International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.3, 134-143 http://ecoevopublisher.com/index.php/ijmec 134 Feature Review Open Access Pan-Genome Analysis of Capra: Revealing the Core and Variable Genomes Shaping Goat Evolution Xuming Lü, Yeping Han Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: yeping.han@jicat.org International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.3 doi: 10.5376/ijmec.2025.15.0014 Received: 06 Apr., 2025 Accepted: 13 May, 2025 Published: 05 Jun., 2025 Copyright © 2025 Lü and Han, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Lü X.M., and Han Y.P., 2025, Pan-genome analysis of capra: revealing the core and variable genomes Shaping goat evolution, International Journal of Molecular Ecology and Conservation, 15(3): 134-143 (doi: 10.5376/ijmec.2025.15.0014) Abstract This study examined the genomic data of wild goats and several domestic goat breeds, taking into account their classification and domestication history. The functions of the core genome and the variable genome were described, and their value in the study of goat evolution and domestication was discussed. The research results show that the core genome stably supports basic life functions, while the variable genome carries many sequence changes related to environmental adaptation and human selection. These changes include gene loss and structural variations formed during domestication, as well as adaptive genes that adapt to different ecological environments. Pan-genome analysis highlights the role of genomic structural changes in the formation of domesticated traits, providing a new perspective for the genetic diversity and breeding potential of goats. This study also compared the pan-genomes of goats with those of other livestock such as pigs, cattle and sheep, thereby providing broader insights into cross-species evolution. At the same time, the technical limitations and future directions of pan-genome research were also discussed, including the use and protection methods of multi-omics data. The goat pan-genome not only enhances the understanding of goat history and adaptability, but also provides useful genetic tools for the breeding and conservation of endangered populations. Keywords Goat (Capra hircus) Pan-genome Core genome Variable genome Domestication; Environmental adaptation 1 Introduction Goats play a crucial role in global agriculture and animal husbandry. They are among the earliest domesticated animals and still provide meat, milk and fiber to this day. It is particularly important for small-scale farmers and residents in remote areas (Lu, 2023). At present, there are already hundreds of varieties in the world. It is distributed from high mountains to hot deserts and has strong adaptability (Nanaei et al., 2023). The advancement of DNA sequencing technology has enabled a clearer understanding of the evolution and traits of goats at the genomic level. Genome-wide analysis thus traced early domestication events and subsequent migration routes (Colli et al., 2018; Daly et al., 2021). Meanwhile, related studies have also compared genetic differences among different varieties and precisely located genes associated with important traits (Brito et al., 2017; Sasazaki et al., 2023). However, a long-standing limitation remains obvious: most studies rely on a single reference genome, and thus may miss some aspects of species genetic diversity (Li et al., 2023a). The concept of "pan-genome" originated from microbiology. The core of it is to gather all the genes of a species - including both the core genes shared by all individuals and the variant genes that only occur in some individuals. In humans and crops, pan-genomics has revealed many previously overlooked gene versions (Gong et al., 2023). Take humans as an example. The latest pan-genome has added approximately 119 million DNA "building blocks" and thousands of duplicate genes, significantly enhancing the ability to detect structural variations (Liao et al., 2023). Similar situations also occur in crops such as tomatoes, among which rare alleles that affect traits such as flavor have been identified (Gao et al., 2019). Pangenomics, on the one hand, broadens the understanding of genetic diversity, and on the other hand, clarifies the sources of individual differences. In recent years, the concept of pan-genome has begun to be applied to the research of livestock genomes and has made initial progress (Gong et al., 2023). It is of great significance to construct a pan-genome for the Capra genus, which includes both many wild relatives and domestic goats. On the one hand, the genomes of wild goat species
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