A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant
文献类型： 外文期刊
作者： Wei, Qingzhen 1 ; Wang, Jinglei 1 ; Wang, Wuhong 1 ; Hu, Tianhua 1 ; Hu, Haijiao 1 ; Bao, Chonglai 1 ;
作者机构： 1.Zhejiang Acad Agr Sci, Inst Vegetable Res, Hangzhou 30021, Peoples R China
期刊名称：HORTICULTURE RESEARCH （ 影响因子：6.793； 五年影响因子：6.589 ）
ISSN： 2662-6810
年卷期： 2020 年 7 卷 1 期
页码：
收录情况： SCI
摘要： Eggplant (Solanum melongenaL.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of similar to 1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). TheS. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using theS. melongena-HQ reference genome and detected a QTL interval of 71.29-78.26 Mb on chromosome E03. The geneSmechr0301963, which belongs to theSUNgene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.
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