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基于下一代测序数据对巨脂鲤（ tambaqui ）、美索不达米亚脂鲤（ pacu ）及其杂交种 tambacu 的骨骼肌进行综合微小RNA组分析。

Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data.

作者信息

Fantinatti Bruno E A, Perez Erika S, Zanella Bruna T T, Valente Jéssica S, de Paula Tassiana G, Mareco Edson A, Carvalho Robson F, Piazza Silvano, Denti Michela A, Dal-Pai-Silva Maeli

机构信息

Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, Sao Paulo, 18618-970, Brazil.

Ninth of July University - UNINOVE, Bauru, Sao Paulo, Brazil.

出版信息

BMC Genomics. 2021 Apr 6;22(1):237. doi: 10.1186/s12864-021-07513-5.

DOI:10.1186/s12864-021-07513-5
PMID:33823787
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8022549/
Abstract

BACKGROUND

Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are good fish species for aquaculture. The tambacu, individuals originating from the induced hybridization of the female tambaqui with the male pacu, present rapid growth and robustness, characteristics which have made the tambacu a good choice for Brazilian fish farms. Here, we used small RNA sequencing to examine global miRNA expression in the genotypes pacu (PC), tambaqui (TQ), and hybrid tambacu (TC), (Juveniles, n = 5 per genotype), to better understand the relationship between tambacu and its parental species, and also to clarify the mechanisms involved in tambacu muscle growth and maintenance based on miRNAs expression.

RESULTS

Regarding differentially expressed (DE) miRNAs between the three genotypes, we observed 8 upregulated and 7 downregulated miRNAs considering TC vs. PC; 14 miRNAs were upregulated and 10 were downregulated considering TC vs. TQ, and 15 miRNAs upregulated and 9 were downregulated considering PC vs. TQ. The majority of the miRNAs showed specific regulation for each genotype pair, and no miRNA were shared between the 3 genotype pairs, in both up- and down-regulated miRNAs. Considering only the miRNAs with validated target genes, we observed the miRNAs miR-144-3p, miR-138-5p, miR-206-3p, and miR-499-5p. GO enrichment analysis showed that the main target genes for these miRNAs were grouped in pathways related to oxygen homeostasis, blood vessel modulation, and oxidative metabolism.

CONCLUSIONS

Our global miRNA analysis provided interesting DE miRNAs in the skeletal muscle of pacu, tambaqui, and the hybrid tambacu. In addition, in the hybrid tambacu, we identified some miRNAs controlling important molecular muscle markers that could be relevant for the farming maximization.

摘要

背景

巨脂鲤（ tambaqui ）和麦瑞加拉鲮（ pacu ）是水产养殖的优良鱼类品种。坦巴库鱼是雌性巨脂鲤与雄性麦瑞加拉鲮诱导杂交产生的个体，生长迅速且健壮，这些特性使坦巴库鱼成为巴西养鱼场的理想选择。在此，我们使用小 RNA 测序来检测麦瑞加拉鲮（ PC ）、巨脂鲤（ TQ ）和杂交坦巴库鱼（ TC ）基因型（每个基因型的幼鱼 n = 5 ）中的全局 miRNA 表达，以更好地了解坦巴库鱼与其亲本物种之间的关系，并基于 miRNA 表达阐明坦巴库鱼肌肉生长和维持所涉及的机制。

结果

关于三种基因型之间差异表达（ DE ）的 miRNA ，与 PC 相比， TC 中有 8 个 miRNA 上调， 7 个下调；与 TQ 相比， TC 中有 14 个 miRNA 上调， 10 个下调；与 TQ 相比， PC 中有 15 个 miRNA 上调， 9 个下调。大多数 miRNA 对每个基因型对都有特定的调控，在上调和下调的 miRNA 中， 3 个基因型对之间没有共享的 miRNA 。仅考虑具有验证靶基因的 miRNA ，我们观察到了 miRNA miR - 144 - 3p 、 miR - 138 - 5p 、 miR - 206 - 3p 和 miR - 499 - 5p 。 GO 富集分析表明，这些 miRNA 的主要靶基因聚集在与氧稳态、血管调节和氧化代谢相关的途径中。

结论

我们的全局 miRNA 分析在麦瑞加拉鲮、巨脂鲤和杂交坦巴库鱼的骨骼肌中提供了有趣的差异表达 miRNA 。此外，在杂交坦巴库鱼中，我们鉴定了一些控制重要分子肌肉标志物的 miRNA ，这些 miRNA 可能与养殖最大化相关。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/2a244c29bf89/12864_2021_7513_Fig13_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/6a93def62ad1/12864_2021_7513_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/2321f296175d/12864_2021_7513_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/8d4dd62978d6/12864_2021_7513_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/2345c995d2d6/12864_2021_7513_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/3c1d1b8af4e6/12864_2021_7513_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/09828bd9a2b4/12864_2021_7513_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/7bd9cd11f3b4/12864_2021_7513_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/39897c3dd80f/12864_2021_7513_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/214136d7c43e/12864_2021_7513_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/56af23295c7d/12864_2021_7513_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/fc61080f24b7/12864_2021_7513_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/bb39331ab11c/12864_2021_7513_Fig12_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7cf4/8022549/2a244c29bf89/12864_2021_7513_Fig13_HTML.jpg

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