Evolutionary dynamics of lincRNA transcription in nine citrus species

First author: Lili Ke; Affiliations: Huazhong Agricultural University (华中农业大学): Wuhan, China

Corresponding author: Qiang Xu

Long intergenic non‐coding RNAs (lincRNAs) play important roles in various biological processes in plants. However, little is known about the evolutionary characteristics of lincRNAs among closely related plant species. Here, we present a large‐scale comparative study of lincRNA transcription patterns in nine citrus species. By strand‐specific RNA‐sequencing, we identified 18,075 lincRNAs (14,575 lincRNA loci) from 34 tissue samples. The results indicated that the evolution of lincRNA transcription is more rapid than that of mRNAs. In total, 82.8%–97.6% of sweet orange (Citrus sinensis) lincRNA genes were shown to have homologous sequences in other citrus genomes. However, only 15.5%–28.8% of these genes had transcribed homologous lincRNAs in these citrus species, presenting a strong contrast to the high conservation of mRNA transcription (81.6%–84.7%). Moreover, primitive and modern citrus lincRNAs were preferentially expressed in reproductive and vegetative organs, respectively. Evolutionarily conserved lincRNAs showed higher and more constitutive expression than species‐specific lincRNAs. Notably, we observed a similar tissue expression pattern of homologous lincRNAs in sweet orange and pummelo (Citrus grandis), suggesting that these lincRNAs may be functionally conserved and selectively maintained. We also identified and validated a lincRNA with the highest expression in fruit that acts as an endogenous target mimic (eTM) of csi‐miR166c, and two lincRNAs that act as a precursor and target of csi‐miR166c, respectively. These lincRNAs together with csi‐miR166c could form an eTM166‐miR166c‐ argeted lincRNA regulatory network that possibly affects citrus fruit development.

长链基因间区非编码lincRNA在植物许多生物学过程中扮演非常重要的作用。然而，lincRNA在近缘植物物种中的演化还鲜有报道。本文，作者对九个柑橘物种lincRNA的转录模式进行了大规模的比较研究。通过链特异性RNA测序，作者从34个组织样本中鉴定到了18,075个lincRNA（共14,575个lincRNA位点）。该研究显示lincRNA转录的演化速度要远快于mRNA。总的来说，82.8%–97.6%的甜橙lincRNA在其他柑橘物种基因组中均有两个同源拷贝的序列。然而，这些lincRNA基因的同源拷贝仅仅只有15.5%–28.8%能够在其他柑橘物种中正常转录，这与mRNA中的81.6%–84.7%比例形成一个强烈对比。此外，原始和现代柑橘lincRNA分别优先在生殖器官和营养器官中表达。演化上保守的lincRNA要比那些物种特异性lincRNA具有更高、更多的组成型表达。有趣的是，作者在甜橙和观察到了柚子中观察到了同源lincRNA相似的组织表达模式，说明这些lincRNA可能在功能上是保守的，并且被选择性的保留了下来。作者还在柑橘果实中鉴定到了一个高表达的lincRNA作为csi‐miR166c的内源靶向mimic，另外还有两个lincRNA分别作为csi‐miR166c的前体和靶标。这些lincRNA与csi‐miR166c一起能够形成一个eTM166‐miR166c靶向的lincRNA调控机制，影响柑橘果实的发育。

通讯：徐强 (http://linx.hzau.edu.cn/szxx/zzjs/gsx/jiaoshou/201403/t20140305_37532.htm)

个人简介：1998-2002年，华中农业大学，园艺学士；2002-2007年，华中农业大学，园艺博士；2009-2010年，美国康奈尔大学合作研究。

研究方向：柑橘果实品质调控机理研究；耐黄龙病基因发掘与耐病机理解析；基于基因组学的分子工具开发及辅助育种。

doi: https://doi.org/10.1111/tpj.14279

Journal: the plant journal

First Published: February 09, 2019