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

參考文獻

¬¬¬References
1. Ai, M., Min, S., Grosjean, Y., Leblanc, C., Bell, R., Benton, R. and Suh, G.S., 2010. Acid sensing by the Drosophila olfactory system. Nature, 468(7324), pp.691-695.
2. Akitake, B., Ren, Q., Boiko, N., Ni, J., Sokabe, T., Stockand, J.D., Eaton, B.A. and Montell, C., 2015. Coordination and fine motor control depend on Drosophila TRPγ. Nature communications, 6(1), p.7288.
3. Anderson, E.W., Fornell, C. and Lehmann, D.R., 1994. Customer satisfaction, market share, and profitability: Findings from Sweden. Journal of marketing, 58(3), pp.53-66.
4. Albertson, R. C., Streelman, J. T., Kocher, T. D., and Yelick, P. C. (2005). Integration and evolution of the cichlid mandible: the molecular basis of alternate feeding strategies. Proceedings of the National Aademy of Sciences, 102(45), 16287-16292.
5. Arnoult L, Su KFY, Manoel D, Minervino C, Magrina J, Gompel N, Prud′homme B 2013. Emergence and Diversification of Fly Pigmentation Through Evolution of a Gene Regulatory Module. Science 339: 1423-1426. doi: 10.1126/science.1233749
6. Babbage, M. (2010). The Pfam protein families database. Nucleic Acids Research, 38 (Database issue), D211-22. doi: 10.1093/nar/gkp985.
7. Baker, B.S., Taylor, B.J. and Hall, J.C., 2001. Are complex behaviors specified by dedicated regulatory genes? Reasoning from Drosophila. Cell, 105(1), pp.13-24.
8. Ballard, J.W.O., 2000. Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup. Journal of molecular evolution, 51, pp.48-63.
9. Bastock, M., 1956. A gene mutation which changes a behavior pattern. Evolution, pp.421-439.
10. Bock, I. R. and M. R. Wheeler. 1972. Studies in Genetics VII. The Drosophila melanogaster species group. The University of Texas Publication 7213: 1-102.
11. Benton, R., Vannice, K.S., Gomez-Diaz, C. and Vosshall, L.B., 2009. Variant ionotropic glutamate receptors as chemosensory receptors in Drosophila. Cell, 136(1), pp.149-162
12. Boughman, J.W., 2002. How sensory drive can promote speciation. Trends in ecology & Evolution, 17(12), pp.571-577.
13. Cande, J., Prud’homme, B. and Gompel, N., 2013. Smells like evolution: the role of chemoreceptor evolution in behavioral change. Current opinion in neurobiology, 23(1), pp.152-158.
14. Cantarel, B.L., Korf, I., Robb, S.M., Parra, G., Ross, E., Moore, B., Holt, C., Alvarado, A.S. and Yandell, M., 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome research, 18(1), pp.188-196.
15. Camacho C, et al. 2009. BLASTþ: architecture and applications. BMC Bioinformatics 10(1):421.
16. Camino, E. M., J. C. Butts, A. Ordway, J. E. Vellky, M. Rebeiz, and T. M. Williams. 2015. The evolutionary origination and diversification of a dimorphic gene regulatory network through parallel innovations in cis and trans. PLoS Genetics 11: e1005136.
17. Cantarel, B.L., Korf, I., Robb, S.M., Parra, G., Ross, E., Moore, B., Holt, C., Alvarado, A.S. and Yandell, M., 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome research, 18(1), pp.188-196.
18. Chakraborty, M., Baldwin-Brown, J.G., Long, A.D. and Emerson, J.J., 2016. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic acids research, 44(19), pp.e147-e147.
19. Chang, C.H. and Larracuente, A.M., 2019. Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome. Genetics, 211(1), pp.333-348.
20. Chang, C.H., Chavan, A., Palladino, J., Wei, X., Martins, N.M.C., Santinha, A.J., Matos, M.R., Ramos, A.P., Irarrazaval, I., Garcia, J.F. and Signor, S.A., 2019. Islands of retroelements are major components of Drosophila centromeres. PLoS biology, 17(3), p.e3000241.
21. Charlesworth, B., Coyne, J.A., Barton, N.H., Charlesworth, D., 1987. The relative rates of evolution of sex chromosomes and autosomes. The American Naturalist 130, 113–146.
22. Chen, S., Zhou, Y., Chen, Y. and Gu, J., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), pp.i884-i890.Chen, N., 2004. Using Repeat Masker to identify repetitive elements in genomic sequences. Current protocols in bioinformatics, 5(1), pp.4-10.
23. Chin, C.S., Alexander, D.H., Marks, P., Klammer, A.A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E.E. and Turner, S.W., 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature methods, 10(6), pp.563-569.
24. Chin, C.S., Peluso, P., Sedlazeck, F.J., Nattestad, M., Concepcion, G.T., Clum, A., Dunn, C., O′Malley, R., Figueroa-Balderas, R., Morales-Cruz, A. and Cramer, G.R., 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nature methods, 13(12), pp.1050-1054.
25. Clyne, P.J., Warr, C.G., Freeman, M.R., Lessing, D., Kim, J. and Carlson, J.R., 1999. A novel family of divergent seven-transmembrane proteins: candidate odorant receptors in Drosophila. Neuron, 22(2), pp.327-338.
26. Coyne, J. A. and H. A. Orr. 1989. Two rules of speciation. In: Otte D, Endler JA (eds) Speciation and its Consequences. Sinauer Associates: Sunderland, MA, pp 180-207.
27. Darwin, C., 1871. Pangenesis. Nature, 3(78), pp.502-503.
28. Deng, M., Wang, Y., Zhang, L., Yang, Y., Huang, S., Wang, J., Ge, H., Ishibashi, T. and Yan, Y., 2019. Single cell transcriptomic landscapes of pattern formation, proliferation and growth in Drosophila wing imaginal discs. Development, 146(18), p.dev179754.
29. Deng, Q., Zeng, Q., Qian, Y., Li, C. and Yang, Y., 2007. Research on the karyotype and evolution of Drosophila melanogaster species group. Journal of Genetics and Genomics, 34(3), pp.196-213.
30. Dennis, G., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. and Lempicki, R.A., 2003. DAVID: database for annotation, visualization, and integrated discovery. Genome biology, 4(9), pp.1-11.
31. de Lima, L.G. and Ruiz-Ruano, F.J., 2022. In-depth Satellitome Analyses of 37 Drosophila species illuminate repetitive DNA evolution in the Drosophila genus. Genome Biology and Evolution, 14(5), p.evac064.
32. Drapeau, M.D., Radovic, A., Wittkopp, P.J. and Long, A.D., 2003. A gene necessary for normal male courtship, yellow, acts downstream of fruitless in the Drosophila melanogaster larval brain. Journal of neurobiology, 55(1), pp.53-72.
33. Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M. and Gingeras, T.R., 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), pp.15-21.
34. Emms, D.M. and Kelly, S., 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome biology, 20, pp.1-14.
35. Falconer DS, Mackay TFC. 1996. Introduction to Quantitative Genetics. UK: Longman Group Ltd.
36. Finn, R.D., Clements, J. and Eddy, S.R., 2011. HMMER web server: interactive sequence similarity searching. Nucleic acids research, 39(suppl_2), pp.W29-W37.
37. Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K. and Holm, L., 2010. The Pfam protein families database. Nucleic acids research, 38(suppl_1), pp.D211-D222.
38. Fuyama Y 1977. A role of visual stimulus in the courtship of Drosophila suzukii. Japanese Journal of Genetics 52: 440.
39. Gibert, J.M., Mouchel-Vielh, E. and Peronnet, F., 2017. Modulation of yellow expression contributes to thermal plasticity of female abdominal pigmentation in Drosophila melanogaster. Scientific Reports, 7(1), pp.1-9.
40. Glassford, W.J., Johnson, W.C., Dall, N.R., Smith, S.J., Liu, Y., Boll, W., Noll, M. and Rebeiz, M., 2015. Co-option of an ancestral Hox-regulated network underlies a recently evolved morphological novelty. Developmental cell, 34(5), pp.520-531.
41. Gompel, N., Prud′homme, B., Wittkopp, P.J., Kassner, V.A. and Carroll, S.B., 2005. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature, 433(7025), pp.481-487.
42. Goel, M., Sun, H., Jiao, W.B. and Schneeberger, K., 2019. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome biology, 20(1), pp.1-13.
43. Gregory, T.R. and Johnston, J.S., 2008. Genome size diversity in the family Drosophilidae. Heredity, 101(3), pp.228-238.
44. Gurevich, A., Saveliev, V., Vyahhi, N. and Tesler, G., 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29(8), pp.1072-1075.
45. Haas, B. and Papanicolaou, A.J.G.S., 2016. TransDecoder (find coding regions within transcripts).
46. Hayward, A. and Gilbert, C., 2022. Transposable elements. Current Biology, 32(17), pp.R904-R909.
47. Hirai, Y. and Kimura, M.T., 1997. Incipient reproductive isolation between two morphs of Drosophila elegans (Diptera: Drosophilidae). Biological Journal of the Linnean Society, 61(4), pp.501-513.
48. Hufnagel, D.E., Hufford, M.B. and Seetharam, A.S., 2020. SequelTools: a suite of tools for working with PacBio Sequel raw sequence data. BMC bioinformatics, 21(1), pp.1-11.
49. Hungate, E.A., Earley, E.J., Boussy, I.A., Turissini, D.A., Ting, C.T., Moran, J.R., Wu, M.L., Wu, C.I. and Jones, C.D., 2013. A locus in Drosophila sechellia affecting tolerance of a host plant toxin. Genetics, 195(3), pp.1063-1075.
50. Ishikawa Y, Kimura MT, Toda MJ 2022. Biology and ecology of the Oriental flower-breeding Drosophila elegans and related species. Fly 16(1):207-220.
51. Jeong, S., Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., 2008. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell, 132(5), 783-793.
52. Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G. and Pesseat, S., 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics, 30(9), pp.1236-1240.
53. Joseph, R.M. and Carlson, J.R., 2015. Drosophila chemoreceptors: a molecular interface between the chemical world and the brain. Trends in Genetics, 31(12), pp.683-695.
54. Jones, C.D., 2005. The genetics of adaptation in Drosophila sechellia. Genetics of Adaptation, pp.137-145.
55. Küpper, C., Stocks, M., Risse, J.E., Dos Remedios, N., Farrell, L.L., McRae, S.B., Morgan, T.C., Karlionova, N., Pinchuk, P., Verkuil, Y.I. and Kitaysky, A.S., 2016. A supergene determines highly divergent male reproductive morphs in the ruff. Nature genetics, 48(1), pp.79-83.
56. Kalvari, I., Argasinska, J., Quinones-Olvera, N., Nawrocki, E.P., Rivas, E., Eddy, S.R., Bateman, A., Finn, R.D. and Petrov, A.I., 2018. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic acids research, 46(D1), pp.D335-D342.
57. Kim, B.Y., Wang, J.R., Miller, D.E., Barmina, O., Delaney, E., Thompson, A., Comeault, A.A., Peede, D., D′Agostino, E.R., Pelaez, J. and Aguilar, J.M., 2021. Highly contiguous assemblies of 101 drosophilid genomes. Elife, 10, p.e66405.
58. Kronforst, M.R., Young, L.G., Kapan, D.D., McNeely, C., O′Neill, R.J. and Gilbert, L.E., 2006. Linkage of butterfly mate preference and wing color preference cue at the genomic location of wingless. Proceedings of the National Academy of Sciences, 103(17), pp.6575-6580.
59. Kriventseva, E.V., Kuznetsov, D., Tegenfeldt, F., Manni, M., Dias, R., Simão, F.A. and Zdobnov, E.M., 2019. OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic acids research, 47(D1), pp.D807-D811.
60. Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K., 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular biology and evolution, 35(6), p.1547.
61. Liao, Y., Smyth, G.K. and Shi, W., 2019. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic acids research, 47(8), pp.e47-e47.
62. Lieber, M. and MacManes, M.D., 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature protocols, 8(8), pp.1494-1512.
63. Lindholm, A. and Breden, F., 2002. Sex chromosomes and sexual selection in poeciliid fishes. The american naturalist, 160(S6), pp.S214-S224.
64. Liu, Y., M. Ramos-Womack, C. Han, P. Reilly, K. L. Brackett, W. Rogers, T. M. Williams, P. Andolfatto, D. L. Stern, and M. Rebeiz. 2019. Changes throughout a genetic network mask the contribution of Hox gene evolution. Current Biology 29: 2157-2166.
65. Love, M., Anders, S. and Huber, W., 2014. Differential analysis of count data–the DESeq2 package. Genome Biol, 15(550), pp.10-1186.
66. Mahram, A. and Herbordt, M.C., 2015. NCBI BLASTP on high-performance reconfigurable computing systems. ACM Transactions on Reconfigurable Technology and Systems (TRETS), 7(4), pp.1-20.
67. Massey, J.H. and Wittkopp, P.J., 2016. The genetic basis of pigmentation differences within and between Drosophila species. Current topics in developmental biology, 119, pp.27-61.
68. Massey, J.H., Li, J., Stern, D.L. and Wittkopp, P.J., 2021. Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola. Heredity, 127(5), pp.467-474.
69. Massey, J.H., Rice, G.R., Firdaus, A.S., Chen, C.Y., Yeh, S.D., Stern, D.L. and Wittkopp, P.J., 2020. Co-evolving wing spots and mating displays are genetically separable traits in Drosophila. Evolution, 74(6), pp.1098-1111.
70. Martin, M., 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), pp.10-12.
71. Matsuo, T., Sugaya, S., Yasukawa, J., Aigaki, T. and Fuyama, Y., 2007. Odorant-binding proteins OBP57d and OBP57e affect taste perception and host-plant preference in Drosophila sechellia. PLoS biology, 5(5), p.e118.
72. McBride, C.S. and Arguello, J.R., 2007. Five Drosophila genomes reveal nonneutral evolution and the signature of host specialization in the chemoreceptor superfamily. Genetics, 177(3), pp.1395-1416.
73. Min, S., Ai, M., Shin, S.A. and Suh, G.S., 2013. Dedicated olfactory neurons mediating attraction behavior to ammonia and amines in Drosophila. Proceedings of the National Academy of Sciences, 110(14), pp.E1321-E1329.
74. Missbach, C., Dweck, H.K., Vogel, H., Vilcinskas, A., Stensmyr, M.C., Hansson, B.S. and Grosse-Wilde, E., 2014. Evolution of insect olfactory receptors. elife, 3, p.e02115.
75. Morgan, Thomas Hunt. Sex-linked inheritance in Drosophila. No. 237. Carnegie institution of Washington, 1916.
76. Negi, A., Liao, B.Y. and Yeh, S.D., 2023. Long-read-based genome assembly of Drosophila gunungcola reveals fewer chemosensory genes in flower-breeding species. Genome Biology and Evolution, 15(3), p.evad048.
77. Ordway, A. J., K. N. Hancuch, W. Johnson, and T. M. Williams. 2014. The expansion of body coloration involves coordinated evolution in cis and trans within the pigmentation regulatory network of Drosophila prostipennie. Developmental Biology 392: 431-440.
78. Pavlou, H.J. and Goodwin, S.F., 2013. Courtship behavior in Drosophila melanogaster: towards a ‘courtship connectome’. Current opinion in neurobiology, 23(1), pp.76-83.
79. Pertea, M., Pertea, G.M., Antonescu, C.M., Chang, T.C., Mendell, J.T. and Salzberg, S.L., 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature biotechnology,33(3), pp.290-295.
80. Peyser, R.D., Lanno, S.M., Shimshak, S.J. and Coolon, J.D., 2017. Analysis of cytochrome P450 contribution to evolved plant toxin resistance in Drosophila sechellia. Insect molecular biology, 26(6), pp.715-720.
81. Prud′homme, B., Gompel, N., Rokas, A., Kassner, V.A., Williams, T.M., Yeh, S.D., True, J.R. and Carroll, S.B., 2006. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature, 440(7087), pp.1050-1053.
82. Puerma, E., Orengo, D.J., Cruz, F., Gómez-Garrido, J., Librado, P., Salguero, D., Papaceit, M., Gut, M., Segarra, C., Alioto, T.S. and Aguadé, M., 2018. The high-quality genome sequence of the oceanic island endemic species Drosophila guanche reveals signals of adaptive evolution in genes related to flight and genome stability. Genome Biology and Evolution, 10(8), pp.1956-1969.
83. Ranz, J.M., González, J., Casals, F. and Ruiz, A., 2003. Low occurrence of gene transposition events during the evolution of the genus Drosophila. Evolution, 57(6), pp.1325-1335.
84. Rebeiz, M., J. E. Pool, V. A. Kassner, C. F. Aquadro, and S. B. Carroll. 2009. Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science 326: 1663-1667.
85. Ritchie, M.G. and Gleason, J.M., 1995. Rapid evolution of courtship song pattern in Drosophila willistoni sibling species. Journal of Evolutionary Biology, 8(4), pp.463-479.
86. Robertson, H.M., Warr, C.G. and Carlson, J.R., 2003. Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster. Proceedings of the National Academy of Sciences, 100(suppl_2), pp.14537-14542.
87. Sánchez-Gracia, A., Vieira, F.G. and Rozas, J., 2009. Molecular evolution of the major chemosensory gene families in insects. Heredity, 103(3), pp.208-216.
88. Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V. and Zdobnov, E.M., 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19), pp.3210-3212.
89. Smit, A.F. and Hubley, R., 2008. RepeatModeler Open-1.0.
90. Stern, D. L. and V. Orgogozo. 2008. The loci of evolution: How predictable is genetic evolution? Evolution 62: 2155-2177.
91. Soderlund, C., Bomhoff, M. and Nelson, W.M., 2011. SyMAP v3. 4: a turnkey synteny system with application to plant genomes. Nucleic acids research, 39(10), pp.e68-e68.
92. Sultana F, Kimura MT, Toda MJ 1999. Anthophilic Drosophila of the elegans species-subgroup from Indonesia, with description of a new species (Diptera: Drosophilidae). Entomol Sci. 2:121- 126.
93. Takahashi, A. 2013. Pigmentation and behavior: Potential association through pleiotropic genes in Drosophila. Genes & Genetic Systems 88: 165-174.
94. Thorvaldsdóttir, H., Robinson, J.T. and Mesirov, J.P., 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in bioinformatics, 14(2), pp.178-192.
95. True, J.R. and Carroll, S.B., 2002. Gene co-option in physiological and morphological evolution. Annual review of cell and developmental biology, 18(1), pp.53-80.
96. Vieira, F.G. and Rozas, J., 2011. Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system. Genome biology and evolution, 3, pp.476-490.
97. Werner, T., Koshikawa, S., Williams, T.M. and Carroll, S.B., 2010. Generation of a novel wing colour pattern by the Wingless morphogen. Nature, 464(7292), pp.1143-1148.
98. Wittkopp, P.J., True, J.R. and Carroll, S.B., 2002. Reciprocal functions of the Drosophila yellow and ebony proteins in the development and evolution of pigment patterns. 1849-1858.
99. Wittkopp, P.J., Williams, B.L., Selegue, J.E. and Carroll, S.B., 2003. Drosophila pigmentation evolution: divergent genotypes underlying convergent phenotypes. Proceedings of the National Academy of Sciences, 100(4), pp.1808-1813.
100. Werner, T., Koshikawa, S., Williams, T.M. and Carroll, S.B., 2010. Generation of a novel wing colour pattern by the Wingless morphogen. Nature, 464(7292), pp.1143-1148.
101. Wood, D.E., Lu, J. and Langmead, B., 2019. Improved metagenomic analysis with Kraken 2. Genome biology, 20, pp.1-13.
102. Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu x, Liu S, Bo X, Yu G., 2021. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation, 2(3), 100141.
103. Yeh, S.D. and True, J.R., 2014. The genetic architecture of coordinately evolving male wing pigmentation and courtship behavior in Drosophila elegans and Drosophila gunungcola. G3: Genes, Genomes, Genetics, 4(11), pp.2079-2093.
104. Yeh, S.D., Liou, S.R. and True, J.R., 2006. Genetics of divergence in male wing pigmentation and courtship behavior between Drosophila elegans and D. gunungcola. Heredity, 96(5), pp.383-395.
105. Zhang, L., Martin, A., Perry, M.W., van der Burg, K.R., Matsuoka, Y., Monteiro, A. and Reed, R.D., 2017. Genetic basis of melanin pigmentation in butterfly wings. Genetics, 205(4), pp.1537-1550.
106. Zhang, L., Yu, J., Guo, X., Wei, J., Liu, T. and Zhang, W., 2020. Parallel mechanosensory pathways direct oviposition decision-making in Drosophila. Current Biology, 30(16), pp.3075-3088.
107. Zhang, Z., Carriero, N., Zheng, D., Karro, J., Harrison, P.M. and Gerstein, M., 2006. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics, 22(12), pp.1437-1439.
108. Zimin, A.V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S.L. and Yorke, J.A., 2013. The MaSuRCA genome assembler. Bioinformatics, 29(21), pp.2669-2677.

指導教授

葉淑丹(Shu-Dan Yeh)

審核日期

2023-6-29

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