Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

中文翻译：

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RNA测序揭示雌性南亚野鲮（Labeo rohita Ham.）繁殖季节性的候选基因和分子机制


鲤鱼、南亚野鲮（Labeo rohita Ham.）是东南亚重要的淡水养殖品种，具有季节性繁殖节律。目前还没有转录组水平的整体研究揭示参与生物钟基因（BCG）调节的昼夜节律的关键候选基因。季节性表现有两个截然不同的繁殖阶段，即产卵后休息和适合揭示相关候选基因的性腺活动开始。它可以通过对参与控制季节性的 BPGL（脑-垂体-性腺-肝脏）轴的组织进行 RNA 测序来破译。这种鱼的 BCG 在不同门中的进化保守程度尚不清楚。由于季节性限制了季风季节以外的种子生产，此类研究可进一步用于提高鱼类生产力。使用 Illumina TruSeq 生成了四种组织（即 BPGL）总共约 150 Gb 的转录组数据。从头组装的BPGL组织揭示了75,554个差异表达转录本、115,534个SSR、65,584个SNP、514个通路、5379个转录因子、187个调节由1576个差异表达转录本代表的候选基因的成熟miRNA，这些都可以以网络基因组资源的形式获得。结果通过 qPCR 得到验证。这是首次报道鲤鱼含有 32 种卡介苗，这些卡介苗广泛存在于鱼类、两栖动物、爬行动物、鸟类、原兽、有袋动物和胎盘哺乳动物中。这是由于响应环境和地球自转的节律性的普遍机制具有适应性和繁殖意义。 这项研究阐明了这种鱼的光周期感应、神经内分泌分泌、肝脏代谢和卵黄合成、性腺成熟、肌肉生长以及感觉和听觉的进化保守机制。研究表明，鱼类除了与提高生殖效率相关之外，还是生物钟研究的良好模型。