比較基因體學區分葉芽線蟲複合種並探討線蟲水平轉移基因

Abstract

葉芽線蟲文為一種植物寄生線蟲屬於Aphelenchoidea總科，宿主範圍超過兩百多種植物，研究顯示不同植物分離的葉芽對於宿主的範圍有所分別，證實葉芽線蟲可能為複合種。論文第一章裡，我們研究葉芽線蟲複合種的不同，四隻屬於此複合種的線蟲基因被定序組裝成基因體，44-47 Mb 大小的基因體幾乎為clade IV線蟲中最小的存在，我們發現葉芽線蟲基因體變小主要是因為轉座子(Transposable elements)在近期演化過程中快速消失有關，隨著葉芽基因體的解序，複合種可以成功的被分成A. oryzae以及A. pseudobesseyi，並且能在28S分子序列得到驗證，僅存的三條染色體顯示葉芽線蟲基因體經歷過染色體融合。

論文第二章，我們探討葉芽線蟲染色體的演化，同線性的基因體研究證實葉芽的三個染色體可能源自於多種染色體融合及裂解，此外我們找出葉芽線蟲的染色體同源片段但雄性葉芽基因序列回貼結果顯示葉芽性別決定機制可能不由單一性染色體決定。我們發現葉芽複合種染色體上重複序列的密集程度也有很大的分別，顯示此複合種正持續分化中。

論文第三章中，植物線蟲生活型態的轉變可能由水平轉移基因造成，因此我們研究線蟲水平轉移基因的演化過程，我比較了Clade IV線蟲的水平轉移基因發現目前植物線蟲的水平轉移基因主要是從兩個演化分支點而來。這些基因大多從細菌轉移而來並且隨著時間推進演化出不同基因數量。水平轉移事件結合物種演化樹使我們能夠了解線蟲水平轉移基因的演化。

Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the Aphelenchoidea lineage that can infect nearly 200 plant species. Research has shown that nematode strains isolated from different plants exhibit varying host range, suggesting that they may be species complex.

In chapter 1, I investigated the differences within A. besseyi species complex. I generated the assemblies belonging to A. besseyi species complex. The assemblies of Aphelenchoides ranged from 44.7-47.4 Mb which is amongst the smallest in the clade IV nematodes. This genome reduction was mainly due to the rapid reduction in transposable elements. Phylogenomic analysis successfully delimited the species complex strains into A. oryzae and A. pseudobesseyi which was consistent with the 28S phylogeny.

In chapter 2, we investigated the chromosome evolution in A. besseyi. Synteny analyses between nematodes suggested that the three chromosomes in A. besseyi may be a result of multiple fission and fusion events. In addition, features enriched in nematode sex chromosome were identified in A. besseyi despite the male reads coverage of A. besseyi were even amongst the three chromosomes suggesting it might possess stochastic sex determination system similar to Bursaphelenchus species. To investigate the differences within A. besseyi species complex, I identified their differential repeat abundance along chromosomes, indicating ongoing genetic differentiation.

In chapter 3, the acquirement of horizontal gene transfer (HGT) genes was proposed to lead the lifestyle changes of PPNs from free-living. We sought to pinpoint the HGT evolution in PPNs. I compared the inferred HGT families across clade IV nematodes, revealing that HGT genes retained in PPNs were mostly acquired from two major episodes. These genes were mainly originated from bacteria but differentially lost between clades. The combination of HGT events and species phylogeny allowed us to pinpoint the HGT evolution in nematodes.