Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum.
Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum.
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转录组分析为红树蕨属 Acrostichum 的系统发育和适应性进化提供了见解
DOI：
10.1038/srep35634
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发表时间：
2016-10-26
影响因子：
4.6
通讯作者：
Shi S
中科院分区：
文献类型：
--
作者：
Zhang Z;He Z;Xu S;Li X;Guo W;Yang Y;Zhong C;Zhou R;Shi S
红树林蕨类Acrostichum生长在极端不稳定的海洋潮间带，条件恶劣，如高盐浓度，潮汐节律和长期气候变化。为了探讨该属植物的系统发育关系和适应性的分子机制，我们对两种Acrostichum，A. aureumandA. speciosum，以及姐妹属Ceratopteris thalictroides中的一个种。我们获得了47，517，36，420和60，823个单基因，其中24.39-45.63%被公共数据库注释。对分歧时间的估算表明，Acrostichum在晚白垩世就已适应于沿海地区，而来自印度西太平洋（IWP）地区的两种红树林蕨类的分歧时间则较晚。两种方法（修改的分支网站模型和Khmethod）被用来确定几个积极选择的基因，这可能有助于差异适应的两个Acrostichumspecies不同的光和盐条件。本研究为红树林蕨类植物在潮间带的进化和适应提供了丰富的转录组数据和新的见解。
The mangrove fern genusAcrostichumgrows in the extremely unstable marine intertidal zone under harsh conditions, such as high salt concentrations, tidal rhythms and long-term climate changes. To explore the phylogenetic relationships and molecular mechanisms underlying adaptations in this genus, we sequenced the transcriptomes of two species ofAcrostichum,A. aureumandA. speciosum, as well as a species in the sister genus,Ceratopteris thalictroides. We obtained 47,517, 36,420 and 60,823 unigenes for the three ferns, of which 24.39–45.63% were annotated using public databases. The estimated divergence time revealed thatAcrostichumadapted to the coastal region during the late Cretaceous, whereas the two mangrove ferns from the Indo West-Pacific (IWP) area diverged more recently. Two methods (the modified branch-site model and the Khmethod) were used to identify several positively selected genes, which may contribute to differential adaptation of the twoAcrostichumspecies to different light and salt conditions. Our study provides abundant transcriptome data and new insights into the evolution and adaptations of mangrove ferns in the inhospitable intertidal zone.
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影响因子：
10.7
作者：
Ding, KY;Zhou, K;Shen, Y
通讯作者：
Shen, Y
使用RNA-Seq从头组装红树林棕榈（Nypa fruticans）编码序列并发现棕榈祖先的全基因组重复
影响因子：
3.7
作者：
He Z;Zhang Z;Guo W;Zhang Y;Zhou R;Shi S
通讯作者：
Shi S
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
4.9
作者：
Aya, Koichiro;Kobayashi, Masaaki;Matsuoka, Makoto
通讯作者：
Matsuoka, Makoto