藍腹鷴全基因體組裝及適應演化研究

Whole-Genome De Novo Assembly and Adaptive Evolution of the Swinhoe's Pheasant

林冠廷(Kuan-Ting Lin)

指導教授 ： 蔡孟勳

國立臺灣大學/生物資源暨農學院/生物科技研究所/碩士(2018年)

https://doi.org/10.6342/NTU201801978

摘要

藍腹鷴又名臺灣藍鷳，為雉科鷳屬鳥類，棲息在台灣2,300公尺以下中海拔山區，目前仍被國際自然保護聯盟紅皮書中列為近危物種。本篇研究利用新世代定序技術，完成藍腹鷴全基因體序列的草圖，成為第一隻完成全基因體定序的鷳屬鳥類，並經由組裝結果統計及鳥類共通的同源基因測試確認其優異品質。這個基因體草圖包含1.05 Gb的序列，16,442個基因序列。比較藍腹鷴和其他鳥類的基因體，藍腹鷴大約在1,160萬年前開始與帝雉分化。在適應環境方面，我們發現藍腹鷴在能量代謝及缺氧反應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被發現，同時，與帝雉相同，藍腹鷴在血紅蛋白基因HbA有一個胺基酸位點發生替換，可以提升攜氧效率，幫助適應山地環境。另外，我們也從先前的研究中了解到雉科經歷了演化輻射，並從藍腹鷴基因體中發現其形態發育相關基因的正向選擇，提供適應過程的基因訊息。最後，為了說明藍腹鷴除了棲地破壞外可能的近危原因，本篇研究分析藍腹鷴及藍腹鷴帝雉共同祖先的免疫相關基因收縮，並進一步探討其MHC-B免疫相關區段的缺失，說明其較容易受外在細菌病原侵染的可能。本篇研究提供了有價值的高品質藍腹鷴全基因體資訊，進並一步探討基因體演化特徵，揭露其環境適應機制與可能遭遇的危機。

關鍵字

藍腹鷴 ； 斯文豪氏鷳 ； 基因體 ； 基因體組裝 ； 次世代定序

並列摘要

The Swinhoe‘s pheasant (Lophura swinhoii), which is a near-threatened species in the IUCN Red List indigenous to Taiwan, belongs to the family Phasianidae in the order Galliformes. This pheasant provides an opportunity to realize evolutionary processes following geographic isolation and the Lophura genus could be a good model to investigate adaptive evolution because of their diversified habitats in Asia. 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 Swinhoe's pheasant genome, which is the first whole-genome assembly among the all twelve gallopheasants (Lophura genus), by integrating sequencing data from Illumina short reads and 10x Genomics linked-reads. Paired-end reads were used to assemble contigs, whereas mate pair and 10x Genomics reads were used for scaffolding. The draft genome contained 1.05 Gb of DNA, 15.3 Mb N50 length and over 90% of complete genes were evaluated by the BUSCO benchmark. The 16,442 predicted genes were identified in the genome. Of these genes, 15,687 were annotated as protein-coding genes. The mitochondrial genome was sequenced and assembled as well as the major histocompatibility complex B-locus (MHC-B) genes were annotated and curated. Compared with other avian genomes, the Swinhoe's pheasant diverged from the Mikado pheasant (Syrmaticus mikado) approximately 11.6 million years ago. Besides, we annotated and analyzed the size changes of gene families among the Swinhoe's pheasant, Mikado pheasant, and their common ancestor. The results indicated that the gene families related to fructose and mannose metabolism showed significant expansion in the Swinhoe's pheasant genome. Conversely, the gene families related to immune system and response to bacterium showed significant contraction. In addition, analyzing the positive selection genes in evolution differences of Swinhoe's pheasant found that the gene families related to morphogenesis were identified. In conclusion, this study provided a valuable genomic resource for the Swinhoe's pheasant and revealed insights into the unique evolutionary characteristics from its genome.

並列關鍵字

Lophura swinhoii ； De novo genome assembly ； Next-generation sequencing ； 10x Genomics

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