De novo transcriptome assembly and sex-biased gene expression in the gonads of Amur catfish (Silurus asotus)

Shen, Fang‐Fang; Long, Yong; Li, Fengyang; Ge, Guodong; Song, Guangliang; Li, Qing; Qiao, Zhengxue

doi:10.1016/j.ygeno.2020.01.026

Cited by 18 publications

(13 citation statements)

References 63 publications

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“…In addition, sequences of human origin (9,196,859 total reads; mean proportion, 21.1%) were removed using DeconSeq software, version 0.4.3 ( 46 ). The data were then further processed using cmpfastq software for separation of paired and unpaired reads ( 47 ).…”

Section: Methodsmentioning

confidence: 99%

Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses

et al. 2021

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Section: Methodsmentioning

confidence: 99%

Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses

et al. 2021

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“…Usually, sex determination in gonochoric species such as P. lividus involves a robust transcriptional regulation (Nef et al 2005). Interestingly, in the majority of these species the male specimens have a higher number of genes being expressed in the gonads (Nef et al 2005, Tao et al 2013, Teaniniuraitemoana et al 2014, Shen et al 2020). Notwithstanding, there are some species where the opposite also occurs (González-Castellano et al 2019, Piprek et al 2019).…”

Section: Resultsmentioning

confidence: 99%

The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: identification of sex-related and lipid biosynthesis genes

Machado

Fernández-Boo

Nande

et al. 2021

Preprint

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Paracentrotus lividus is the most abundant, distributed and desirable echinoid species in Europe. Although, economically important, this species has scarce genomic resources available. Here, we produced and comprehensively characterized the male and female gonad transcriptome of P. lividus. The P. lividus transcriptome assembly has 53,865 transcripts, an N50 transcript length of 1,842 bp and an estimated gene completeness of 97.4% and 95.6% in Eukaryota and Metazoa BUSCO databases, respectively. Differential gene expression analyses yielded a total of 3371 and 3351 up regulated genes in P. lividus male and female gonad tissues, respectively. Additionally, we analysed and validated a catalogue of pivotal transcripts involved in sexual development and determination (206 transcripts) as well as in biosynthesis and storage of lipids (119 transcripts) in male and female specimens. This study provides a valuable transcriptomic resource and will contribute for the future conservation of the species as well as the exploitation in aquaculture settings.HighlightsAssembly of a reference transcriptome of Paracentrotus lividus gonads.Differential gene expression between males and female gonads of Paracentrotus lividus.Identification and validation of pivotal genes involved in biosynthesis and storage of lipids.

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“…Transcriptomic analysis between different sexes has been carried out in many aquaculture species to identify sex-specific markers and understand sex differentiation processes and sexual development ( Ding et al, 2020 ; Lobo et al, 2020 ; Shen et al, 2020 ; Wang et al, 2020b ). In this study, we compared the expression patterns in male and female hypothalamus and pituitary tissues.…”

Section: Discussionmentioning

confidence: 99%

Updated Genome Assembly of Bighead Carp (Hypophthalmichthys nobilis) and Its Differences Between Male and Female on Genomic, Transcriptomic, and Methylation Level

Zhou

Liu

et al. 2021

Front. Genet.

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Cyprinidae is one of the largest family in freshwater fishes, and it is most intensively cultured fish taxon of the world. However, studies about sex determination in this large family is still rear, and one of the reasons is lack of high quality and complete genome. Here, we used nanopore to sequence the genome of a male bighead carp, obtaining contig N50 = 24.25 Mb, which is one of the best assemblies in Cyprinidae. Five males and five females were re-sequenced, and a male-specific region on LG19 was confirmed. We find this region holds many male-specific markers in other Cyprinidae fishes, such as grass carp and silver carp. Transcriptome analyses of hypothalamus and pituitary tissues showed that several sex-specific differentially expressed genes were associated with steroid biosynthesis. The UCH64E gene, located in the male-specific region on LG19, showed higher expression levels in male than female tissues of bighead carp. The methyl-RAD of hypothalamus tissues between males and females indicated that the sexual methylation differences are significant in bighead carp. We also compared the methylation sites recognized using methyl-RAD and nanopore raw reads and found that approximately 73% of the methylation sites identified using methyl-RAD were within nanopore CpG sites.

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De novo transcriptome assembly and sex-biased gene expression in the gonads of Amur catfish (Silurus asotus)

Cited by 18 publications

References 63 publications

Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses

Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses

The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: identification of sex-related and lipid biosynthesis genes

Updated Genome Assembly of Bighead Carp (Hypophthalmichthys nobilis) and Its Differences Between Male and Female on Genomic, Transcriptomic, and Methylation Level

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