Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
Biomolecules. 2024 Aug 23;14(9):1045. doi: 10.3390/biom14091045.
Slimming grass carp is a commercial variety with good body form and meat quality, which is cultured by starving common grass carp in a clean flowing water environment. Compared to common grass carp, slimming grass carp has a far higher economic value. Until now, no molecular study has concentrated on the regulation mechanism of the muscle characteristics of slimming grass carp. This study first reported the gene expression profile of the muscle characteristics of slimming grass carp based on the level of extrachromosomal circular DNAs (eccDNAs). EccDNAs are double-stranded circular DNAs derived from genomic DNAs and play crucial roles in the functional regulation of a wide range of biological processes, none of which have been shown to occur in fish. Here, muscle eccDNAs from slimming grass carp and common grass carp were both generally sequenced, and the information, as well as the expression profile of eccDNAs, were compared and analysed. The findings reveal that 82,238 and 25,857 eccDNAs were detected from slimming grass carp and common grass carp, respectively. The length distribution of eccDNAs was in the range of 1~1000 bp, with two peaks at about 200 bp and 400 bp. When the expression profiles of eccDNAs between slimming grass carp and common grass carp were compared, 3523 up-regulated and 175 down-regulated eccDNAs were found. Enrichment analysis showed that these eccDNA genes were correlated with cellular structure and response, cell immunology, enzyme activity, etc. Certain differentially expressed eccDNAs involved in muscle characteristics were detected, which include myosin heavy chain, myosin light chain, muscle segment homeobox C, calsequestrin, calmodulin, etc., among which the majority of genes were linked to muscle structure and contraction. This indicates that during the process of cultivating from common grass carp to slimming grass carp, the treatment primarily affected muscle structure and contraction, making the meat quality of slimming grass carp different from that of common grass carp. This result provides molecular evidence and new insights by which to elucidate the regulating mechanism of muscle phenotypic characterisation in slimming grass carp and other fish.
瘦身草鱼是一种体型和肉质良好的商业品种，它是通过在清洁的流动水环境中饥饿普通草鱼来培育的。与普通草鱼相比，瘦身草鱼具有更高的经济价值。到目前为止，还没有关于瘦身草鱼肌肉特征调节机制的分子研究。本研究首次基于染色体外环状 DNA（eccDNA）水平报道了瘦身草鱼肌肉特征的基因表达谱。eccDNA 是源自基因组 DNA 的双链环状 DNA，在广泛的生物学过程的功能调节中发挥着关键作用，在鱼类中尚未发现这种情况。在这里，分别对瘦身草鱼和普通草鱼的肌肉 eccDNA 进行了全面测序，并比较和分析了这些信息和 eccDNA 的表达谱。研究结果表明，从瘦身草鱼和普通草鱼中分别检测到 82238 个和 25857 个 eccDNA。eccDNA 的长度分布在 1~1000bp 之间，有两个峰，约为 200bp 和 400bp。当比较瘦身草鱼和普通草鱼的 eccDNA 表达谱时，发现 3523 个 eccDNA 上调，175 个 eccDNA 下调。富集分析表明，这些 eccDNA 基因与细胞结构和反应、细胞免疫学、酶活性等有关。检测到某些与肌肉特征相关的差异表达的 eccDNA，包括肌球蛋白重链、肌球蛋白轻链、肌节同源盒 C、钙网蛋白、钙调蛋白等，其中大多数基因与肌肉结构和收缩有关。这表明在从普通草鱼培育到瘦身草鱼的过程中，处理主要影响肌肉结构和收缩，使瘦身草鱼的肉质与普通草鱼不同。这一结果为阐明瘦身草鱼和其他鱼类肌肉表型特征的调节机制提供了分子证据和新的见解。
