Genome‐wide survey of open chromatin regions in two swallowtail butterflies Papilio machaon and P. bianor. Issue 2 (31st July 2022)

• Record Type: Journal Article
• Authors: Wan, Wen‐ting; Hu, Ping; Chang, Zhou; Ren, Yan‐dong; Dong, Zhi‐wei; Yang, Jie; Pan, Xiang‐yu; He, Jin‐wu; Liu, Wei; Liu, Gui‐chun; Zhao, Ruo‐ping; Mao, Chu‐yang; Li, Jun; Wang, Wen; Li, Xue‐yan
• Is Part Of: Archives of insect biochemistry and physiology. Volume 111:Issue 2(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-07-31
• Subjects: ATAC‐seq -- butterflies -- chromatin accessibility -- regulatory elements; Insects -- Physiology -- Periodicals; Insect biochemistry -- Periodicals; 595.701572
• DOI: 10.1002/arch.21952
• Languages: English
• ISSNs: 0739-4462

Abstract

Abstract: Papilio machaon was assigned as the type species for all butterflies by Linnaeus and P. bianor is a congener but exhibits a great difference in morphology (especially larva and adult color pattern) and larval host plants from P. machaon . Thus, they are the ideal models to investigate genetic mechanisms underlying morphology and plasticity between congeners. The reference genomes of both species were dissected in our previous studies, but little is known about their regulatory genome and the epigenetic regulation of gene expression throughout developmental stages. Here, we profiled the chromatin accessibility and gene expression of three developmental stages (the 4th instar larva [L4], the 5th instar larva [L5], and pupa [P]) using transposase accessible chromatin sequencing (ATAC‐seq) and RNA‐seq. Results showed that many accessible chromatin peaks were identified at three developmental stages (peak number, P. machaon : 44, 977 [L4], 36, 919 [L5], 47, 147 [P]; P. bianor : 20, 341 [L4], 44, 668 [L5], 62, 249 [P]). Moreover, the number of differentially accessible peaks and differentially expressed genes between larval stages of each butterfly species are significantly fewer than that between larval and pupal stages, suggesting a higher similarity within larvae and a significant difference between larvae and pupae. This study added the annotated information of chromatin accessibility genome‐wide of the two papilionid species and will promote the investigation of gene regulation in butterfly evolution. Abstract : Chromatin accessibility and gene expression of three developmental stages of Papilio machaon and P. bianor was characterized using transposase accessible chromatin sequencing (ATAC‐seq) and RNA‐seq. We identify over 20, 000 accessible chromatin peaks at different developmental stages, which showed a significant signal at the transcription start site regions. This data set provides clues for possible regulatory elements in the butterfly genome in studying the molecular basis of phenotypic trait differences among different ontogenetic stages and between species. Research highlights: 1. We identify over 20, 000 accessible chromatin peaks at different developmental stages of Papilio machaon and P. bianor, which showed a significant signal at the transcription start site regions. 2. The number of differentially accessible peaks and differentially expressed genes between larval stages of each butterfly species are significantly fewer than that between larval and pupal stages. 3. The annotated information on chromatin accessibility genome‐wide of the two papilionid species will provide a valuable resource for investigating the phenotypic evolution of butterflies.