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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-02-01
|
| Series: | BMC Genomic Data |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12863-024-01208-y |
| _version_ | 1797273028267081728 |
|---|---|
| author | Fei Zhu Jing Lu Ke Sun Cao Deng Yu Xu |
| author_facet | Fei Zhu Jing Lu Ke Sun Cao Deng Yu Xu |
| author_sort | Fei Zhu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-07T14:38:41Z |
| format | Article |
| id | doaj.art-4382f6f6d3354cb494932bd205f187b0 |
| institution | Directory Open Access Journal |
| issn | 2730-6844 |
| language | English |
| last_indexed | 2024-03-07T14:38:41Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomic Data |
| spelling | doaj.art-4382f6f6d3354cb494932bd205f187b02024-03-05T20:29:48ZengBMCBMC Genomic Data2730-68442024-02-0125111110.1186/s12863-024-01208-yPolyploidization of Indotyphlops braminus: evidence from isoform-sequencingFei Zhu0Jing Lu1Ke Sun2Cao Deng3Yu Xu4School of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversityDepartment of Bioinformatics, DNA Stories Bioinformatics CenterSchool of Life Sciences, Guizhou Normal UniversityAbstract 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.https://doi.org/10.1186/s12863-024-01208-yIndotyphlops braminusPolyploidizationTranscriptomeSequencingEvolution |
| spellingShingle | Fei Zhu Jing Lu Ke Sun Cao Deng Yu Xu Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing BMC Genomic Data Indotyphlops braminus Polyploidization Transcriptome Sequencing Evolution |
| title | Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing |
| title_full | Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing |
| title_fullStr | Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing |
| title_full_unstemmed | Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing |
| title_short | Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing |
| title_sort | polyploidization of indotyphlops braminus evidence from isoform sequencing |
| topic | Indotyphlops braminus Polyploidization Transcriptome Sequencing Evolution |
| url | https://doi.org/10.1186/s12863-024-01208-y |
| work_keys_str_mv | AT feizhu polyploidizationofindotyphlopsbraminusevidencefromisoformsequencing AT jinglu polyploidizationofindotyphlopsbraminusevidencefromisoformsequencing AT kesun polyploidizationofindotyphlopsbraminusevidencefromisoformsequencing AT caodeng polyploidizationofindotyphlopsbraminusevidencefromisoformsequencing AT yuxu polyploidizationofindotyphlopsbraminusevidencefromisoformsequencing |