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

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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.

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Abbreviations

AA:

Alternative accept site

AD:

Alternative donor site

ARF:

Auxin response factor

AS:

Alternative splicing

CDS:

Sequence coding for amino acids in protein

DEG:

Differentially expressed genes

FPKM:

Fragments per kilobase of transcript per million mapped reads

GO:

Gene ontology

ES:

Exon skipping

IR:

Intron retention

ORF:

Open reading frame

pre-mRNA:

Precursor Messenger RNA

PCA:

Principal component analysis

RRM:

RNA recognition motif

SE:

Skipped exon

SR:

Serine/arginine-rich

SqRT-PCR:

Semi-quantitative reverse transcription and polymerase chain reaction

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Acknowledgments

National High Technology Research and Development Program of China “Moso Bamboo Functional Genomics Research” (Grant No. 2013AA102607-4), Fundamental Research Funds of ICBR (Grant No. 1632015009), and Fundamental Research Funds of ICBR (Grant No. 1632016003).

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    Authors and Affiliations

    1. Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Center for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Chaoyang District, Beijing, 100102, People’s Republic of China

      Long Li, Tao Hu, Xueping Li, Shaohua Mu, Zhanchao Cheng, Wei Ge & Jian Gao

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    Correspondence to Jian Gao.

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    Communicated by A. K. Tyagi.

    L. Li and T. Hu contributed equally to this work.

    Electronic supplementary material

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    438_2016_1212_MOESM1_ESM.pdf

    Online resource 1 Fig. S1: Mapping result of the RNA-seq reads; Fig. S2: Phylogenetic relationships among different samples based on isoform expressions; Fig. S3: Validation of AS events based on RT-PCR; Fig. S4: Expression level of AS genes and non-AS genes at different growth stages; Fig. S5: FPKM value distribution of the first, second, and third most abundant isoforms at different shoot growth stages (CK, S1–S7); Fig. S6: The relationship between the number of identified isoforms and gene expression level at different shoot growth stage (CK, S1-S7); Fig. S7: Functional categorization (FDR < 0.01) of AS-occurring genes in shoot growth; Fig. S8: Enriched biological process GO terms of AS genes; Fig. S9: K-means clustering of differentially expressed isoforms; Expression and conserved domain analysis of isoforms from five plant growth and hormone signing associated families: (a) transport inhibitor response 1 (TIR1), (b) auxin-responsive protein IAA (AUX/IAA), (c) auxin-responsive GH3, and (d) MADS; Fig. S11: Distribution of different types of alternative splicing events in different species. (PDF 5257 kb)

    438_2016_1212_MOESM2_ESM.xlsx

    Online resource 2 Table S1: Primers used to amplify AS events; Table S2: Gene models of all identified isoforms; Table S3: AS events in moso bamboo; Table S4: GC content, exon number, and mRNA length of all moso bamboo genes; Table S5: Expression values of all identified isoforms during shoot growth; Table S6: GO annotation of all moso bamboo genes; Table S7: List of differentially expressed isoforms and their structures. (XLSX 64402 kb)

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    Li, L., Hu, T., Li, X. et al. Genome-wide analysis of shoot growth-associated alternative splicing in moso bamboo. Mol Genet Genomics 291, 1695–1714 (2016). https://doi.org/10.1007/s00438-016-1212-1

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