We performed transcriptomic profiling from seven larval stages of tropical gar (Atractosteus tropicus), an endemic fish inhabiting the riverscape of southeast Mexico with a growing aquaculture interest. de novo assembly generated 108,932 transcripts, grouped into 80,065 genes, with an average contig length of 792 bp and an N50 value of 1447 bp. A total of 50,377 open reading frames (ORF) were detected, and 34,192 hits were identified against SwissProt; we detected 96% of the metazoan orthologs (BUSCO metazoan odb9) as full-length features. Differential expression (DE) analyses were conducted by grouping samples as biological replicates in three developmental categories or stages: embryo-to-larvae transition (0–1 days after hatch (DAH)), mouth opening larvae (3–5 DAH) and lecithoexotrophic larvae (7–9 DAH). Enrichment analyses of overrepresented gene ontology terms in differentially expressed genes were also performed. Promising candidate nutritional markers were selected by a combination of semantic searches over annotations in three different operational categories: functional role as a digestive enzyme, metabolic hormones and organogenesis of digestive system. The results of this study provide for the first time an overview of early developmental transcriptome profiles in the gar and identify candidate nutritional markers, which can be used as indicators of digestive system development.

中文翻译：

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在热带雀鲷（Atractosteus tropicus）早期发育过程中通过从头转录组测序发现营养基因组标记

我们对热带雀鲷( Atractosteus tropicus ) 的七个幼虫阶段进行了转录组分析，这是一种栖息在墨西哥东南部河流景观中的特有鱼类，对水产养殖的兴趣日益浓厚。从头组装产生了 108,932 个转录本，分为 80,065 个基因，平均重叠群长度为 792 bp，N50 值为 1447 bp。共检测到 50,377 个开放阅读框 (ORF)，针对 SwissProt 确定了 34,192 个命中；我们检测到 96% 的后生动物直向同源物 (BUSCO metazoan odb9) 作为全长特征。差异表达 (DE) 分析是通过将样品分组为三个发育类别或阶段的生物复制品来进行的：胚胎到幼虫的转变（孵化后 0-1 天（DAH）），张口幼虫（3-5 DAH）和卵形外养幼虫（7-9 DAH）。还对差异表达基因中过度表达的基因本体术语进行了富集分析。通过对三个不同操作类别的注释进行语义搜索的组合来选择有希望的候选营养标记：作为消化酶的功能作用、代谢激素和消化系统的器官发生。这项研究的结果首次提供了 gar 中早期发育转录组谱的概述，并确定了可用作消化系统发育指标的候选营养标记。