Dataset Information

Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing.

ABSTRACT:

Background

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

Methods

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.

Results

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.

SUBMITTER: Zhu F

PROVIDER: S-EPMC10895795 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Publications

Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing.

Zhu Fei F Lu Jing J Sun Ke K Deng Cao C Xu Yu Y

BMC genomic data 20240226 1

<h4>Background</h4>Indotyphlops braminus, the only known triploid parthenogenetic snake, is a compelling species for revealing the mechanism of polyploid emergence in vertebrates.<h4>Methods</h4>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.<h4>Results</h4>A total of 51,849 nonredundant full-length transcript assemblies (with an N50 ...[more]

PMID: 38408920

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Project description:BackgroundCancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing has utility in providing a cost-effective approach for evaluating isoform expression, although short-read assembly displays limitations in the accurate inference of full-length transcripts. Long-read RNA sequencing (Iso-Seq), using the Pacific Biosciences (PacBio) platform, can overcome such limitations by providing full-length isoform sequence resolution which requires no read assembly and represents native expressed transcripts. A constraint of the Iso-Seq protocol is due to fewer reads output per instrument run, which, as an example, can consequently affect the detection of lowly expressed transcripts. To address these deficiencies, we developed a concatenation workflow, PacBio Full-Length Isoform Concatemer Sequencing (PB_FLIC-Seq), designed to increase the number of unique, sequenced PacBio long-reads thereby improving overall detection of unique isoforms. In addition, we anticipate that the increase in read depth will help improve the detection of moderate to low-level expressed isoforms.ResultsIn sequencing a commercial reference (Spike-In RNA Variants; SIRV) with known isoform complexity we demonstrated a 3.4-fold increase in read output per run and improved SIRV recall when using the PB_FLIC-Seq method compared to the same samples processed with the Iso-Seq protocol. We applied this protocol to a translational cancer case, also demonstrating the utility of the PB_FLIC-Seq method for identifying differential full-length isoform expression in a pediatric diffuse midline glioma compared to its adjacent non-malignant tissue. Our data analysis revealed increased expression of extracellular matrix (ECM) genes within the tumor sample, including an isoform of the Secreted Protein Acidic and Cysteine Rich (SPARC) gene that was expressed 11,676-fold higher than in the adjacent non-malignant tissue. Finally, by using the PB_FLIC-Seq method, we detected several cancer-specific novel isoforms.ConclusionThis work describes a concatenation-based methodology for increasing the number of sequenced full-length isoform reads on the PacBio platform, yielding improved discovery of expressed isoforms. We applied this workflow to profile the transcriptome of a pediatric diffuse midline glioma and adjacent non-malignant tissue. Our findings of cancer-specific novel isoform expression further highlight the importance of long-read sequencing for characterization of complex tumor transcriptomes.

Dataset Information

Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing.

Background

Methods

Results

Publications

Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing.

Similar Datasets

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