Matsumoto Yuki, Yik-Lok Chung 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, Yagura Masaru, Niimura Yoshihito, Nakamura Yasukazu
Research and Development Section, Anicom Specialty Medical Institute Inc., Yokohama, Kanagawa, Japan; Data Science Center, Azabu University, Sagamihara, Kanagawa, Japan.
School of Life Sciences and the Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.
J Adv Res. 2024 Oct 28. doi: 10.1016/j.jare.2024.10.023.
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.
The goal was to develop Anicom American Shorthair 1.0 (AnAms1.0), a reference-grade chromosome-scale cat genome assembly.
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.
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.
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.
全面的基因组资源有助于深入了解生物学特征，包括与性状/疾病相关的基因座。目前家猫（Felis catus）的参考基因组组装版本Felis_Catus_9.0（felCat9）源自阿比西尼亚猫的序列，可能无法充分代表一般猫种群，限制了可推断的遗传变异范围。
目标是开发Anicom美国短毛猫1.0（AnAms1.0），这是一个参考级别的染色体规模的猫基因组组装。
与之前依赖阿比西尼亚猫序列的组装不同，AnAms1.0是由更受欢迎的美国短毛猫品种的序列构建而成，该品种与比阿比西尼亚猫更多的品种相关。通过结合先进的基因组技术，包括PacBio长读长测序以及基于Hi-C和光学图谱数据的序列支架构建，我们将AnAms1.0与现有的猫科动物基因组组装（20个支架，支架N50 > 150 Mbp）进行了比较。通过基于同源性和从头开始的基因注释（通过Iso-Seq和RNA-Seq）来识别新的编码基因和剪接变体。
AnAms1.0显示出比现有的猫科动物基因组组装更好的连续性和准确性。与felCat9相比，使用AnAms1.0我们鉴定出了超过1500个结构变异和2900万个重复序列。此外，我们鉴定出了>1600个新的蛋白质编码基因。值得注意的是，还鉴定出了嗅觉受体结构变异和与心肌病相关的变异。
AnAms1.0有助于发现与家猫正常和疾病表型相关的新基因。分析的数据可在Cats-I（https://cat.annotation.jp/）上公开获取，我们将其作为一个积累和共享基因组资源的平台，以发现新的遗传特征并推动兽医学发展。
