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 the phylogenetically distant and 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 structural variations.

Results

AnAms1.0 demonstrated superior contiguity and accuracy than existing Felidae genome assemblies. Using AnAms1.0, we identified over 1.5 thousand structural variations and 29 million repetitions compared to felCat9. Additionally, we identified > 1,800 novel protein-coding genes and structural variants. 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.

中文翻译：

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具有改进注释的染色体规模组装提供了对家猫全品种基因组结构和多样性的见解

 介绍

全面的基因组资源提供了对生物学特征的见解，包括性状/疾病相关的遗传位点。家猫 （Felis catus） 的当前参考基因组组装 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，从而限制了可推断遗传变异的程度。

 目标

目标是开发 Anicom American Shorthair 1.0 （AnAms1.0），这是一种参考级染色体规模的猫基因组组装。

 方法

与之前依赖阿比西尼亚猫序列的组装相比，AnAms1.0 是由系统发育遥远且更流行的美国短毛猫品种的序列构建的，该品种比阿比西尼亚猫相关。通过结合先进的基因组学技术，包括 PacBio 长读长测序和基于 Hi-C 和光学映射数据的序列支架，我们将 AnAms1.0 与现有的 Felidae 基因组组装（20 个支架，支架 N50 > 150 Mbp）进行了比较。通过 Iso-Seq 和 RNA-seq 进行基于同源的基因和从头计算的基因注释用于鉴定新的编码基因和结构变异。

 结果

AnAms1.0 表现出优于现有 Felidae 基因组组装的连续性和准确性。使用 AnAms1.0，与 felCat9 相比，我们鉴定了超过 1500 个结构变异和 2900 万个重复。此外，我们还鉴定了 > 1,800 个新的蛋白质编码基因和结构变体。值得注意的是，鉴定出嗅觉受体结构变异和心肌病相关变异。

 结论

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/） 上公开访问，我们建立了一个平台，用于积累和共享基因组资源，以发现新的遗传特征并推进兽医学。