Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing

TL;DR

This study uses sequencing to explore the genetic makeup of a unique triploid snake species, providing insights into genome duplication events.

Contribution

The study generates the first full-length transcriptome of Indotyphlops braminus using isoform sequencing, offering evidence of a recent genome duplication.

Findings

A full-length transcriptome of I. braminus was assembled with 51,849 nonredundant transcripts.

Phylogenetic analysis suggests divergence of subgenomes occurred 11.5–15 million years ago.

The transcriptome provides preliminary evidence of a recent genome duplication event.

Abstract

Indotyphlops braminus, the only known triploid parthenogenetic snake, is a compelling species for revealing the mechanism of polyploid emergence in vertebrates.

In this study, we applied PacBio isoform sequencing technology to generate the first full-length transcriptome of I. braminus, aiming to improve the understanding of the molecular characteristics of this species.

A total of 51,849 nonredundant full-length transcript assemblies (with an N50 length of 2980 bp) from I. braminus were generated and fully annotated using various gene function databases. Our analysis provides preliminary evidence supporting a recent genome duplication event in I. braminus. Phylogenetic analysis indicated that the divergence of I. braminus subgenomes occurred approximately 11.5 ~ 15 million years ago (Mya). The full-length transcript resource generated as part of this research will facilitate transcriptome analysis and genomic evolution studies in the future.

The online version contains supplementary material available at 10.1186/s12863-024-01208-y.

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