De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms.
De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms.
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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
DOI：
10.1371/journal.pone.0145385
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Shi S
中科院分区：
文献类型：
--
作者：
He Z;Zhang Z;Guo W;Zhang Y;Zhou R;Shi S
苹果树是槟榔科红树林中唯一的单子叶树种。这一物种是有记录以来最早的红树林化石。果蝇如何适应恶劣且不稳定的潮间带是一个有趣的问题。然而，保存在NCBI中的60个基因片段不足以解决这个问题。在这项研究中，我们使用下一代测序技术对果蝇转录组进行了测序、组装和注释。总共19,918,800个干净的成对末端读数被从头组装成45,368个单基因，N50长度为1,096个碱基对。用Blast2GO对41.35%的未登录基因进行了功能标注。我们鉴定了许多注释为“对压力的反应”的基因和15个假定的阳性选择基因。鉴定了简单序列重复序列，并与其他棕榈树进行了比较。利用基因组数据推算出果树与其他棕榈树的分化时间为7500万年前，这与化石记录是一致的。在计算同义替换率后，我们发现两个全基因组重复事件是由普通棕榈树和其他棕榈树共享的。这些重复事件为槟榔科后来的2000多个物种形成事件提供了大量的原料。本研究为果树和棕榈树的进一步功能和进化研究提供了高质量的资源。
Nypa fruticans (Arecaceae) is the only monocot species of true mangroves. This species represents the earliest mangrove fossil recorded. How N. fruticans adapts to the harsh and unstable intertidal zone is an interesting question. However, the 60 gene segments deposited in NCBI are insufficient for solving this question. In this study, we sequenced, assembled and annotated the transcriptome of N. fruticans using next-generation sequencing technology. A total of 19,918,800 clean paired-end reads were de novo assembled into 45,368 unigenes with a N50 length of 1,096 bp. A total of 41.35% unigenes were functionally annotated using Blast2GO. Many genes annotated to “response to stress” and 15 putative positively selected genes were identified. Simple sequence repeats were identified and compared with other palms. The divergence time between N. fruticans and other palms was estimated at 75 million years ago using the genomic data, which is consistent with the fossil record. After calculating the synonymous substitution rate between paralogs, we found that two whole-genome duplication events were shared by N. fruticans and other palms. These duplication events provided a large amount of raw material for the more than 2,000 later speciation events in Arecaceae. This study provides a high quality resource for further functional and evolutionary studies of N. fruticans and palms in general.