Long-Read Transcriptome of Equine Bronchoalveolar Cells

Sophie Elena Sage; Pamela Nicholson; Tosso Leeb; Vinzenz Gerber; Vidhya Jagannathan

doi:10.3390/genes13101722

Long-Read Transcriptome of Equine Bronchoalveolar Cells

Genes (Basel). 2022 Sep 25;13(10):1722. doi: 10.3390/genes13101722.

Authors

Sophie Elena Sage¹, Pamela Nicholson², Tosso Leeb³, Vinzenz Gerber¹, Vidhya Jagannathan³

Affiliations

¹ Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.
² Next Generation Sequencing Platform, University of Bern, 3001 Bern, Switzerland.
³ Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.

Abstract

We used Pacific Biosciences long-read isoform sequencing to generate full-length transcript sequences in equine bronchoalveolar lavage fluid (BALF) cells. Our dataset consisted of 313,563 HiFi reads comprising 805 Mb of polished sequence information. The resulting equine BALF transcriptome consisted of 14,234 full-length transcript isoforms originating from 7017 unique genes. These genes consisted of 6880 previously annotated genes and 137 novel genes. We identified 3428 novel transcripts in addition to 10,806 previously known transcripts. These included transcripts absent from existing genome annotations, transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. We provide transcript-level data for equine BALF cells as a resource to the scientific community.

Keywords: Equus caballus; Iso-Seq; annotation; asthma; bioinformatics; horse; lung.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Genome*
Horses / genetics
Molecular Sequence Annotation
Protein Isoforms
Sequence Analysis, RNA / methods
Transcriptome* / genetics

Substances

Protein Isoforms

Grants and funding

This research was funded by the Swiss National Science Foundation (Grant No. 31003A-162548/1) and the Internal Research Fund of the Swiss Institute of Equine Medicine, Bern, Switzerland (ISMEquine Research No. 33-890).