Systematic Collection and Analysis of Alternative Splicing Events in Potato Plants

Abstract

: Potato [ Solanum tuberosum L.] is one of the major food plants with complete genome sequences available. Plant genes are subjected to alternative splicing (AS), a process increases both transcriptome and proteome diversities. The work reports a systematic genome-wide study on identification and analysis of AS events by integrating multiple sources of sequencing data in potato plants. A collection of 291,071 expressed sequence tags (ESTs) and mRNA sequences were cleaned and assembled into 150,435 unique transcripts and 87,992 of them were mapped to potato genome. In addition, a total of 5.8 billion out of 7.7 billion RNA-sequencing (RNA-seq) reads, which were collected from 227 samples deposited from 10 published projects, were mapped to potato genome. Combining all mapping data results in identification of a total of 226,769 AS events, which were further classified into basic events (49.0%) and complex events (51.0%), that were generated from 24,650 genes. The basic AS events include intron retention (9.5%), alternative acceptor sites (19.2%), alternative donor site (8.2%), and exon skipping (12.1%). The AS rate of annotated gene models was estimated to be ~45.8% in potato plants. Comparative analysis identified 2,929 alternatively splice genes conserved among potato, tomato, soybean and maize plants. The work provides an important resource for further functional characterization of these genes in potato biology.