A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution
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DOI：
10.1038/s41598-019-47985-w
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发表时间：
2019-08-13
影响因子：
4.6
通讯作者：
Rotino, Giuseppe Leonardo
中科院分区：
文献类型：
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作者：
Barchi, Lorenzo;Pietrella, Marco;Rotino, Giuseppe Leonardo
多刺茄属植物约有 450 个物种，是茄科中最大的单系类群，但目前缺少该类群的高质量基因组组装。我们获得了茄子（Solanum melongena）的染色体锚定基因组组装，包含34,916个基因，证实茄科二倍体基因数量约为35,000个。对番茄 (S. lycopersicum)、马铃薯 (S. tuberosum) 和辣椒 (Capsicum annuum) 的比较基因组研究强调了茄科中 miRNA:mRNA 调控对和 R 型防御基因的快速进化，并为辣椒属中甾体配糖生物碱化合物的缺乏提供了基因组基础。使用简约方法，我们重建了主要茄科分支的关键创建者的假定染色体互补体以及导致现存物种及其祖先核型的重排。四个基因组中存在的 10% 至 15% 的基因是由前 γ、γ 和 T 古多倍体事件产生的同线性旁系同源物（ohnologs），并且富含转录因子。我们的数据表明，控制果实成熟的基本基因网络在不同的茄科分支中是保守的，并且更年期的果实成熟涉及该网络中相对较少的组成部分的差异调节，包括 CNR 和乙烯生物合成基因。
With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-gamma, gamma and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.