Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats.
Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats.
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DOI：
10.1186/s12864-015-1498-0
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发表时间：
2015-04-17
期刊：
影响因子：
4.4
通讯作者：
Varotto C
中科院分区：
文献类型：
--
作者：
Hu S;Sablok G;Wang B;Qu D;Barbaro E;Viola R;Li M;Varotto C
质体基因组，也称为质体，是由选择力作用于它们编码的基本细胞功能而形成的，因此它们被期望保留不同植物物种在进化过程中所进行的适应性路径的特征。为了识别与适应不同生态位相关的正选择的分子特征，我们用Solexa技术对两种具有不同生境偏好的同属紫云英科物种，碎米荠和碎米荠的质体进行了测序。在深入表征质体组组织、重复模式和基因空间之后，新测序的质体彼此之间的比较以及与GenBank中可获得的15个完全测序的拟南芥科质体的比较揭示了碎米荠属谱系中IR边界的动态变化。我们进一步检测到的75个蛋白质编码基因的10个被检查的质体的正选择的签名，确定了一系列的叶绿体功能puperly参与家庭内的适应性过程。例如，在RUBISCO中发现的处于正选择下的三个残基可能参与调节RUBISCO聚集/活化和拟南芥科中的酶特异性。此外，我们的研究结果指出，在碎米荠塑性体的差异进化速率。总的来说，我们的结果支持在C. resedifolia，可能是适应高海拔环境的结果。我们进一步提供了第一个表征的选择性模式塑造的紫云英科质体，这可能有助于阐明在这个重要的植物家族的适应和进化的驱动力。本文的在线版本（doi：10.1186/s12864-015-1498-0）包含补充材料，可供授权用户使用。
Plastid genomes, also known as plastomes, are shaped by the selective forces acting on the fundamental cellular functions they code for and thus they are expected to preserve signatures of the adaptive path undertaken by different plant species during evolution. To identify molecular signatures of positive selection associated to adaptation to contrasting ecological niches, we sequenced with Solexa technology the plastomes of two congeneric Brassicaceae species with different habitat preference, Cardamine resedifolia and Cardamine impatiens. Following in-depth characterization of plastome organization, repeat patterns and gene space, the comparison of the newly sequenced plastomes between each other and with 15 fully sequenced Brassicaceae plastomes publically available in GenBank uncovered dynamic variation of the IR boundaries in the Cardamine lineage. We further detected signatures of positive selection in ten of the 75 protein-coding genes of the examined plastomes, identifying a range of chloroplast functions putatively involved in adaptive processes within the family. For instance, the three residues found to be under positive selection in RUBISCO could possibly be involved in the modulation of RUBISCO aggregation/activation and enzymatic specificty in Brassicaceae. In addition, our results points to differential evolutionary rates in Cardamine plastomes. Overall our results support the existence of wider signatures of positive selection in the plastome of C. resedifolia, possibly as a consequence of adaptation to high altitude environments. We further provide a first characterization of the selective patterns shaping the Brassicaceae plastomes, which could help elucidate the driving forces underlying adaptation and evolution in this important plant family. The online version of this article (doi:10.1186/s12864-015-1498-0) contains supplementary material, which is available to authorized users.
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影响因子：
6.9
作者：
Braukmann T;Kuzmina M;Stefanovic S
通讯作者：
Stefanovic S
DOI：
10.1073/pnas.0910097107
发表时间：
2010-01-05
影响因子：
11.1
作者：
Bourrellier, Ana Belen Feria;Valot, Benoit;Hodges, Michael
通讯作者：
Hodges, Michael
影响因子：
3.7
作者：
Huang YY;Matzke AJ;Matzke M
通讯作者：
Matzke M
影响因子：
3.7
作者：
Kapralov MV;Smith JA;Filatov DA
通讯作者：
Filatov DA
影响因子：
3.7
作者：
Huang, Jin-Ling;Sun, Gui-Ling;Zhang, Da-Ming
通讯作者：
Zhang, Da-Ming