Long-read RNA Sequencing Improves the Annotation of the Equine Transcriptome

Sichong Peng; Anna R. Dahlgren; Erin N. Hales; Alexa M Barber; Ted Kalbfleisch; Jessica L. Petersen; Rebecca R. Bellone; Mariusz Mackowski; Katia Cappelli; Stefano Capomaccio; Stephen J. Coleman; O. Distl; Elena Giulotto; Bianca Waud; Natasha Anne Hamilton; Tosso Leeb; Gabriella Lindgren; LA. Lyons; Molly E. McCue; JN. MacLeod; Julia Metzger; J.R. Mickelson; B. J. Murphy; Ludovic Orlando; Cecilia Penedo; T. Raudsepp; Eric Strand; Teruaki Tozaki; Dagmar S. Trachsel; BD. Velie

doi:10.1101/2022.06.07.495038

GenomicsbioRxivJun 7, 2022

Preprint

Long-read RNA Sequencing Improves the Annotation of the Equine Transcriptome

Sichong Peng iD, Anna R. Dahlgren iD, Erin N. Hales iD, Alexa M Barber iD, Ted Kalbfleisch iD, Jessica L. Petersen iD, Rebecca R. Bellone iD, Mariusz Mackowski iD, Katia Cappelli iD, Stefano Capomaccio iD, Stephen J. Coleman iD, O. Distl iD, Elena Giulotto iD, Bianca Waud, Natasha Anne Hamilton iD, Tosso Leeb iD, Gabriella Lindgren iD, LA. Lyons, Molly E. McCue iD, JN. MacLeod, Julia Metzger iD, J.R. Mickelson, B. J. Murphy, Ludovic Orlando iD, Cecilia Penedo, , Carrie J. Finno iD

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Abstract

1A high-quality reference genome assembly, a biobank of diverse equine tissues from the Functional Annotation of the Animal Genome (FAANG) initiative, and incorporation of long-read sequencing technologies, have enabled efforts to build a comprehensive and tissue-specific equine transcriptome. The equine FAANG transcriptome reported here provides up to 45% improvement in transcriptome completeness across tissue types when compared to either RefSeq or Ensembl transcriptomes. This transcriptome also provides major improvements in the identification of alternatively spliced isoforms, novel noncoding genes, and 3 transcription termination site (TTS) annotations. The equine FAANG transcriptome will empower future functional studies of important equine traits while providing future opportunities to identify allele-specific expression and differentially expressed genes across tissues.