ArticlePloS one2011
First survey of the wheat chromosome 5A composition through a next generation sequencing approach.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides.Plant biotechnology journal · 2018Article
- Article
- Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order.BMC genomics · 2017Article
- Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii.Frontiers in plant science · 2016Article
- Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides.Scientific reports · 2015Article
- The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements.BMC genomics · 2015Article
- Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes.BMC genomics · 2015Article
- New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing.Plant science : an international journal of experimental plant biology · 2015Article
- Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications.BMC genomics · 2014Article
- Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.The Plant journal : for cell and molecular biology · 2014Article
- New wheat microRNA using whole-genome sequence.Functional & integrative genomics · 2014Article
- Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Next-generation survey sequencing and the molecular organization of wheat chromosome 6B.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution.Genome biology · 2013Article
- Article
- Flow sorting and sequencing meadow fescue chromosome 4F.Plant physiology · 2013Article
- Identification of new stress-induced microRNA and their targets in wheat using computational approach.Plant signaling & behavior · 2013Article
- Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting.BMC genomics · 2013Article
- Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat.BMC genomics · 2013Article
- Wheat Zapper: a flexible online tool for colinearity studies in grass genomes.Functional & integrative genomics · 2013Article
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Wheat is one of the world's most important crops and is characterized by a large polyploid genome. One way to reduce genome complexity is to isolate single chromosomes using flow cytometry. Low coverage DNA sequencing can provide a snapshot of individual chromosomes, allowing a fast characterization of their main features and comparison with other genomes. We used massively parallel 454 pyrosequencing to obtain a 2x coverage of wheat chromosome 5A. The resulting sequence assembly was used to identify TEs, genes and miRNAs, as well as to infer a virtual gene order based on the synteny with other grass genomes. Repetitive elements account for more than 75% of the genome. Gene content was estimated considering non-redundant reads showing at least one match to ESTs or proteins. The results indicate that the coding fraction represents 1.08% and 1.3% of the short and long arm respectively, projecting the number of genes of the whole chromosome to approximately 5,000. 195 candidate miRNA precursors belonging to 16 miRNA families were identified. The 5A genes were used to search for syntenic relationships between grass genomes. The short arm is closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; the long arm to regions of Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosomes 9 and 3. From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome.
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