果蠅基因與調情—以比較基因體學解碼果蠅翅斑和翅膀展示的共同演化

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娜吉(Ateesha Negi) 查詢紙本館藏

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論文名稱

果蠅基因與調情—以比較基因體學解碼果蠅翅斑和翅膀展示的共同演化
(Fly Gene and Flirting: Comparative Genomics to Unravel the Co-evolving Wing-spot and Mating Display in Drosophila)

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至系統瀏覽論文 (2025-6-30以後開放)

摘要(中)

體色是動物中一種最多樣且常為自然選汰或性選汰作用的性狀，而某些果蠅物種的雄性具有性別專一的黑色翅斑，被認為賦予雄性交配優勢，並與向雌蟲展示翅膀的行為在演化上相關聯。雖然之前研究已經發現此兩種性狀之間存在遺傳相關性，但分子層面上的遺傳機制仍然未明。本研究的目的是透過比較具有翅斑和翅膀展示性狀的牽牛花果蠅(D. elegans)與缺乏這些性狀的高山果蠅(D. gunungcola)兩物種，探討果蠅翅斑和翅膀展示共同演化的遺傳機制，並填補先前研究中未明之處。由於缺乏高山果蠅的基因體資料，本研究首先壢用 PacBio Sequel 平台對經過多代近親交配的高山果蠅品系進行全基因體的長片段定序，獲得約 12Gb 的原始定序資料，進而完成了幾乎覆蓋染色體全長的基因體組裝。經基因註釋後，獲得 13,950 個蛋白質編碼基因，比對黑腹果蠅和牽牛花果蠅的基因體結果顯示，所組裝的基因體具有完整性。此外，利用 Benchmarking Universal Single-Copy Orthologs (BUSCOs)分析顯示，在此一組裝好的基因體中，98.8% BUSCOs 為全長，這也支持此基因體組裝的高度完整性。接著，研究分析了果蠅的嗅覺受體基因家族，發現牽牛花果蠅和高山果蠅的基因體中皆缺失了與嗅覺相關的 Or49a 和 Or67a 兩基因，此兩姊妹物種皆以花作為繁殖場所，因此基因的缺失可能會影響著牽牛花果蠅亞種群生態專一化和繁殖習性，並顯示遺傳學、行為和生態適應之間複雜的交互作用。接下來，研究採用比較轉錄體學方法，探討可能驅動牽牛花果蠅翅斑和翅膀展示之間共同演化的遺傳機制，研究結果顯示發現，兩個知名轉錄因子基因，即參與黑色素生合成的 bifid 基因和影響求偶行為的 fruitless 基因，在牽牛花果蠅雄蟲中表現量增加。本篇論文的研究成果為果蠅性狀共演化和生態專一化的遺傳和演化提供了重要見解，不僅展示了先進基因體技術和方法的價值，也為進一步研究果蠅的遺傳、行為和生態適應之間複雜的交互作用設立了一個平台。

摘要(英)

Pigmentation is one of the traits that exhibits the most variation among animals and is commonly subjected to either or both, natural and sexual selection. Male-specific wing pigmentation, conferring mating advantage, displays an evolutionary association with frontal wing display across various Drosophila species groups. Though a genetic correlation between these traits has been suggested, the explicit genetic mechanism at the molecular level has remained elusive. The present study bridges this knowledge gap by investigating the genetic mechanisms underpinning the co- evolution of wing-spot and mating display in Drosophila, with a primary focus on D. elegans, the species with wing spots and wing display, and D. gunungcola, the sister species lacking both traits. As a crucial step, a reference-quality annotated genome was assembled for D. gunungcola, a species previously lacking such a resource. The PacBio Sequel platform enabled the sequencing of the inbred line of D. gunungcola, generating around 12 Gb of raw sequencing data and facilitating a nearly complete genome assembly at the chromosomal level. The genome assembly revealed a total of 13,950 protein-coding genes, indicating a high level of completeness when compared to other Drosophila species like D. melanogaster and D. elegans. This assertion is supported quantitatively through Benchmarking Universal Single-Copy Orthologs (BUSCOs) analysis, which showed 98.8% of BUSCOs present in full length. Further investigation into the olfactory receptor gene families in Drosophila disclosed intriguing genetic findings. Notably, the genes Or49a and OR67a, essential for olfaction, were found to be absent in flower-breeding sibling species within the Drosophila elegans species subgroup. The implications of these gene loss events could be far-reaching, potentially affecting ecological specialization and breeding habits, and hinting at a complex interplay between genetics, behavior, and ecological adaptation. Employing comparative transcriptomics, this study has unveiled genetic mechanisms potentially driving the co-evolution of wing spots and mating displays in D. elegans. The transcription factors bifid and fruitless, known to play roles in melanin biosynthesis and courtship behavior respectively, were found to be specifically upregulated in male D. elegans, a species known for its wing spots and mating displays. This thesis offers valuable insights into the genetics and evolution of Drosophila, with particular emphasis on trait co-evolution and ecological specialization. It not only underscores the value of advanced genomic technologies and methodologies, but also sets a platform for future investigations into the fascinating interplay between genetics, behavior, and ecological adaptations in Drosophila.

關鍵字(中)

★ 牽牛花果蠅亞種群
★ 基因體組裝
★ 食花果蠅
★ 翅斑
★ 翅膀展示
★ 比較轉錄體學

關鍵字(英)

★ Drosophila elegans species subgroup
★ Genome assembly
★ Flower-breeders
★ Wing-spot
★ Mating display
★ Comparative transcriptomics

論文目次

中文摘要......................................................................................................... i
Abstract........................................................................................................... ii
Acknowledgments............................................................................................. iv
Table of Contents............................................................................................... vii
List of Figures................................................................................................... ix
List of Tables ................................................................................................... xii
Abbreviations................................................................................................... xiv
Chapter I. Introduction to novel traits and co-evolution in Drosophila........................ 1
Chapter II. Long-read-based assembly and annotation of the Drosophila gunungcola genome: a valuable resource for evolutionary studies................................................
14
Abstract........................................................................................................ 14
Introduction.................................................................................................. 15
Material and Methods..................................................................................... 17
Results......................................................................................................... 26
Discussion.................................................................................................... 31
Chapter III. Chemosensory Receptors Comparison of Flower-Breeding Drosophila elegans Species Subgroup reveals loss of Or49a and Or67a.......................................
51
Abstract........................................................................................................ 51
Introduction................................................................................................... 52
Material and Methods...................................................................................... 54
Results.......................................................................................................... 56
Discussion..................................................................................................... 58
Chapter IV. Comparative transcriptomics reveals candidate genes for co-evolving wing spot and mating displays in Drosophila elegans species-subgroup..............................
74
Abstract........................................................................................................ 74
Introduction................................................................................................... 75
Material and Methods...................................................................................... 78
Results.......................................................................................................... 85
Discussion..................................................................................................... 95
Chapter V. Conclusion and Future Direction........................................................... 136
References........................................................................................................ 138
Appendix A. Code availability for chapter II…....................................................... 148
Appendix B. QC and alignment metrics for chapter IV............................................. 154
Appendix C. Code availability for chapter IV......................................................... 157
Appendix D. GO and KEGG analysis for chapter IV................................................. 159
Appendix E. D. elegans male-biased DEGs............................................................ 185

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指導教授

葉淑丹(Shu-Dan Yeh)

審核日期

2023-6-29

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