Genome-Wide Survey of Alternative Splicing in Actinidia chinensis
2015
Alternative splicing can increase the diversity and complexity
of proteome greatly through creating multiple mRNA transcripts from
a single gene. RNA-seq data from different organs (leaf, immature
fruit, half-ripe fruit and mature fruit) of Actinidia chinensis had been used to identify the alternative splicing events using
the A. chinensis genome as reference,
and totally 32180 alternative splicing events were discovered from
the A. chinensis genome (39040 genes) corresponding
to 11651 genes (29% of the total genome). Intron retention events
showed the highest frequency (more than 50%) among all the different
alternative splicing events. The frequency of events with alternative
3′ splice sites was twice than the alternative 5′ splice
sites. GO enrichment analysis result showed that the alternative splicing
gene was mainly enriched in enzyme regulation and nucleotide binding
related GO categories. The alternative splicing events in different
organs of A. chinensis seemed to preferentially occur
in genes with important function. The genes of leaf were associated
with the function of actin and microtubule. The genes of immature
fruit decided the function of two-component signal system. The genes
of half-ripe fruit were connected with phospholipid synthesis process.
The genes in mature fruit were associated with signal transduction.
In addition, 55.6% of vitamin related genes had been found to have
alternative splicing changes, which were significantly higher than
the average changes of the genome (the average splicing change level
was 29.6%). Those explained that alternative splicing events played
an important role in the process of vitamin synthesis. In this paper,
through the genome-wide analysis of alternative splicing in A. chinensis , a powerful resource for understanding the
complex genome of A. chinensis was provided. The
result was also useful to molecular breeding in kiwifruit.
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