Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae)
Background Genetic pathways involved with flower color and shape are thought to play an important role in the development of flowers associated with different pollination syndromes, such as those associated with bee, butterfly, or hummingbird pollination. Because pollination syndromes are complex tr...
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PeerJ Inc.
2020-03-01
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| Online Access: | https://peerj.com/articles/8778.pdf |
| _version_ | 1797425679306850304 |
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| author | Wade R. Roberts Eric H. Roalson |
| author_facet | Wade R. Roberts Eric H. Roalson |
| author_sort | Wade R. Roberts |
| collection | DOAJ |
| description | Background Genetic pathways involved with flower color and shape are thought to play an important role in the development of flowers associated with different pollination syndromes, such as those associated with bee, butterfly, or hummingbird pollination. Because pollination syndromes are complex traits that are orchestrated by multiple genes and pathways, the gene regulatory networks have not been explored. Gene co-expression networks provide a systems level approach to identify important contributors to floral diversification. Methods RNA-sequencing was used to assay gene expression across two stages of flower development (an early bud and an intermediate stage) in 10 species of Achimenes (Gesneriaceae). Two stage-specific co-expression networks were created from 9,503 orthologs and analyzed to identify module hubs and the network periphery. Module association with bee, butterfly, and hummingbird pollination syndromes was tested using phylogenetic mixed models. The relationship between network connectivity and evolutionary rates (dN/dS) was tested using linear models. Results Networks contained 65 and 62 modules that were largely preserved between developmental stages and contained few stage-specific modules. Over a third of the modules in both networks were associated with flower color, shape, and pollination syndrome. Within these modules, several hub nodes were identified that related to the production of anthocyanin and carotenoid pigments and the development of flower shape. Evolutionary rates were decreased in highly connected genes and elevated in peripheral genes. Discussion This study aids in the understanding of the genetic architecture and network properties underlying the development of floral form and provides valuable candidate modules and genes for future studies. |
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| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:19:33Z |
| publishDate | 2020-03-01 |
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| spelling | doaj.art-771e2dfaeb6e40f4a210c8e6cb9cffa62023-12-02T21:53:52ZengPeerJ Inc.PeerJ2167-83592020-03-018e877810.7717/peerj.8778Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae)Wade R. Roberts0Eric H. Roalson1School of Biological Sciences, Washington State University, Pullman, WA, USASchool of Biological Sciences, Washington State University, Pullman, WA, USABackground Genetic pathways involved with flower color and shape are thought to play an important role in the development of flowers associated with different pollination syndromes, such as those associated with bee, butterfly, or hummingbird pollination. Because pollination syndromes are complex traits that are orchestrated by multiple genes and pathways, the gene regulatory networks have not been explored. Gene co-expression networks provide a systems level approach to identify important contributors to floral diversification. Methods RNA-sequencing was used to assay gene expression across two stages of flower development (an early bud and an intermediate stage) in 10 species of Achimenes (Gesneriaceae). Two stage-specific co-expression networks were created from 9,503 orthologs and analyzed to identify module hubs and the network periphery. Module association with bee, butterfly, and hummingbird pollination syndromes was tested using phylogenetic mixed models. The relationship between network connectivity and evolutionary rates (dN/dS) was tested using linear models. Results Networks contained 65 and 62 modules that were largely preserved between developmental stages and contained few stage-specific modules. Over a third of the modules in both networks were associated with flower color, shape, and pollination syndrome. Within these modules, several hub nodes were identified that related to the production of anthocyanin and carotenoid pigments and the development of flower shape. Evolutionary rates were decreased in highly connected genes and elevated in peripheral genes. Discussion This study aids in the understanding of the genetic architecture and network properties underlying the development of floral form and provides valuable candidate modules and genes for future studies.https://peerj.com/articles/8778.pdfFlowersCo-expression clusteringGesneriaceaeEvolutionary ratesPollination syndromeRNA-seq |
| spellingShingle | Wade R. Roberts Eric H. Roalson Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae) PeerJ Flowers Co-expression clustering Gesneriaceae Evolutionary rates Pollination syndrome RNA-seq |
| title | Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae) |
| title_full | Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae) |
| title_fullStr | Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae) |
| title_full_unstemmed | Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae) |
| title_short | Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae) |
| title_sort | co expression clustering across flower development identifies modules for diverse floral forms in achimenes gesneriaceae |
| topic | Flowers Co-expression clustering Gesneriaceae Evolutionary rates Pollination syndrome RNA-seq |
| url | https://peerj.com/articles/8778.pdf |
| work_keys_str_mv | AT waderroberts coexpressionclusteringacrossflowerdevelopmentidentifiesmodulesfordiversefloralformsinachimenesgesneriaceae AT erichroalson coexpressionclusteringacrossflowerdevelopmentidentifiesmodulesfordiversefloralformsinachimenesgesneriaceae |