結合次世代與長片段定序組裝大岩桐及俄氏草之基因組與轉錄體

Abstract

苦苣苔科花朵具呈現多樣性特色並分布全球，在生態與園藝上具有重要的意義。在苦苣苔科中，俄氏草(Titanotrichum oldhamii)是位於台灣的本土觀賞植物，其具有從有性生殖花反轉成無性繁殖體特性；大岩桐(Sinningia speciosa)是位於巴西並在園藝上廣受歡迎的植物，其花朵的多樣性也讓達爾文為之著迷。俄氏草與大岩桐是未來新興模式植物，在我們實驗室研究俄氏草花反轉與大岩桐花對稱之潛在基因。然而卻沒有高品質的俄氏草與大岩桐之基因體問世，如此嚴重影響到更進一步的研究工作。為了獲得高品質的俄氏草與大岩桐之基因體，我結合三代(TGS; Oxford Nanopore Technology)長片段定序，加上次世代(NGS; Illumina)雙端高質量短序列(150 bp)，以長接短策略進行全新混合組裝(de novo hybrid assemble)，透過CLC軟體和MaSuRCA組裝。這樣結合長片段與精準Illumina短片段之組裝策略可以解決長片段定序高錯誤率的問題。我也將俄氏草與大岩桐之不同器官轉錄體原始定序資料進行轉錄體組裝，組裝好之轉錄體有高N50值與功能性分析驗證，使其組裝更完備。最後透過組裝葉綠體基因體，結構分析葉綠體基因體編碼區序列，建立分子標記與演化樹，利於推論苦苣苔科的親緣關係。本論文研究中，進行俄氏草與大岩桐基因體與轉錄體之定序與組裝，對於苦苣苔科中這些新興模式植物的科學探索和園藝改良提供了關鍵的見解與和研究資源。

Gesnariaceae species displays floral diversity and is distributed globally with ecological and and horticultural significance. Within Gensariaceae, Titanotrichum oldhamii is native ornamental in Taiwan with its sexual flower is capable to reverse into asexual propagules. Sinningia speciosa is a popular Barzilian horticultural plant that Charles Darwin was fascinated on its rich flower diversity upon human slection. Both of them are emerging plant models and well-studied for the underlying genetic of flower reversal and floral symmetry in our lab. However, the lacking of high-quality sequenced genome of both species hinders further research works. In order to obtain the first high-quality sequenced genomes in Gesnariaceae, I combined the long reads from the third-generation sequencing (TGS; Oxford Nanopore Technology) with the high quality pair-end short reads (150 bp) from the next-generation sequencing (NGS; Illumina) to generate de novo hybrid genome assemblies of T. oldhamii and S. speciosa using the QIAGEN CLC genomic workbench and hybrid genome assemlbing by MaSuRCA. This strategy combines long reads with accurate Illumina sequencing short reads to solve the high error rate problem from long reads. I also assembled T. oldhamii and S. speciosa transcriptome from different development organs for best k-mer length to obtain high quality transcriptomes with long N50 with draft annotation. Plastomes of these species were sequenced for their usage of inferring phylogeny of Gesneriaceae species. The genomes and transcriptomes of T. oldhamii and S. speciosa sequenced in this study present pivotal insights into and resources for scientific exploration and horticultural improvement of these emerging plant models in Gesneriaceae.