Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
| Autor: | Jason R. Miller, Kelly P. Steele, Nevin D. Young, Robert M. Stupar, Junqi Liu, Roxanne Denny, Thiruvarangan Ramaraj, Peng Zhou, Joseph Guhlin, Peter Tiffin, Joann Mudge, Kevin A. T. Silverstein, Andrew Farmer |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
DNA Copy Number Variations lcsh:QH426-470 lcsh:Biotechnology Pairwise Genome Comparison Biology Leucine-Rich Repeat Proteins Ortholog Group Genome Dispensable Genome Nucleotide diversity Short InDels Structural variation 03 medical and health sciences lcsh:TP248.13-248.65 Medicago truncatula Genetics Gene family Copy-number variation Gene Heat-Shock Proteins Plant Proteins 2. Zero hunger Comparative Genomic Hybridization High-Throughput Nucleotide Sequencing Proteins food and beverages Sequence Analysis DNA biology.organism_classification Syntenic Block lcsh:Genetics 030104 developmental biology RNA Plant Sequence Alignment Genome Plant Reference genome Research Article Biotechnology |
| Zdroj: | BMC Genomics, Vol 18, Iss 1, Pp 1-14 (2017) BMC Genomics |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/s12864-017-3654-1 |
| Popis: | Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Results Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation. Conclusions Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3654-1) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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