Deep spatiotemporal transcriptome analysis provides new insights into early development of koi carp (Cyprinus carpio var. koi)

Abstract

Koi carp, a colorful variety of the common carp (Cyprinus carpio), is a rich genetic resource for studies on skin color differentiation and pigmentation, as well as for breeding and selection of ornamental fish species. An improved comprehension of the genetic regulation of early developmental processes in koi will facilitate future applications of precision breeding and gene editing related to pigment cell development. A comparative transcriptome analysis of six early developmental stages, namely Mu (multicellular cleavage), Bl (blastocyst), Ga (gastrulation), Ne (neurulation), Oc (organogenesis) and 7Dph (7 days post hatching) on a global scale was performed. 124.9 Gb of clean data was generated from 18 transcriptomes with a mapping efficiency of over 87.86%. A total of 49,717 known and 3384 novel genes were identified, of which 77, 153, 89, 132, 158 and 1071 were specifically expressed in each stage, respectively, while 35,009 genes were present at an expression level in all six stages. Furthermore, 33,986 differentially expressed genes (DEGs) were identified in comparison between adjacent stages, and 30 expression patterns were acquired, including continuously increasing or decreasing, significantly increasing or decreasing from a certain stage, and irregular dynamic fluctuations. The Ga vs. Bl group was enriched in several biological processes and metabolic pathways related to the transition from the maternal to the zygotic stage and showed the largest trend in transcriptomic changes (10,714 up- and 8515 down-regulated). Moreover, some genes involved in DNA replication, transcription, protein synthesis, ribosomes, immunology, neural crest cell development, and pigment cell differentiation were also highly enriched (e.g., eif3, cox1, cox2, tyk2, pkz, pax3, pax7, gch2, xdh, etc.). The results of RNA-Seq were confirmed by qPCR of 15 genes from different metabolic pathways, and the spatiotemporal expression profiles of nine genes involved in xanthophore and erythrophore differentiation and pigmentation were also examined. Our findings offer fresh insights into the molecular regulation of early koi carp development and provide a solid foundation for future investigations and functional studies of DEGs.