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. 2013 Jul 12;8(7):e68452.
doi: 10.1371/journal.pone.0068452. Print 2013.

Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome

Fanyue Sun  1 , Shikai Liu, Xiaoyu Gao, Yanliang Jiang, Dayan Perera, Xiuli Wang, Chao Li, Luyang Sun, Jiaren Zhang, Ludmilla Kaltenboeck, Rex Dunham, Zhanjiang Liu
Affiliations

Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome

Fanyue Sun et al. PLoS One. .

Abstract

Background: Catfish has a male-heterogametic (XY) sex determination system, but genes involved in gonadogenesis, spermatogenesis, testicular determination, and sex determination are poorly understood. As a first step of understanding the transcriptome of the testis, here, we conducted RNA-Seq analysis using high throughput Illumina sequencing.

Methodology/principal findings: A total of 269.6 million high quality reads were assembled into 193,462 contigs with a N50 length of 806 bp. Of these contigs, 67,923 contigs had hits to a set of 25,307 unigenes, including 167 unique genes that had not been previously identified in catfish. A meta-analysis of expressed genes in the testis and in the gynogen (double haploid female) allowed the identification of 5,450 genes that are preferentially expressed in the testis, providing a pool of putative male-biased genes. Gene ontology and annotation analysis suggested that many of these male-biased genes were involved in gonadogenesis, spermatogenesis, testicular determination, gametogenesis, gonad differentiation, and possibly sex determination.

Conclusion/significance: We provide the first transcriptome-level analysis of the catfish testis. Our analysis would lay the basis for sequential follow-up studies of genes involved in sex determination and differentiation in catfish.

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Conflict of interest statement

Competing Interests: The co-author Zhanjiang Liu is a PLOS ONE Editorial Board member. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. GO term classifications of channel catfish testis transcriptome.
GO annotations were based on zebrafish RefSeq and GO-terms were processed by Blast2Go and categorized at level 2 into three major functional categories (biological process, cellular component, and molecular function).
Figure 2
Figure 2. Putative catfish spermatogenic pathway based on RNA-Seq expression signatures in channel catfish testis.
Figure 3
Figure 3. Linkage group distribution of the male-biased genes.
Note that the proportion of male-biased genes per linkage group is similar except for chromosomes 1, 6, 8, 7, 24 and 27 (shown in red for linkage groups with high numbers of male-biased genes and in yellow for linkage groups with low numbers of male-biased genes).
See this image and copyright information in PMC

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Grants and funding

This project was supported by Agriculture and Food Research Initiative (AFRI) Competitive Grants no. 2009-35205-05101, 2010-65205-20356 and 2012-67015-19410 from the USDA National Institute of Food and Agriculture (NIFA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.