Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP.
Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP.
复制标题
DOI：
10.1038/srep16958
复制
发表时间：
2015-11-23
影响因子：
4.6
通讯作者：
Bailey CD
中科院分区：
文献类型：
--
作者：
Dugas DV;Hernandez D;Koenen EJ;Schwarz E;Straub S;Hughes CE;Jansen RK;Nageswara-Rao M;Staats M;Trujillo JT;Hajrah NH;Alharbi NS;Al-Malki AL;Sabir JS;Bailey CD
豆科植物因其结构重排和序列变异的多样性而成为研究被子植物质体组进化的模式。然而，大多数已知的豆类质体来自少数属，代表了蝶形花科亚科的一个谱系子集。我们调查的两个新测序的质体（印加和银合欢）和两个最近发表的质体（金合欢和Prosopis）的基础上，在亚科含羞草的质体进化，并讨论在其他豆科植物和rosid质体基因组的背景下的结果。含羞草质体具有典型的被子植物基因内容和一般组织，以及蛋白质编码基因进化的一般缓慢速率，但它们是豆科植物中已知最大的。增加的长度结果从串联重复扩增和一个不寻常的13 kb的IR-SSC边界移动金合欢和印加。拟态质体具有额外的有趣的功能，包括损失的clpP内含子1 Inga，加速的进化速度在clpP相思和Inga，和dN/dS的比例一致的中性和积极的选择几个基因。这些新的质体和结果为豆科植物比较基因组学、植物育种和质体基因工程提供了重要的资源，同时进一步阐明了豆科植物和被子植物质体进化的复杂性。
The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.