NDLI: Genome-wide analysis of shoot growth-associated alternative splicing in moso bamboo

Content Provider	Springer Nature Link
Author	Li, Long Hu, Tao Li, Xueping Mu, Shaohua Cheng, Zhanchao Ge, Wei Gao, Jian
Copyright Year	2016
Abstract	Alternative splicing (AS) significantly enhances transcriptome complexity and is differentially regulated in a wide variety of physiological processes in plants, including shoot growth. Presently, the functional implications and conservation of AS occurrences are not well understood in the moso bamboo genome. To analyze the global changes in AS during moso bamboo shoot growth, fast-growing shoots collected at seven different heights and culms after leaf expansion were sequenced using the Illumina HiSeq™ 2000 sequencing platform. It was found that approximately 60.74 % of all genes were alternatively spliced, with intron retention (IR) being the most frequent AS event (27.43 %). Statistical analysis demonstrated that variations of AS frequency and AS types were significantly correlated with changes in gene features and gene transcriptional level. According to the phylogenetic analysis of isoform expression data and AS frequency, the bamboo shoot growth could be divided into four different growth periods, including winter bamboo shoot (S1), early growth period (S2–S5), late growth period (S6 and S7), and mature period (CK). In addition, our data also showed that the winter bamboo shoot had the highest number of AS events. Twenty-six putative Serine/arginine-rich (SR) proteins were identified, producing a total of 109 transcripts. AS events were frequently and specifically regulated by SR splicing factors throughout shoot growth, resulting in changes to the original open reading frame (ORF) and subsequently changes to conserved domains. The AS product-isoforms showed regular expression change during the whole shoot growth period, thus influencing shoot growth. All together, these data indicate that AS events are adjusted to different growth stages, providing briefness and efficient means of gene regulation. This study will provide a very useful clue for future functional analyses.
Starting Page	1695
Ending Page	1714
Page Count	20
File Format	PDF
ISSN	16174615
Journal	Molecular and General Genetics MGG
Volume Number	291
Issue Number	4
e-ISSN	16174623
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2016-05-11
Publisher Place	Berlin/Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Alternative splicing (AS) Serine/arginine-rich (SR) protein Transcriptome sequencing Shoot growth Moso bamboo Cell Biology Biochemistry Microbial Genetics and Genomics Plant Genetics & Genomics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine Molecular Biology

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