A high-continuity and annotated tomato reference genome.
BMC Genomics, 2021/12/15;22(1):898.
Su X[1], Wang B[1], Geng X[1], Du Y[1], Yang Q[1], Liang B[1], Meng G[1], Gao Q[2], Yang W[3], Zhu Y[4], Lin T[5]
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PMID: 34911432DOI: 10.1186/s12864-021-08212-x
Impact factor: 4.547
Abstract
background: Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development.
results: Here, we assembled an updated reference genome of S. lycopersicum cv. Heinz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes of S. lycopersicum and S. pimpinellifolium LA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. We also used a recombinant inbred line (RIL) population to generate a high-density genetic map with high resolution and accuracy. Using these resources, we identified a number of candidate genes that were likely to be related to important agronomic traits in tomato.
conclusion: Our results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology.
Keywords: QTL analysis; comparative genomics; de novo tomato genome; high-density genetic map
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