Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar
Abstract Background The tropical gar (Atractosteus tropicus) is the southernmost species of the seven extant species of gar fishes in the world. In Mexico and Central America, the species is an important food source due to its nutritional quality and low price. Despite its regional importance and in...
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| Format: | Article |
| Language: | English |
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BMC
2017-04-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3652-3 |
| _version_ | 1828171123329597440 |
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| author | Kayla M. Cribbin Corey R. Quackenbush Kyle Taylor Lenin Arias-Rodriguez Joanna L. Kelley |
| author_facet | Kayla M. Cribbin Corey R. Quackenbush Kyle Taylor Lenin Arias-Rodriguez Joanna L. Kelley |
| author_sort | Kayla M. Cribbin |
| collection | DOAJ |
| description | Abstract Background The tropical gar (Atractosteus tropicus) is the southernmost species of the seven extant species of gar fishes in the world. In Mexico and Central America, the species is an important food source due to its nutritional quality and low price. Despite its regional importance and increasing concerns about overexploitation and habitat degradation, basic genetic information on the tropical gar is lacking. Determining genetic information on the tropical gar is important for the sustainable management of wild populations, implementation of best practices in aquaculture settings, evolutionary studies of ancient lineages, and an understanding of sex-specific gene expression. In this study, the transcriptome of the tropical gar was sequenced and assembled de novo using tissues from three males and three females using Illumina sequencing technology. Sex-specific and highly differentially expressed transcripts in brain and muscle tissues between adult males and females were subsequently identified. Results The transcriptome was assembled de novo resulting in 80,611 transcripts with a contig N50 of 3,355 base pairs and over 168 kilobases in total length. Male muscle, brain, and gonad as well as female muscle and brain were included in the assembly. The assembled transcriptome was annotated to identify the putative function of expressed transcripts using Trinotate and SwissProt, a database of well-annotated proteins. The brain and muscle datasets were then aligned to the assembled transcriptome to identify transcripts that were differentially expressed between males and females. The contrast between male and female brain identified 109 transcripts from 106 genes that were significantly differentially expressed. In the muscle comparison, 82 transcripts from 80 genes were identified with evidence for significant differential expression. Almost all genes identified as differentially expressed were sex-specific. The differentially expressed transcripts were enriched for genes involved in cellular functioning, signaling, immune response, and tissue-specific functions. Conclusions This study identified differentially expressed transcripts between male and female gar in muscle and brain tissue. The majority of differentially expressed transcripts had sex-specific expression. Expanding on these findings to other developmental stages, populations, and species may lead to the identification of genetic factors contributing to the skewed sex ratio seen in the tropical gar and of sex-specific differences in expression in other species. Finally, the transcriptome assembly will open future research avenues on tropical gar development, cell function, environmental resistance, and evolution in the context of other early vertebrates. |
| first_indexed | 2024-04-12T03:22:33Z |
| format | Article |
| id | doaj.art-0b9362b20b804c4cb0a1c876dc3878ea |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T03:22:33Z |
| publishDate | 2017-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-0b9362b20b804c4cb0a1c876dc3878ea2022-12-22T03:49:50ZengBMCBMC Genomics1471-21642017-04-011811910.1186/s12864-017-3652-3Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical garKayla M. Cribbin0Corey R. Quackenbush1Kyle Taylor2Lenin Arias-Rodriguez3Joanna L. Kelley4School of Biological Sciences, Washington State UniversitySchool of Biological Sciences, Washington State UniversitySchool of Biological Sciences, Washington State UniversityDivisión Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT)School of Biological Sciences, Washington State UniversityAbstract Background The tropical gar (Atractosteus tropicus) is the southernmost species of the seven extant species of gar fishes in the world. In Mexico and Central America, the species is an important food source due to its nutritional quality and low price. Despite its regional importance and increasing concerns about overexploitation and habitat degradation, basic genetic information on the tropical gar is lacking. Determining genetic information on the tropical gar is important for the sustainable management of wild populations, implementation of best practices in aquaculture settings, evolutionary studies of ancient lineages, and an understanding of sex-specific gene expression. In this study, the transcriptome of the tropical gar was sequenced and assembled de novo using tissues from three males and three females using Illumina sequencing technology. Sex-specific and highly differentially expressed transcripts in brain and muscle tissues between adult males and females were subsequently identified. Results The transcriptome was assembled de novo resulting in 80,611 transcripts with a contig N50 of 3,355 base pairs and over 168 kilobases in total length. Male muscle, brain, and gonad as well as female muscle and brain were included in the assembly. The assembled transcriptome was annotated to identify the putative function of expressed transcripts using Trinotate and SwissProt, a database of well-annotated proteins. The brain and muscle datasets were then aligned to the assembled transcriptome to identify transcripts that were differentially expressed between males and females. The contrast between male and female brain identified 109 transcripts from 106 genes that were significantly differentially expressed. In the muscle comparison, 82 transcripts from 80 genes were identified with evidence for significant differential expression. Almost all genes identified as differentially expressed were sex-specific. The differentially expressed transcripts were enriched for genes involved in cellular functioning, signaling, immune response, and tissue-specific functions. Conclusions This study identified differentially expressed transcripts between male and female gar in muscle and brain tissue. The majority of differentially expressed transcripts had sex-specific expression. Expanding on these findings to other developmental stages, populations, and species may lead to the identification of genetic factors contributing to the skewed sex ratio seen in the tropical gar and of sex-specific differences in expression in other species. Finally, the transcriptome assembly will open future research avenues on tropical gar development, cell function, environmental resistance, and evolution in the context of other early vertebrates.http://link.springer.com/article/10.1186/s12864-017-3652-3Atractosteus tropicusTropical garDifferential expressionTranscriptome assemblyEarly vertebrates |
| spellingShingle | Kayla M. Cribbin Corey R. Quackenbush Kyle Taylor Lenin Arias-Rodriguez Joanna L. Kelley Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar BMC Genomics Atractosteus tropicus Tropical gar Differential expression Transcriptome assembly Early vertebrates |
| title | Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar |
| title_full | Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar |
| title_fullStr | Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar |
| title_full_unstemmed | Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar |
| title_short | Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar |
| title_sort | sex specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar |
| topic | Atractosteus tropicus Tropical gar Differential expression Transcriptome assembly Early vertebrates |
| url | http://link.springer.com/article/10.1186/s12864-017-3652-3 |
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