榕小蜂科的化學感受器基因家族演化

化學受器是昆蟲主要的感覺器官，昆蟲利用嗅覺來感知食物、配偶、宿主、掠食者等外在因子。榕小蜂科的物種丟失了大多數的化學受器基因，可能與其封閉的特殊生活史有關。即使如此，榕小蜂的嗅覺在其與榕樹的互利共生關係中至關重要，榕小蜂主要透過辨識榕樹隱頭果氣味，來達到專一性授粉。本論文透過定序兩種榕小蜂的基因體跟轉錄體，研究小蜂的化學受器基因如何與其宿主共演化。本文第一章使用粒線體基因標記，進行系統發生以及族群遺傳分析，進而釐清兩研究物種Wiebesia pumilae, W. sp3和他們的近親W. sp1之間的親緣關係、天然分佈位置、自然宿主，並揭露W. sp3有數個族群源於人為引入，且在其入侵地發生多次獨立轉換宿主，由原本共生的愛玉 (Ficus pumila var. awkeotsang)轉至薜荔 (Ficus pumila var. pumila)。經由回顧前人在入侵族群做的物候調查，我提出一個可能機轉解釋榕小蜂的宿主轉換在不同榕樹性別系統之最終演化結果。本文第二章提供詳細的生物資訊流程描述組裝及注釋兩研究物種的基因體以及粒線體基因體，並進行種間基因演化速率分析。本文第三章探討不同演化層面和尺度下，榕小蜂嗅覺基因與其宿主的共演化。在精細演化尺度，利用近期與宿主達成共演化的W. pumilae和W. sp3的基因體與轉錄體，發現在科內基因拷貝數保守的嗅覺基因出現種間差異表達現象。而在跨越整個榕小蜂科的廣大演化尺度，藉由比較W. pumilae、W. sp3和Ceratosolen solmsi三物種，發現在嗅覺受器 (olfactory receptor)出現各支系獨有的適應性基因串聯重複 (adaptive tandem gene duplication)，極有可能是與宿主榕樹氣味長期共適應、共演化的結果。最後我比較與不同性別系統榕樹共生之榕小蜂，發現三個在榕小蜂科中出現縮減的嗅覺基因家族，於雌雄同株榕樹的小蜂Elisabethiella stueckenbergi都出現較多的基因數目擴張，可能與雌雄同株榕樹小蜂具有更頻繁的宿主轉換有關。

關鍵字

榕小蜂；嗅覺；共演化；基因體組裝；寄主專一性

並列摘要

Pollinating fig wasps (Agaonidae) have one of the most reduced chemosensory genes in insects, which is probably associated with specialized life cycle in obligate mutualism. On the other hand, olfaction plays a crucial role in maintaining host specificity in the fig-fig wasp coevolution. In this thesis, I sequenced genomic and transcriptomic data from two fig wasp species to understand how reduced chemosensory genes maintain host-specificity during species divergence. The first chapter describes the evolutionary relationships of the two studied fig wasps (Wiebesia pumilae and W. sp3), their close species (W. sp1), and their associated hosts (Ficus pumila var. pumila and Ficus pumila var. awkeotsang), which revealed that while originally an endemic species, recent human intervention had resulted in introduced populations along with recurrent host-shifting in W. sp3. Possible mechanism for distinct co-pollinator pattern seen in different fig sexual systems was also proposed. The second chapter provides bioinformatics pipelines to generate high quality nuclear genomes and mitochondrial genomes of both species using next generation sequencing, and assess the evolutionary rates in protein-coding genes between them. The final chapter characterizes chemosensory gene evolution of fig wasp from multiple evolutionary perspectives. For fine scale evolution, utilizing the genome and transcriptome of W. sp3 and W. pumilae, both of which codiverged recently with their host, I discovered that regulatory changes at copy-number conservative chemosensory genes are associated with local coadaptations. For large scale evolution, by comparing the two Wiebesia species with Ceratosolen solmsi, I found that lineage-specific adaptive tandem gene duplications in olfactory receptors (OR) family may drive phenotypic coevolution with figs. For olfactory evolution in wasps belonging to different sexual systems of hosts, larger expanded gene families were found in the ancestrally contracted gene families: OR, gustatory receptor (GR) and odorant-binding protein (OBP) in the monoecious fig wasp Elisabethiella stueckenbergi, possibly reflecting differences in host-shifting frequency.

並列關鍵字

fig wasp ； olfaction ； coevolution ； genome assembly ； host specificity

參考文獻

Akiva, E., Brown, S., Almonacid, D. E., Barber, A. E., Custer, A. F., Hicks, M. A., … Babbitt, P. C. (2014). The Structure–Function Linkage Database. Nucleic Acids Research, 42(D1), D521–D530. https://doi.org/10.1093/nar/gkt1130

Google Scholar

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

Google Scholar

Andrews, S. (2010). FastQC A Quality Control tool for High Throughput Sequence Data. Retrieved June 1, 2018, from https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Google Scholar

Attwood, T. K., Coletta, A., Muirhead, G., Pavlopoulou, A., Philippou, P. B., Popov, I., … Mitchell, A. L. (2012). The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012. Database, 2012(0), bas019-bas019. https://doi.org/10.1093/database/bas019

Google Scholar

Bailey, J. A., Liu, G., & Eichler, E. E. (2003). An Alu Transposition Model for the Origin and Expansion of Human Segmental Duplications. The American Journal of Human Genetics, 73(4), 823–834. https://doi.org/10.1086/378594

Google Scholar

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榕小蜂科的化學感受器基因家族演化

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