家畜单细胞转录组学数据库的研究现状与展望

doi:10.11843/j.issn.0366-6964.2026.01.001

Abstract

Abstract:

This article aims to elucidate how single-cell omics technologies advance livestock research and provides a systematic review of the construction process， current applications， and major challenges of single-cell transcriptomic databases in domestic animals. It seeks to offer data references and analytical frameworks for researchers， thereby promoting deeper application of this technology in livestock studies. This review conducted a comprehensive review and integrated analysis of existing single-cell transcriptomic database resources for livestock， summarizing their construction methodologies and application pathways， while also discussing current technical bottlenecks. The review demonstrates that single-cell transcriptomics offers novel perspectives and abundant data resources for elucidating mechanisms of livestock diseases， molecular breeding， and health management， while also revealing significant challenges in areas such as data integration and annotation standardization. Future efforts should focus on constructing high-quality databases， developing analysis algorithms tailored to livestock species， and promoting multi-omics integration to fully leverage the potential of single-cell technologies in the development of animal husbandry.

Key words: livestock, single-cell transcriptomics, database

CLC Number:

S813

WANG Jian, LI Ruixing, LIU Qiaoming, LI Yuanfang. Research Status and Prospects of Livestock Single-cell Transcriptomics Databases[J]. Acta Veterinaria et Zootechnica Sinica, 2026, 57(1): 1-12.

Figures/Tables 2

Fig.1

Table 1

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数据库名称 Database name	数据库详情 Database details	物种类型 Species types	功能特点 Functional features	网址 Website	文献 Reference
PBatlas	1个物种，1个样本，5个大脑区域，32 250个细胞	家猪	细胞聚类与基因表达分析、细胞通讯分析、疾病风险基因分析	http：//120.79.46.200：82	［33］
CCL	1个物种，30多个数据集，13种组织	奶牛	细胞类型注释、比较分析和标记基因查询	http：//cattlecelllandscape.zju.edu.cn	［40］
DCA	1个物种，84种细胞类型，27万多个细胞	驴	基因表达查询、细胞通讯分析、转录因子查询	https：//egrb.qau.edu.cn/	［42］
CattleCA	1个物种，59种细胞类型，170多万个细胞	牛	基因表达查询和标记基因查询	https：//ngdc.cncb.ac.cn/cattleca/	［41］
ChickenGTEx	1个物种，127 598个细胞	鸡	基因表达查询	https：//chicken.farmgtex.org/	［39］
CDCP	641个数据集，2万多个样本，9 800万多个细胞	家猪、家鸡、家牛、家兔和绵羊	允许查询特定细胞类型或集群中不同基因的表达	https：//db.cngb.org/cdcp/	［13］
SCEA	21个物种，355个数据集，1 700万多个细胞	家鸡，家兔和绵羊	集成化scRNA-seq分析流程、t-SNE绘图网页部件	https：//www.ebi.ac.uk/gxa/sc/home	［43］
SPEED	127个物种，630多万个细胞，85种疾病类型	家猪、家鸡、家兔、绵羊和家牛	细胞通讯分析、基因间互作、跨物种进化分析	http：//speedatlas.net	［44］
SCP	831个数据集，5 754万多个细胞	家猪、家鸡、家牛、绵羊	基因表达查询、细胞聚类分析、标记基因查询	https：//singlecell.broadinstitute.org/single_cell	［45］

Research Status and Prospects of Livestock Single-cell Transcriptomics Databases

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