Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta
Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA seq...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-11-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/3998.pdf |
| _version_ | 1797418793273655296 |
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| author | Kishor Dhaygude Kalevi Trontti Jenni Paviala Claire Morandin Christopher Wheat Liselotte Sundström Heikki Helanterä |
| author_facet | Kishor Dhaygude Kalevi Trontti Jenni Paviala Claire Morandin Christopher Wheat Liselotte Sundström Heikki Helanterä |
| author_sort | Kishor Dhaygude |
| collection | DOAJ |
| description | Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon. |
| first_indexed | 2024-03-09T06:38:05Z |
| format | Article |
| id | doaj.art-3ff97ba2dd7442009e3fc54181aa1847 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:38:05Z |
| publishDate | 2017-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-3ff97ba2dd7442009e3fc54181aa18472023-12-03T10:54:49ZengPeerJ Inc.PeerJ2167-83592017-11-015e399810.7717/peerj.3998Transcriptome sequencing reveals high isoform diversity in the ant Formica exsectaKishor Dhaygude0Kalevi Trontti1Jenni Paviala2Claire Morandin3Christopher Wheat4Liselotte Sundström5Heikki Helanterä6Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, FinlandDepartment of Biosciences, Neurogenomics Laboratory, University of Helsinki, Helsinki, FinlandCentre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, FinlandCentre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, FinlandDepartment of Zoology Ecology, Stockholm University, Stockholm, SwedenCentre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, FinlandCentre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, FinlandTranscriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.https://peerj.com/articles/3998.pdfPool-seqRNA-sequencingAntsTranscriptome de novo assemblyHymenopteraTranscriptomics |
| spellingShingle | Kishor Dhaygude Kalevi Trontti Jenni Paviala Claire Morandin Christopher Wheat Liselotte Sundström Heikki Helanterä Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta PeerJ Pool-seq RNA-sequencing Ants Transcriptome de novo assembly Hymenoptera Transcriptomics |
| title | Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta |
| title_full | Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta |
| title_fullStr | Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta |
| title_full_unstemmed | Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta |
| title_short | Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta |
| title_sort | transcriptome sequencing reveals high isoform diversity in the ant formica exsecta |
| topic | Pool-seq RNA-sequencing Ants Transcriptome de novo assembly Hymenoptera Transcriptomics |
| url | https://peerj.com/articles/3998.pdf |
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