一个高连续性和注释的番茄参考基因组。

A high-continuity and annotated tomato reference genome.

机构信息

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.

Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.

出版信息

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

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.

背景

遗传和功能基因组学研究需要高质量的基因组组装。番茄（Solanum lycopersicum）是一种重要的园艺作物，是研究果实发育的理想模式物种。

结果

我们组装了一个更新的 Heinz 1706 番茄 cv.的参考基因组，长度为 799.09 Mb，包含 34,384 个预测的蛋白编码基因和 65.66%的重复序列。通过比较番茄和 S. pimpinellifolium LA2093 的基因组，我们发现了大量可能与人类选择相关的基因组片段，这些片段可能在番茄的驯化中发挥了关键作用。我们还使用重组自交系（RIL）群体生成了具有高分辨率和高精度的高密度遗传图谱。利用这些资源，我们鉴定了一些候选基因，这些基因可能与番茄的重要农艺性状有关。