CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris)

Abstract Background The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and trans...

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Bibliographic Details
Published in:BMC Genomics
Main Authors: In Seok Yang, Insu Jang, Jin Ok Yang, Jinhyuk Choi, Min-Seo Kim, Ka-Kyung Kim, Byung-Joon Seung, Jae-Ho Cheong, Jung-Hyang Sur, Hojung Nam, Byungwook Lee, Junho Kim, Sangwoo Kim
Format: Article in Journal/Newspaper
Language:English
Published: BMC 2023
Subjects:
Domestic dog
Canine mammary tumor
SNP
Transcriptome
Transcript isoform
Database
Biotechnology
TP248.13-248.65
Genetics
QH426-470
Canis lupus
Online Access:https://doi.org/10.1186/s12864-023-09655-0
https://doaj.org/article/79b86829fd834ed6b7380de75438a87d
Description
Summary:Abstract Background The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. Results We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. Conclusions CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ .

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