A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis.
A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis.
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DOI：
10.1371/journal.pone.0183778
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Ma XF
中科院分区：
文献类型：
--
作者：
Zhao P;Wang L;Zhao X;Chen G;Ma XF
矮Braya humilis是菊科Euclidieae族的成员。该物种对不同的气候带和纬度具有广泛的适应性，因为它的分布范围从北方亚洲到北方北美的北极高山地区。在中国，B. humilis主要分布在青藏高原及其邻近的干旱地区。在这项研究中，我们使用Illumina平台对来自QTP附近干旱地区的样本进行测序，共产生46，485个高度准确的unigenes，其中78.41%通过BLAST与公共蛋白质数据库进行了注释。B。humilis转录组的特征在于与其近亲拟南芥相比具有高水平的序列保守性。我们还使用相互blast来鉴定B之间共享的直向同源基因。humilis和其他四个已测序的菊科物种（即A. thaliana，A. lyrata、Capsella rubella和Thellungiella parvula）。为了能够精确地表征直序基因，还包括了早期发散的基部被子植物Amborella dipoda。在应用更严格的标准确定e值、氨基酸命中长度和同一性值以进一步减少该列表之前，总共鉴定了6，689个正向同源基因。这导致了B的381个核心直系同源基因的最终列表。humilis;其中39个基因与盐胁迫和渗透胁迫反应有关，并估算了该物种和A.拟南芥直向同源物显示这些基因在B中处于纯化选择下。卑微的在B中检测到6个基因的表达。盐胁迫和渗透胁迫处理的矮牵牛幼苗。与拟南芥中的对应物相比，这些直向同源基因的表达模式表明它们在序列和功能上都是保守的。研究结果表明，B.矮生植物主要是先存遗传成分的结果。未来的工作将需要表征这些orthopathic基因在自然人群中的表达模式，并将提供进一步的见解适应机制的基础广泛的B。humilis适应
Braya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B. humilis is mainly found on the Qinghai—Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78.41% were annotated by BLASTing versus public protein databases. The B. humilis transcriptome is characterized by a high level of sequence conservation compared with its close relative, Arabidopsis thaliana. We also used reciprocal blast to identify shared orthologous genes between B. humilis and four other sequenced Brassicaceae species (i.e. A. thaliana, A. lyrata, Capsella rubella, and Thellungiella parvula). To enable precise characterization of orthologous genes, the early-diverging basal angiosperm Amborella trichopoda was also included. A total of 6,689 orthologous genes were identified before stricter criteria for the determination of e-values, amino acid hit lengths, and identity values was applied to further reduce this list. This led to a final list of 381 core orthologous genes for B. humilis; 39 out of these genes are involved in salt and osmotic stress responses and estimations of nonsynonymous/synonymous substitution ratios for this species and A. thaliana orthologs show that these genes are under purifying selection in B. humilis. Expression of six genes was detected in B. humilis seedlings under salt and osmotic stress treatments. Comparable expression patterns to their counterparts in Arabidopsis suggest that these orthologous genes are both sequence and functional conservation. The results of this study demonstrate that the environmental adaptations of B. humilis are mainly the results of preexisting genetic components. Future work will be required to characterize the expression patterns of these orthologous genes in natural populations and will provide further insights into the adaptive mechanisms underlying the wide range of B. humilis adaptations.
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影响因子：
56.9
作者：
Chamala, Srikar;Chanderbali, Andre S.;Barbazuk, W. Brad
通讯作者：
Barbazuk, W. Brad
影响因子：
7.4
作者：
Oh, Dong-Ha;Dassanayake, Maheshi;Bohnert, Hans J.
通讯作者：
Bohnert, Hans J.
影响因子：
7.2
作者：
Toufighi, K;Brady, SM;Provart, NJ
通讯作者：
Provart, NJ
DOI：
10.1111/tpj.12267
发表时间：
2013-09
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Dorn KM;Fankhauser JD;Wyse DL;Marks MD
通讯作者：
Marks MD
影响因子：
48
作者：
Mortazavi, Ali;Williams, Brian A.;Wold, Barbara
通讯作者：
Wold, Barbara