September 22, 2019  |  

Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis).

Authors: Zhao, Hansheng and Gao, Zhimin and Wang, Le and Wang, Jiongliang and Wang, Songbo and Fei, Benhua and Chen, Chunhai and Shi, Chengcheng and Liu, Xiaochuan and Zhang, Hailin and Lou, Yongfeng and Chen, LianFu and Sun, Huayu and Zhou, Xianqiang and Wang, Sining and Zhang, Chi and Xu, Hao and Li, Lichao and Yang, Yihong and Wei, Yanli and Yang, Wei and Gao, Qiang and Yang, Huanming and Zhao, Shancen and Jiang, Zehui

Bamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies.Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo.These fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.

Journal: GigaScience
DOI: 10.1093/gigascience/giy115
Year: 2018

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