台灣水鹿全基因體組裝及鹿角的演化分析

De Novo genome assembly and antler evolution of Formosan sambar deer (Rusa unicolor swinhoei)

劉晏均(Yan-Jun Liu)

指導教授 ： 莊曜宇

共同指導教授 ： 蔡孟勲(Mong-Hsun Tsai)

國立臺灣大學/電機資訊學院/生醫電子與資訊學研究所/碩士(2020年)

https://doi.org/10.6342/NTU202000195

摘要

台灣水鹿又名四目鹿，目前被歸類為台灣特有亞種。本篇研究利用10x定序技術，完成台灣水鹿全基因體的序列草圖，並經由組裝結果的統計結果與偶蹄類共通的同源基因進行測試來確認其優異品質。其基因體草圖包含2.71Gb的序列，21,398個蛋白質編譯碼基因序列。將台灣水鹿與其他偶蹄類動物進行比較，發現鹿科與牛科大約在2,530萬年前開始分化。在角骨骼演化方面，我們發現有角下目物種生物礦物組織發育和內骨型態發育相關的同源基因家族有明顯擴張，類似功能的基因在正向選擇基因上也有發現，同時，我們根據正向選擇與基因家族擴張的分析中，找出多個有角下目的基因家族與顱神經脊細胞生成有關，揭示了有角下目的單一進化起源的假說。另外，在鹿角演化方面，我們發現鹿科動物在軟骨分化與神經分化相關的同源基因家族有明顯擴張，並且類似功能的基因在正向選擇基因上也有發現，並揭示了鹿角再生在演化上的機制。最後，本篇研究找出台灣水鹿鹿角快速生長的相關基因，並說明軟骨細胞增殖和分化以及蛋白合成的轉錄因子和訊號分子與鹿角的生長息息相關。本篇研究提供了有價值的高品質台灣水鹿的全基因體訊息，並進一步探討基因體演化特徵，揭示角骨骼，鹿角在演化上的機制以及鹿角生長的相關機制。

關鍵字

台灣水鹿 ； 基因體 ； 基因體組裝 ； 10X Genomics

並列摘要

The Formosan sambar deer (Rusa unicolor swinhoei) which is an endemic species in Taiwan. This deer provides an opportunity to realize the antler and horn evolutionary processes. Currently, rapid development of next-generation sequencing technology provides an opportunity to get wealth of information from animal genomes. Furthermore, the whole-genome sequencing is a critical foundation for genomic research. In this study, we sequenced high quality Formosan sambar deer genome, which is the first whole-genome assembly by using only 10x Genomics linked-reads. The draft genome contained 2.71 Gb of DNA, 14.1 Mb N50 length and over 90 % of complete genes were evaluated by the BUSCO benchmark. The 23,110 predicted genes were identified in the genome. Of these genes, 21,398 were annotated as protein-coding genes. Comparing with other artiodactyls, the Formosan sambar deer diverged from bovine families approximately 25.3 million years ago. First, we annotated and analyzed the size changes of gene families in the pecora The results indicated that the gene family related to biomineralization and epidermal growth showed significant expansion. In addition, analyzing the positive selection genes in evolution found that the gene families related to crest neural growth were identified.
Then, we annotated and analyzed the size changes of gene families in the and among pecora and the common ancestor of and Formosan sambar deer and white tail deer. The results indicated that the gene family related to epidermal growth and Nervous system development showed significant expansion. In conclusion, this study provided a valuable genomic resource for the Formosan sambar deer and reveal insights into the antler and horn evolutionary characteristics form its genome.

並列關鍵字

Formosan sambar deer ； De novo genome assembly ； 10x Genomics

參考文獻

1. Gilbert, C., A. Ropiquet, and A. Hassanin, Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): systematics, morphology, and biogeography. Molecular phylogenetics and evolution, 2006. 40(1): p. 101-117.

2. Douzery, E. and E. Randi, The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic content. Molecular Biology and Evolution, 1997. 14(11): p. 1154-1166.

3. Hundertmark, K.J., et al., Genetic relationships deduced from cytochrome-b sequences among moose. Alces, 2002. 38: p. 113-122.

4. Ohtaishi, N. and Y. Gao, A review of the distribution of all species of deer (Tragulidae, Moschidae and Cervidae) in China. Mammal Review, 1990. 20(2‐3): p. 125-144.

5. Demarchi, M.W. and F.L. Bunnell, Estimating Forest Canopy Effects on Summer Thermal Cover for Cervidae (Deer Family). Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere, 1993. 23(11): p. 2419-2426.