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通过长读长测序对两个番茄祖先种，即醋栗番茄和樱桃番茄进行从头基因组组装。

De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum  lycopersicum var. cerasiforme, by long-read sequencing.

作者信息

Takei Hitomi, Shirasawa Kenta, Kuwabara Kosuke, Toyoda Atsushi, Matsuzawa Yuma, Iioka Shinji, Ariizumi Tohru

机构信息

Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.

Research Fellow of Japan Society for Promotion of Science (JSPS), Kojimachi, Tokyo 102-0083, Japan.

出版信息

DNA Res. 2021 Jan 19;28(1). doi: 10.1093/dnares/dsaa029.

DOI:10.1093/dnares/dsaa029
PMID:33475141
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7934570/
Abstract

The ancestral tomato species are known to possess genes that are valuable for improving traits in breeding. Here, we aimed to construct high-quality de novo genome assemblies of Solanum pimpinellifolium 'LA1670' and S. lycopersicum var. cerasiforme 'LA1673', originating from Peru. The Pacific Biosciences (PacBio) long-read sequences with 110× and 104× coverages were assembled and polished to generate 244 and 202 contigs spanning 808.8 Mbp for 'LA1670' and 804.5 Mbp for 'LA1673', respectively. After chromosome-level scaffolding with reference guiding, 14 scaffold sequences corresponding to 12 tomato chromosomes and 2 unassigned sequences were constructed. High-quality genome assemblies were confirmed using the Benchmarking Universal Single-Copy Orthologs and long terminal repeat assembly index. The protein-coding sequences were then predicted, and their transcriptomes were confirmed. The de novo assembled genomes of S. pimpinellifolium and S. lycopersicum var. cerasiforme were predicted to have 71,945 and 75,230 protein-coding genes, including 29,629 and 29,185 non-redundant genes, respectively, as supported by the transcriptome analysis results. The chromosome-level genome assemblies coupled with transcriptome data sets of the two accessions would be valuable for gaining insights into tomato domestication and understanding genome-scale breeding.

摘要

已知野生番茄物种拥有对改良育种性状有价值的基因。在此，我们旨在构建来自秘鲁的醋栗番茄‘LA1670’和樱桃番茄变种‘LA1673’的高质量从头基因组组装。对覆盖度为110倍和104倍的太平洋生物科学公司（PacBio）长读长序列进行组装和优化，分别生成了244个和202个重叠群，‘LA1670’的重叠群跨度为8.088亿碱基对，‘LA1673’的重叠群跨度为8.045亿碱基对。在参考引导下进行染色体水平的支架构建后，构建了对应于12条番茄染色体的14个支架序列和2个未分配序列。使用基准通用单拷贝直系同源基因和长末端重复序列组装指数对高质量基因组组装进行了验证。然后预测了蛋白质编码序列，并对其转录组进行了验证。转录组分析结果支持，醋栗番茄和樱桃番茄变种的从头组装基因组预计分别有71945个和75230个蛋白质编码基因，其中包括29629个和29185个非冗余基因。这两个种质的染色体水平基因组组装与转录组数据集相结合，将有助于深入了解番茄驯化过程并理解基因组规模的育种。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/e5f112444893/dsaa029f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/1f7f3ab86fd7/dsaa029f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/6ebcd79ef173/dsaa029f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/501b71263688/dsaa029f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/e5f112444893/dsaa029f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/1f7f3ab86fd7/dsaa029f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/6ebcd79ef173/dsaa029f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/501b71263688/dsaa029f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8db8/7934570/e5f112444893/dsaa029f4.jpg

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