The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene familie...

在此，我们报道了康氏茄（Solanum commersonii）的基因组序列草案。该序列以马铃薯（Solanum tuberosum）基因组序列为参考构建，包含约830兆碱基（megabase），N50为44303碱基对（base pair, bp），并锚定到12条染色体（chromosome）上。与马铃薯相比，康氏茄的杂合度（heterozygosity）显著降低（1.5% vs. 53%至59%），基因组大小的差异主要源于基因间序列（intergenic sequence）长度的变异。通过从头预测（ab initio prediction）结合RNA-seq数据支持的基因注释，我们得到了一个包含1703个预测微小核糖核酸（microRNA）、18882个长链非编码核糖核酸（long noncoding RNA）（其中20%靶向冷响应基因）以及39290个蛋白编码基因（protein-coding gene）的目录。这些蛋白编码基因中包含大量非冗余核苷酸结合位点编码基因，以及126个马铃薯中缺失的冷相关基因。系统发育分析（phylogenetic analysis）表明，栽培马铃薯与康氏茄的谱系在约230万年前发生分化。三个复制时期对应于特定基因家族的基因组富集……