菱叶绣线菊彩叶园艺品种‘粉霜’和‘黄金喷泉’的叶绿体基因组研究

Chloroplast Genome Analyses of Spiraea × vanhouttei ‘Pink Ice’ and ‘Gold Fountain’

摘要:

基于菱叶绣线菊(Spiraea×vanhouttei)培育出了很多的彩叶园艺品种，其中‘粉霜’彩叶绣线菊(‘Pink Ice’)和‘黄金喷泉’菱叶绣线菊(‘Gold Fountain’)是两个性状优良的品种，这两个彩叶品种的形成机制尚缺乏深入研究。该研究基于二代测序的浅层测序技术，对‘粉霜’和‘黄金喷泉’的叶绿体基因组进行组装、注释、绘制其叶绿体基因组图谱；结合网上已有的绣线菊属植物的叶绿体全基因组开展比较基因组学研究。结果表明，两个品种的叶绿体基因组均为典型的四分体结构，即含有1个LSC、1个SSC及2个IR；‘粉霜’和‘黄金喷泉’的叶绿体基因组大小分别为155 953和155 941 bp，各含有130个基因，包括85个蛋白编码基因，37个转运RNA基因和8个核糖体RNA基因；分别含有67、69个简单重复序列，其中，单核苷酸重复序列最多。筛选出这两个叶绿体基因组内7个高变异区域，分别为trnH_GUG-psbA、trnK_UUU、trnR_UCU-atpA、trnT_ GCU-psbD、ndhC、rpl32、ycf1。菱叶绣线菊、‘粉霜’和‘黄金喷泉’虽有非常近缘的关系，但并未聚成单系。该研究首次获得了两种绣线菊属彩叶品种的叶绿体基因组，为进一步理解绣线菊属及其彩叶园艺品种的亲缘关系提供了大量有用信息，并为今后该属更多园艺资源的发掘奠定了基础。

Abstract:

Several foliage horticultural varieties have been bred based on Spiraea × vanhouttei, including ‘Pink Ice’ and ‘Gold Fountain’, which exhibit excellent horticultural traits. However, the underlying mechanism of these two colorful leaf varieties remain poorly understood. To address this knowledge gap, the complete chloroplast genomes of ‘Pink Ice’ and ‘Gold Fountain’ were assembled by using genome skimming sequencing. Comparative genomic analysis of all available chloroplast genomes of the genus Spiraea to date was studied, including variation hotspot analysis, simple repetitive sequence analysis, and phylogenetic analysis. The results showed that both varieties had a typical quadripartite structure, consisting of one LSC, one SSC, and two IRs. The chloroplast genomes of ‘Pink Ice’ and ‘Gold Fountain’ were 155 953 and 155 941 bp in size, respectively, and each contains 130 genes, including 85 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. The two chloroplast genomes also contained 67 and 69 simple repetitive sequences, respectively, with single nucleotide repeat sequences being the most abundant. There were seven highly variable regions within these two chloroplast genomes, including trnH_GUG-psbA, trnK_UUU, trnR_UCU-atpA, trnT_GCU-psbD, ndhC, rpl32, and ycf1. Finally, phylogenetic analysis revealed that ‘Pink Ice’ and ‘Gold Fountain’ could not be considered a monophyletic group, despite their close relationship. Overall, these would provide valuable insights into the chloroplast genomes of two foliage varieties of Spiraea, which would aid in the development of more horticultural resources for this genus in the future.