Abstract Implementation of massive sequencing techniques in aquaculture has led to increase genomic resources of different species and have generated useful specific markers to improve their management. In this regard, transcriptomic approaches have been widely used to easily obtain gene expression profiles and understand the regulation of molecular pathways of interest in aspects as development and nutrition. The three spot cichlid (Amphilophus trimaculatus) is a native fish from South Mexico, with commercial regional importance and aquaculture potential. However, there is no genomic information available for the species that could allow the analysis in physiological processes of metabolic pathways to contribute or improve its culture. Hence, a comprehensive transcriptome of three different developmental stages: early (3–5 dpf larvae), mid (8–13 dpf larvae) and late (16–25 dpf larvae), were obtained using Illumina Hi-seq 2000 platform. De novo assembly generated 237,164 transcripts grouped in 196,186 genes with an average contig length of 778 bp and an N50 value of 1546 bp. Conceptual translation yielded in 78,883 proteins, of which 35,033 are complete proteins. By analyzing the transcriptomic profile and differential expression among developmental stages, we identified nutritional markers involved in digestive enzyme, metabolic hormone, and organogenesis of the digestive system. Likewise, in order to confirm the transcriptomic results obtained, histological analyzes were performed using hematoxylin-eosin (H&E) staining, finding that the most important morphological changes occur in the mid stage (endo-exptrophic larvae, 8 dpf and exotrophic larvae, 13 dpf), coinciding with the maximum expressions of the candidate genes for nutritional markers.

中文翻译：

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三斑慈鲷 Amphilophus trimaculatus 早期个体发育过程中从头 RNAseq 鉴定的营养基因组标记

摘要 大规模测序技术在水产养殖中的实施导致不同物种的基因组资源增加，并产生了有用的特异性标记来改善其管理。在这方面，转录组学方法已被广泛用于轻松获取基因表达谱并了解在发育和营养等方面感兴趣的分子途径的调节。三斑慈鲷 (Amphilophus trimaculatus) 是来自南墨西哥的本地鱼类，具有商业区域重要性和水产养殖潜力。然而，没有可用于该物种的基因组信息可以允许在代谢途径的生理过程中进行分析以促进或改善其培养。因此，三个不同发育阶段的综合转录组：早期（3-5 dpf 幼虫）、使用 Illumina Hi-seq 2000 平台获得中期（8-13 dpf 幼虫）和晚期（16-25 dpf 幼虫）。从头组装产生了 237,164 个转录本，分为 196,186 个基因，平均重叠群长度为 778 bp，N50 值为 1546 bp。概念翻译产生了 78,883 种蛋白质，其中 35,033 种是完整蛋白质。通过分析发育阶段之间的转录组学特征和差异表达，我们确定了涉及消化酶、代谢激素和消化系统器官发生的营养标志物。同样，为了确认获得的转录组学结果，使用苏木精 - 伊红（H＆E）染色进行组织学分析，发现最重要的形态变化发生在中期（内养幼虫，8 dpf和外养幼虫，13 dpf ),