Development of microsatellite markers by de novo transcriptome sequencing of flatfish Cyclopsetta fimbriata and Syacium papillosum (family: Paralichthyidae)

IF 1 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-04-05 DOI:10.1016/j.genrep.2025.102219

Rubí Fabiola Alderete-Domínguez , Jesús Alejandro Zamora-Briseño , Monica Améndola-Pimenta , Juan Pablo Ek-Huchim , Jaime Zaldivar-Rae , Rossanna Rodríguez-Canul

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Abstract

Flounder fish Cyclopsetta fimbriata and Syacium papillosum (Family: Paralichidae) inhabit the Gulf of Mexico (GoM) where there is a constant menace of oil spill events. Both can be sentinel species for pollutants associated with human activities, but the absence of markers has hampered their genetic studies. In this study we constructed two de novo transcriptomes of C. fimbriata and S. papillosum collected at 40–100 m below the sea surface and were used to develop microsatellite markers. A total of 42,273,686 and 38,304,544 raw reads were obtained for C. fimbriata and S. papillosum. After cleaning, we recovered 25,087,948 (59.3 %) reads with Q value >30 for S. papillosum and 22,062,086 (50 %) reads with Q value >30 for C. fimbriata. The transcriptome of C. fimbriata had 69,333 transcripts with an average GC content of 47.68 %. The length of contigs ranged from 248 bp to 15,452 bp, with an N50 length of 1608 bp. The S. papillosum transcriptome had 75,623 transcripts with an average GC content of 48.27 % with a length of contigs ranging from 181 bp to 16,638 bp, with an N50 length of 1582 bp. Then, 38 microsatellite loci for C. fimbriata and 40 microsatellite loci for S. papillosum were tested on 30 individuals of each species and 20 polymorphic microsatellite loci (50 %) were obtained for S. papillosum and 13 (34.21 %) for C. fimbriata. The Polymorphism Information Content (PIC) values were 0.8 for C. fimbriata and 0.9 for S. papillosum. Their utility for subsequent genetic population studies is discussed.

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利用新转录组测序技术开发拟比目鱼（Cyclopsetta fibriata）和拟鱼科（Syacium papillosum）微卫星标记

比目鱼 Cyclopsetta fimbriata 和 Syacium papillosum（科：比目鱼属）栖息在墨西哥湾（GoM），那里经常受到漏油事件的威胁。这两种生物都是人类活动相关污染物的哨兵物种，但由于缺乏标记物，它们的遗传研究受到了阻碍。在这项研究中，我们构建了在海面以下 40-100 米处采集的 C. fimbriata 和 S. papillosum 的两个全新转录组，并将其用于开发微卫星标记。C. fimbriata和S. papillosum的原始读数分别为42,273,686和38,304,544。经过清理，我们为 S. papillosum 恢复了 25,087,948 个（59.3%）Q 值为 30 的读数，为 C. fimbriata 恢复了 22,062,086 个（50%）Q 值为 30 的读数。C. fimbriata 的转录组有 69,333 个转录本，平均 GC 含量为 47.68%。等位基因长度从 248 bp 到 15,452 bp 不等，N50 长度为 1608 bp。S.papillosum转录组有75623个转录本，平均GC含量为48.27%，等位基因长度从181 bp到16638 bp不等，N50长度为1582 bp。然后，在每个物种的 30 个个体上测试了 38 个 C. fimbriata 和 40 个 S. papillosum 的微卫星位点，结果发现 S. papillosum 有 20 个多态微卫星位点（50%），C. fimbriata 有 13 个多态微卫星位点（34.21%）。C. fimbriata 的多态性信息含量（PIC）值为 0.8，S. papillosum 为 0.9。讨论了它们在后续遗传种群研究中的用途。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.