以比較轉錄體分析線蟲發育期間的協同演化

Abstract

線蟲是物種豐富度極高的動物，具有多樣的棲息地和生活方式，其中包括腐生性，以及能夠寄生動物或植物的寄生性物種。寄生性線蟲的感染能力會隨著發育階段產生變化，從而感染宿主並完成生命週期。雖然線蟲寄生性的出現已經被證實是多次獨立演化的結果，寄生過程中的共同壓力，例如在生活週期中轉換和適應棲息環境以及規避和對抗宿主的免疫系統，導致寄生性的線蟲發展出相似的表現型和發育時期。透過比較8個線蟲物種發育時期的48個轉錄組，此研究發現不同發育時期的轉錄組廣泛的分為胚胎、幼蟲以及成蟲三個群集，代表線蟲生命週期的基因表現在一定程度上具有保守性。組織特異性基因（例如卵母細胞和皮下組織）在各個發育時期具有不同的程度的基因表現，能夠部分闡述此種模式。線蟲普遍具有3至5個幼蟲階段，這些階段的轉錄組在每個物種之內高度相關，說明幼蟲階段之間存在高度依賴性。在隱桿線蟲屬 (Caenorhabditis elegans-briggsae) 以及類圓蟲屬 (Strongyloides stercoralis-venezuelensis) 的同屬物種比較之中，我們發現大約50％的基因具有多效性，不會專一表現在特定的發育時期，其直系同源基因也有半數具有多效性，但表現模式在不同物種之間並不相似。基因表現的高頻率轉換導致鄰近發育時期的協同演化，進而在線蟲進化過程中產生了具有物種特性的轉錄組。綜合而言，此研究初探胚胎發育時期後的線蟲轉錄組演化。

Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free-living while others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. Though parasitism has independently arisen multiple times over evolutionary history, the common pressures of parasitism—such as adapting to the host environment, evading and subverting the host immune system, and changing environments across the life cycle—have led parasites to develop similar phenotypes and developmental stages. In this study, we compared 48 transcriptomes of different developmental stages across eight nematode species. The transcriptomes were found clustered broadly into embryo, larva and adult categories, suggesting that gene expression is conserved to some extent across the entire nematode life cycle. Such patterns were partly accounted for by tissue-specific genes—such as those in oocytes and the hypodermis—being expressed at different proportions. Although nematodes typically have 3-5 larval stages, the transcriptomes for these stages were found to be highly correlated within each species, suggesting high dependence among larval stages. In the case of Caenorhabditis elegans-briggsae and Strongyloides stercoralis-venezuelensis comparisons, we found that around 50% of genes were pleiotropic; half of their orthologs were also pleiotropic, but expressed in different stages. Such frequent rewiring of expression has resulted in concerted transcriptome evolution across adjacent stages, thus generating an individualized species transcriptome in the course of nematode evolution. Our study provides a first insight into the evolution of nematode transcriptome beyond embryonic development.