A high-continuity and annotated tomato reference genome

Xiao Su; Baoan Wang; Xiaolin Geng; Yuefan Du; Qinqin Yang; Bin Liang; Ge Meng; Qiang Gao; Wencai Yang; Yingfang Zhu; Tao Lin

doi:10.1186/s12864-021-08212-x

A high-continuity and annotated tomato reference genome

BMC Genomics. 2021 Dec 15;22(1):898. doi: 10.1186/s12864-021-08212-x.

Authors

Xiao Su^#¹, Baoan Wang^#¹, Xiaolin Geng^#¹, Yuefan Du¹, Qinqin Yang¹, Bin Liang¹, Ge Meng¹, Qiang Gao², Wencai Yang³, Yingfang Zhu⁴, Tao Lin⁵

Affiliations

¹ State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China.
² Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
³ State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China. yangwencai@cau.edu.cn.
⁴ State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China. zhuyf@henu.edu.cn.
⁵ State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China. lintao35@cau.edu.cn.

^# Contributed equally.

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.

MeSH terms

Chromosome Mapping
Domestication
Genomics
Humans
Solanum lycopersicum* / genetics
Solanum* / genetics