Chloroplast Genomes and Comparative Analyses among Thirteen Taxa within Myrsinaceae s.str. Clade (Myrsinoideae, Primulaceae)
Chloroplast Genomes and Comparative Analyses among Thirteen Taxa within Myrsinaceae s.str. Clade (Myrsinoideae, Primulaceae)
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紫金牛科 13 个类群叶绿体基因组及比较分析
DOI：
10.3390/ijms20184534
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发表时间：
2019-09-02
影响因子：
5.6
通讯作者：
Hao, Gang
中科院分区：
文献类型：
--
作者：
Yan, Xiaokai;Liu, Tongjian;Hao, Gang
紫薇科。报春花科报春花总科的热带木本代表枝，现有约1300种。由于以前的研究中遗传标记和/或分类单元样本数量有限，该分支的属界和排列尚不清楚。本文对紫薇科13个分类群的叶绿体基因组进行了分析。对进化支进行了测序和特征分析。这些cp基因组是典型的四分圆分子，在大小和基因含量上高度保守。鉴定出3个假基因，其中ycf15在5个分类群中完全缺失。非编码区和大单拷贝区（LSC）比其他区域具有更高的核苷酸多样性（Pi）。在所有cp基因组中共发现10个热点片段和796个SSR位点。系统发育分析的结果支持单系紫薇科植物的观点。进化支有两个亚进化支。内务（HK）基因的非同义取代率（dN）高于光合（PS）基因，但两者具有几乎相同的同义取代率（dS）。结果表明，与HK基因相比，PS基因受到更强的功能约束。该研究为紫金桃科植物的系统发育重建提供了高变分子标记，有助于更好地理解紫金桃科植物质体基因的进化。进化枝。
The Myrsinaceae s.str. clade is a tropical woody representative in Myrsinoideae of Primulaceae and has ca. 1300 species. The generic limits and alignments of this clade are unclear due to the limited number of genetic markers and/or taxon samplings in previous studies. Here, the chloroplast (cp) genomes of 13 taxa within the Myrsinaceae s.str. clade are sequenced and characterized. These cp genomes are typical quadripartite circle molecules and are highly conserved in size and gene content. Three pseudogenes are identified, of which ycf15 is totally absent from five taxa. Noncoding and large single copy region (LSC) exhibit higher levels of nucleotide diversity (Pi) than other regions. A total of ten hotspot fragments and 796 chloroplast simple sequence repeats (SSR) loci are found across all cp genomes. The results of phylogenetic analysis support the notion that the monophyletic Myrsinaceae s.str. clade has two subclades. Non-synonymous substitution rates (dN) are higher in housekeeping (HK) genes than photosynthetic (PS) genes, but both groups have a nearly identical synonymous substitution rate (dS). The results indicate that the PS genes are under stronger functional constraints compared with the HK genes. Overall, the study provides hypervariable molecular markers for phylogenetic reconstruction and contributes to a better understanding of plastid gene evolution in Myrsinaceae s.str. clade.