Open Access

ARTICLE

Exploring Splicing Variants and Novel Genes in Sacred Lotus Based on RNA-seq Data

Xinyi Zhang, Zimeng Yu, Pingfang Yang^*

State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China

* Corresponding Author: Pingfang Yang. Email:

Phyton-International Journal of Experimental Botany 2023, 92(6), 1665-1679. https://doi.org/10.32604/phyton.2023.029482

Received 21 February 2023; Accepted 06 March 2023; Issue published 11 April 2023

Abstract

Sacred lotus (Nelumbo nucifera) is a typical aquatic plant, belonging to basal eudicot plant, which is ideal for genome and genetic evolutionary study. Understanding lotus gene diversity is important for the study of molecular genetics and breeding. In this research, public RNA-seq data and the annotated reference genome were used to identify the genes in lotus. A total of 26,819 consensus and 1,081 novel genes were identified. Meanwhile, a comprehensive analysis of gene alternative splicing events was conducted, and a total of 19,983 “internal” alternative splicing (AS) events and 14,070 “complete” AS events were detected in 5,878 and 5,881 multi-exon expression genes, respectively. Observations made from the AS events show the predominance of intron retention (IR) subtype of AS events representing 33%. IR is followed by alternative acceptor (AltA), alternative donor (AltD) and exon skipping (ES), highlighting the universality of the intron definition model in plants. In addition, functional annotations of the gene with AS indicated its relationship to a number of biological processes such as cellular process and metabolic process, showing the key role for alternative splicing in influencing the growth and development of lotus. The results contribute to a better understanding of the current gene diversity in lotus, and provide an abundant resource for future functional genome analysis in lotus.

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Keywords

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Supplementary Material

Supplementary Material File

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