| Item type |
学術雑誌論文 / Journal Article(1) |
| 公開日 |
2025-01-15 |
| タイトル |
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タイトル |
Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats |
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言語 |
en |
| 言語 |
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言語 |
eng |
| 資源タイプ |
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資源タイプ識別子 |
http://purl.org/coar/resource_type/c_6501 |
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資源タイプ |
journal article |
| 著者 |
Matsumoto, Yuki
Chung, Yik-Lok,Claire
Isobe, Sachiko
Sakamoto, Mika
Lin, Xiao
Chan, Ting-Fung
Hirakawa, Hideki
Ishihara, Genki
Lam, Hon-Ming
Nakayama, Shinobu
Sasamoto, Shigemi
Tanizawa, Yasuhiro
Watanabe, Akiko
Watanabe, Kei
Masaru, Yagura
Niimura, Yoshihito
Nakamura, Yasukazu
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| Abstract |
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内容記述タイプ |
Abstract |
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内容記述 |
Introduction
Comprehensive genomic resources offer insights into biological features, including traits/disease-related genetic loci. The current reference genome assembly for the domestic cat (Felis catus), Felis_Catus_9.0 (felCat9), derived from sequences of the Abyssinian cat, may inadequately represent the general cat population, limiting the extent of deducible genetic variations.
Objectives
The goal was to develop Anicom American Shorthair 1.0 (AnAms1.0), a reference-grade chromosome-scale cat genome assembly.
Methods
In contrast to prior assemblies relying on Abyssinian cat sequences, AnAms1.0 was constructed from the sequences of more popular American Shorthair breed, which is related to more breeds than the Abyssinian cat. By combining advanced genomics technologies, including PacBio long-read sequencing and Hi-C- and optical mapping data-based sequence scaffolding, we compared AnAms1.0 to existing Felidae genome assemblies (20 scaffolds, scaffolds N50 > 150 Mbp). Homology-based and ab initio gene annotation through Iso-Seq and RNA-Seq was used to identify new coding genes and splice variants.
Results
AnAms1.0 demonstrated superior contiguity and accuracy than existing Felidae genome assemblies. Using AnAms1.0, we identified over 1.5 thousand structural variants and 29 million repetitions compared to felCat9. Additionally, we identified > 1,600 novel protein-coding genes. Notably, olfactory receptor structural variants and cardiomyopathy-related variants were identified.
Conclusion
AnAms1.0 facilitates the discovery of novel genes related to normal and disease phenotypes in domestic cats. The analyzed data are publicly accessible on Cats-I (https://cat.annotation.jp/), which we established as a platform for accumulating and sharing genomic resources to discover novel genetic traits and advance veterinary medicine. |
|
言語 |
en |
| 書誌情報 |
Journal of Advanced Research
発行日 2024-10
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| 出版者 |
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出版者 |
Elsevier BV |
| DOI |
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識別子タイプ |
DOI |
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関連識別子 |
10.1016/j.jare.2024.10.023 |
| 著者版フラグ |
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出版タイプ |
VoR |
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出版タイプResource |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| 査読 |
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内容記述タイプ |
Other |
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内容記述 |
査読あり |
1-s2.0-S2090123224004788-main.pdf (2.5 MB)
