染色體層級的基因體組裝揭示了溪鱧的特殊適應特徵

Abstract

溪鱧屬於條鰭魚綱，鰕虎目溪鱧科，分布於印尼–澳大拉西亞群島、菲律賓、台灣等地的淡水區域。溪鱧科被認為是鰕虎目中較為古老的分支之一，所以對於研究鰕虎目的起源相當重要。我們從台灣各地採集了數個樣本抽取DNA組裝基因體，並從多個組織如肌肉、肝臟、眼睛、腦和鼻子等處抽取RNA分析其轉錄體，並與另外九種鰕虎魚類以及兩個外群比較。我組出來的基因體大小約為607Mb，是所有分析物種中基因組最小的。這是因為溪鱧基因組的重複序列僅佔整個基因組的28.2%，而其他鰕虎魚類則有約40-60%的重複序列。根據重複序列地景圖(repeat landscape)，除了溪鱧之外，其他物種在過去的演化階段都曾歷經了重複序列擴增的現象。因此溪鱧相對小的基因組是因為他不曾經歷重複序列擴增的演化。我的組裝含有有23條染色體層級的片段，完整BUSCO值為98.43%。共註釋了25259個基因。基因的數量比較進階的鰕虎多但和外群的基因數目較為接近。基因演化速率的分析發現溪鱧的演化速率相較於其他魚類慢，這可能與溪鱧重複序列改變較少有關。對基因功能群的分析發現與側線發育有關的基因較其他魚類少，然而在與神經突觸有關的基因有擴增的現象。此外有關頭顱發育的基因在溪鱧有擴增的現象，這可能與他為了適應激流的環境而形成的扁平狀頭顱有關。另外溪鱧在與腎臟發育與滲透壓調節相關的基因的增加可能與他延長的海洋飄流其以及下海產卵的特性有關。PSMC所推估的溪鱧族群大小在450,000年前約為50萬隻。

Loach goby (Rhyacichthys aspro) is an Actinopterygii fish which belongs to the family Rhyacichthyidae in the order Gobiiformes. It is distributed in tropical freshwaters of the Indo-Australasian archipelago, Philippines, and Taiwan. Rhyacichthyidae is recognized as one of the most primitive families within Gobiiformes, making it particularly interesting regarding the evolutionary history of Gobiiformes. In this study, the genome and transcriptome of loach goby from different tissues, including muscle, liver, eyes, brain, and nose were sequenced from multiple individuals. The assembled genome is approximately 607Mb in size, with 23 chromosome-level contigs and a complete Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 98.43%. The loach goby has the smallest genome size compared to nine other Gobiiformes species and two outgroup species. The proportion of repetitive sequences in the entire genome is approximately 28.2%, whereas in other compared species, this proportion ranges from approximately 40-60%. Based on the results of repeat landscape and CAFÉ analysis, all species except the loach goby have experienced repeat element expansions. A total of 25,259 genes were annotated. The gene number is larger than that of more advanced Gobiiformes but similar to the outgroup of Gobiiformes. The evolutionary rate of the loach goby is slower than its gobioid counterparts which may be resulted in the less repeat element alteration in this species. Functional gene analysis shows loach goby has fewer genes related to lateral line development but have neuron synapse related genes expansion. Genes related to skull developments has expansion, likely due to its adaptation to torrential currents. Moreover, genes related to kidney development and osmoregulation also show sign of expansion, which could be linked to their catadromous life style. Loach goby migrate downstream into the sea for spawning and the fry undergo an extended oceanic drift period before migrating back to the rivers. The population demography estimated from pairwise sequentially markovian coalescent (PSMC) shows the population size of loach goby is approximately 5x105 around 450,000 years before present.