A high-continuity and annotated tomato reference genome

BMC Genomics

Qiang Gao¹  Xiaolin Geng²  Wencai Yang²  Yuefan Du²  Baoan Wang²  Qinqin Yang²  Xiao Su²  Ge Meng²  Bin Liang²  Tao Lin²  Yingfang Zhu³ 

[1] Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University;State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University;State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University;

关键词: de novo tomato genome;    comparative genomics;    high-density genetic map;    QTL analysis;   

DOI  :  10.1186/s12864-021-08212-x

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown