Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family.
Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family.
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对两种活体菊科（毛茛目）物种的完整质体组测序揭示了不寻常的重排和 ndh 基因家族的丢失
DOI：
10.1186/s12864-017-3956-3
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发表时间：
2017-08-09
期刊：
影响因子：
4.4
通讯作者：
Wang H
中科院分区：
文献类型：
--
作者：
Sun Y;Moore MJ;Lin N;Adelalu KF;Meng A;Jian S;Yang L;Li J;Wang H
在早分化的13个科中，只有由Circaeaster和Kingdonia两个单型属组成的Circaeasteraceae （Ranunculales）缺乏已发表的完整质体序列。此外，Circaeasteraceae与Lardizabalaceae在系统发育上的姊妹地位仅在先前使用较小数据集的研究中得到微弱或中等程度的支持。此外，先前的质体体研究已经记录了早期分化的eudicots中一些新的结构重排。因此，对环菜科植物的质体体进行测序，对于更好地了解早分化菊科植物质体体的进化，以及进一步研究环菜科植物的系统发育位置具有重要意义。使用Illumina HiSeq 2000，对Circaeasteraceae的两个活成员：circaeasteragrestis和Kingdonia uniflora的完整质体进行了测序。比较了这两种质体的结构和基因含量，并与其他早分化的桉叶质体进行了比较。摘要对一组包含79个基因、99个分类群（包括早分化的所有科的样本）的数据进行了系统发育分析，以确定Circaeasteraceae的系统发育位置。这两个质体都具有典型的陆生植物质体的四分体结构。然而，在两个质体的大单拷贝区都发现了一个大的~49 kb的反转和一个小的~3.5 kb的反转，而Circaeaster具有许多其他重排，特别是在倒置重复中。此外，在英国发现infA是假基因，accD缺失，而在英国，除了ndhE和ndhJ外，所有ndh基因都是假基因（ΨndhA， ΨndhB， ΨndhD， ΨndhH和ΨndhK）或缺失（ndhC, ndhF， ndhI和ndhG）。在系统发育分析中，Circaeasteraceae与Lardizabalaceae是姊妹科。首次对Circaeasteraceae的质体组测序发现了一些不寻常的重排和ndh基因的缺失，并证实了Circaeasteraceae与Lardizabalaceae之间的姐妹关系。本研究为研究毛茛属植物早期分化的质体结构演化和更好地理解毛茛属植物内部的相互关系提供了新的视角。
Among the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae. Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora. Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses. The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales.
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作者：
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