Full-length transcriptome sequencing reveals extreme incomplete annotation of the goat genome.
Anim Genet
; 54(4): 421-424, 2023 Aug.
Article
de En
| MEDLINE
| ID: mdl-36849788
ABSTRACT
Despite recent advances in generating high-quality reference genome assemblies, the genome sequences for most livestock species, including goats, are still poorly annotated. Single-molecule long-read sequencing has greatly facilitated gene annotation by obtaining full-length transcripts. In this study, we generated full-length transcriptome data for samples from abomasum (n = 2) and testicle (n = 1), using PacBio Iso-Seq technology. We further combined these data with published data from abomasum (5ZY, SRR8618141) to evaluate and improve the gene annotation of the goat genome. We identified 14.5-16.3% of novel genes per sample from the four Iso-Seq datasets. At the transcript level, 40.6% of them were novel, including 29.7% novel transcripts from known genes and 10.9% from novel genes. We further verified the expression of novel genes in four additional RNA-seq data and found that the expression level of novel genes was significantly lower than that of known genes, indicating that the lowly expressed genes tend to be missed in the current genome annotation. This study shows the superiority of full-length transcriptome data in gene annotation, and more such data are required to improve the gene annotation for goat genome and other species.
Mots clés
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
Capra
/
Transcriptome
Limites:
Animals
Langue:
En
Journal:
Anim Genet
Sujet du journal:
GENETICA
/
MEDICINA VETERINARIA
Année:
2023
Type de document:
Article
Pays d'affiliation:
Chine