate genomics to apply the genome more efficiently for their genomic and transcriptomic sequence data.
| S-EPMC7114785 | biostudies-literature
Project description:Numerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTL mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTL mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTL were not distributed homogeneously along chromosome arms. Their frequencies increased in the proximal-to-distal direction but declined in the most distal regions and were weakly correlated with recombination rates along the chromosome arms. Databases for projected SSR markers and QTL were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTL were used to estimate standard deviations ([Formula: see text]) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations [Formula: see text] were modeled as an exponential decay function of recombination rates along the Ae. tauschii chromosomes. We implemented four hypothesis tests for determining the membership of query QTL. The hypothesis tests and estimation procedure for [Formula: see text] were implemented in a web portal for meta-analysis of projected QTL. Twenty-one QTL for Fusarium head blight resistance mapped on wheat chromosomes 3A, 3B, and 3D were analyzed to illustrate the use of the portal for meta-QTL analyses.
| S-EPMC6404623 | biostudies-literature
Project description:As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant wheat varieties.
| S-EPMC4855405 | biostudies-literature
Project description:The D-genome progenitor of wheat (Triticum aestivum), Aegilops tauschii, possesses numerous genes for resistance to abiotic stresses, including drought. Therefore, information on the genetic architecture of A. tauschii can aid the development of drought-resistant wheat varieties. Here, we evaluated 13 traits in 373 A. tauschii accessions grown under normal and polyethylene glycol-simulated drought stress conditions and performed a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers. We identified 208 and 28 SNPs associated with all traits using the general linear model and mixed linear model, respectively, while both models detected 25 significant SNPs with genome-wide distribution. Public database searches revealed several candidate/flanking genes related to drought resistance that were grouped into three categories according to the type of encoded protein (enzyme, storage protein, and drought-induced protein). This study provided essential information for SNPs and genes related to drought resistance in A. tauschii and wheat, and represents a foundation for breeding drought-resistant wheat cultivars using marker-assisted selection.
| S-EPMC5004832 | biostudies-other
Project description:Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.
| S-EPMC6240028 | biostudies-literature
Project description:Aegilops tauschii is the D-genome progenitor of hexaploid wheat (Triticum aestivum). It is considered to be an important source of genetic variation for wheat breeding, and its genome is an invaluable reference for wheat genomics. We conducted a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers across 322 diverse accessions of Ae. tauschii that were systematically phenotyped for 29 morphological traits in order to identify marker-trait associations and candidate genes, assess genetic diversity, and classify the accessions based on phenotypic data and genotypic comparison. Using the general linear model and mixed linear model, we identified a total of 18 SNPs significantly associated with 10 morphological traits. Systematic search of the flanking sequences of trait-associated SNPs in public databases identified several genes that may be linked to variations in phenotypes. Cluster analysis using phenotypic data grouped accessions into four clusters, while accessions in the same cluster were not from the same Ae. tauschii subspecies or from the same area of origin. This work establishes a fundamental research platform for association studies in Ae. tauschii and also provides useful information for understanding the genetic mechanism of agronomic traits in wheat.
| S-EPMC4622089 | biostudies-literature