Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera
RNA-seq has proven to be a powerful tool to unravel various aspects of the transcriptome, especially the quantification of alternative splicing (AS) that leads to isoform diversity. The honey bee (Apis mellifera) is an important model organism for studying the molecular underpinnings of behavioral p...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2019-04-01
|
| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.118.200857 |
| _version_ | 1818888188720054272 |
|---|---|
| author | Kavya Kannan Molly Shook Yang Li Gene E. Robinson Jian Ma |
| author_facet | Kavya Kannan Molly Shook Yang Li Gene E. Robinson Jian Ma |
| author_sort | Kavya Kannan |
| collection | DOAJ |
| description | RNA-seq has proven to be a powerful tool to unravel various aspects of the transcriptome, especially the quantification of alternative splicing (AS) that leads to isoform diversity. The honey bee (Apis mellifera) is an important model organism for studying the molecular underpinnings of behavioral plasticity and social behavior, and recent RNA-seq studies of honey bees have revealed AS patterns and their regulation by DNA methylation. However, tissue-specific AS patterns have not been fully explored. In this paper, we characterized AS patterns in two different honey bee tissue types, and also explored their conservation and regulation. We used the RNA-seq data from brain and fat body to improve the existing models of honey bee genes and identified tissue-specific AS patterns. We found that AS genes show high conservation between honey bee and Drosophila melanogaster. We also confirmed and extended previous findings of a correlation between gene body DNA methylation and AS patterns, providing further support for the role of DNA methylation in regulating AS. In addition, our analysis suggests distinct functional roles for tissue-specific alternatively spliced genes. Taken together, our work provides new insights into the conservation and dynamics of AS patterns across different tissue types. |
| first_indexed | 2024-12-19T16:49:09Z |
| format | Article |
| id | doaj.art-d916d4dd64814e9da982f4e2110dec68 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-19T16:49:09Z |
| publishDate | 2019-04-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-d916d4dd64814e9da982f4e2110dec682022-12-21T20:13:35ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362019-04-01941055106310.1534/g3.118.2008579Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis melliferaKavya KannanMolly ShookYang LiGene E. RobinsonJian MaRNA-seq has proven to be a powerful tool to unravel various aspects of the transcriptome, especially the quantification of alternative splicing (AS) that leads to isoform diversity. The honey bee (Apis mellifera) is an important model organism for studying the molecular underpinnings of behavioral plasticity and social behavior, and recent RNA-seq studies of honey bees have revealed AS patterns and their regulation by DNA methylation. However, tissue-specific AS patterns have not been fully explored. In this paper, we characterized AS patterns in two different honey bee tissue types, and also explored their conservation and regulation. We used the RNA-seq data from brain and fat body to improve the existing models of honey bee genes and identified tissue-specific AS patterns. We found that AS genes show high conservation between honey bee and Drosophila melanogaster. We also confirmed and extended previous findings of a correlation between gene body DNA methylation and AS patterns, providing further support for the role of DNA methylation in regulating AS. In addition, our analysis suggests distinct functional roles for tissue-specific alternatively spliced genes. Taken together, our work provides new insights into the conservation and dynamics of AS patterns across different tissue types.http://g3journal.org/lookup/doi/10.1534/g3.118.200857Honey beealternative splicingRNA-seqtranscriptomecomparative genomics |
| spellingShingle | Kavya Kannan Molly Shook Yang Li Gene E. Robinson Jian Ma Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera G3: Genes, Genomes, Genetics Honey bee alternative splicing RNA-seq transcriptome comparative genomics |
| title | Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera |
| title_full | Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera |
| title_fullStr | Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera |
| title_full_unstemmed | Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera |
| title_short | Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera |
| title_sort | comparative analysis of brain and fat body gene splicing patterns in the honey bee apis mellifera |
| topic | Honey bee alternative splicing RNA-seq transcriptome comparative genomics |
| url | http://g3journal.org/lookup/doi/10.1534/g3.118.200857 |
| work_keys_str_mv | AT kavyakannan comparativeanalysisofbrainandfatbodygenesplicingpatternsinthehoneybeeapismellifera AT mollyshook comparativeanalysisofbrainandfatbodygenesplicingpatternsinthehoneybeeapismellifera AT yangli comparativeanalysisofbrainandfatbodygenesplicingpatternsinthehoneybeeapismellifera AT geneerobinson comparativeanalysisofbrainandfatbodygenesplicingpatternsinthehoneybeeapismellifera AT jianma comparativeanalysisofbrainandfatbodygenesplicingpatternsinthehoneybeeapismellifera |