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Evolutionary dynamics of linc RNA transcription in nine citrus species
Author(s) -
Ke Lili,
Zhou Zhiwei,
Xu XiWen,
Wang Xia,
Liu Yuanlong,
Xu Yuantao,
Huang Yue,
Wang Shuting,
Deng Xiuxin,
Chen LingLing,
Xu Qiang
Publication year - 2019
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.14279
Subject(s) - biology , gene , homologous chromosome , transcription (linguistics) , rna , intergenic region , citrus × sinensis , genetics , genome , orange (colour) , horticulture , philosophy , linguistics
Summary Long intergenic non‐coding RNA s (linc RNA s) play important roles in various biological processes in plants. However, little information is known about the evolutionary characteristics of linc RNA s among closely related plant species. Here, we present a large‐scale comparative study of linc RNA transcription patterns in nine citrus species. By strand‐specific RNA ‐sequencing, we identified 18 075 linc RNA s (14 575 linc RNA loci) from 34 tissue samples. The results indicated that the evolution of linc RNA transcription is more rapid than that of mRNA s. In total, 82.8–97.6% of sweet orange ( Citrus sinensis ) linc RNA genes were shown to have homologous sequences in other citrus genomes. However, only 15.5–28.8% of these genes had transcribed homologous linc RNA s in these citrus species, presenting a strong contrast to the high conservation of mRNA transcription (81.6–84.7%). Moreover, primitive and modern citrus linc RNA s were preferentially expressed in reproductive and vegetative organs, respectively. Evolutionarily conserved linc RNA s showed higher expression levels and lower tissue specificity than species‐specific linc RNA s. Notably, we observed a similar tissue expression pattern of homologous linc RNA s in sweet orange and pummelo ( Citrus grandis ), suggesting that these linc RNA s may be functionally conserved and selectively maintained. We also identified and validated a linc RNA with the highest expression in fruit that acts as an endogenous target mimic ( eTM ) of csi‐miR166c, and two linc RNA s that act as a precursor and target of csi‐miR166c, respectively. These linc RNA s together with csi‐miR166c could form an eTM 166‐miR166c‐targeted linc RNA regulatory network that possibly affects citrus fruit development.