Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data

Xuelian Ma; Hansheng Zhao; Hengyu Yan; Minghao Sheng; Yaxin Cao; Kebin Yang; Hao Xu; Wenying Xu; Zhimin Gao; Zhen Su

doi:10.1016/j.csbj.2021.04.068

Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data

Comput Struct Biotechnol J. 2021 Apr 30:19:2708-2718. doi: 10.1016/j.csbj.2021.04.068. eCollection 2021.

Authors

Xuelian Ma¹, Hansheng Zhao², Hengyu Yan^{1

3}, Minghao Sheng¹, Yaxin Cao¹, Kebin Yang², Hao Xu², Wenying Xu¹, Zhimin Gao², Zhen Su¹

Affiliations

¹ State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
² Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China.
³ College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China.

Abstract

Bamboo, one of the most crucial nontimber forest resources worldwide, has the capacity for rapid growth. In recent years, the genome of moso bamboo (Phyllostachys edulis) has been decoded, and a large amount of transcriptome data has been published. In this study, we generated the genome-wide profiles of the histone modification H3K4me3 in leaf, stem, and root tissues of bamboo. The trends in the distribution patterns were similar to those in rice. We developed a processing pipeline for predicting novel transcripts to refine the structural annotation of the genome using H3K4me3 ChIP-seq data and 29 RNA-seq datasets. As a result, 12,460 novel transcripts were predicted in the bamboo genome. Compared with the transcripts in the newly released version 2.0 of the bamboo genome, these novel transcripts are tissue-specific and shorter, and most have a single exon. Some representative novel transcripts were validated by semiquantitative RT-PCR and qRT-PCR analyses. Furthermore, we put these novel transcripts back into the ChIP-seq analysis pipeline and discovered that the percentages of H3K4me3 in genic elements were increased. Overall, this work integrated transcriptomic data and epigenomic data to refine the annotation of the genome in order to discover more functional genes and study bamboo growth and development, and the application of this predicted pipeline may help refine the structural annotation of the genome in other species.

Keywords: Epigenomic data; Genome annotation; H3K4me3; Moso bamboo; Transcriptomic data.