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A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant 被引量:17
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作者 Qingzhen Wei Jinglei Wang +3 位作者 Wuhong Wang Tianhua Hu Haijiao Hu chonglai bao 《Horticulture Research》 SCIE 2020年第1期806-820,共15页
Eggplant(Solanum melongena L.)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 eg... Eggplant(Solanum melongena L.)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~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%).The S.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 singlenucleotide 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 the S.melongena-HQ reference genome and detected a QTL interval of 71.29–78.26 Mb on chromosome E03.The gene Smechr0301963,which belongs to the SUN gene 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 http://eggplant-hq.cn.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. 展开更多
关键词 TRAITS linkage assembly
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