平頷鱲基因體組裝與染色體演化分析

Abstract

平頷鱲(Zacco platypus)屬於鯉形目(Cypriniformes)鲴科(Xenocyprididae)，是分布於中國東部、韓國和日本的溪魚，後被引進臺灣淡水河流域。本研究組裝的染色體層級平頷鱲基因體包含24條染色體，大小為847Mb，其中重複序列長466Mb (55.02%)，共註釋了27,249個基因，完整BUSCO值為96.7%。 與具有39條染色體的馬口鱲(Opsariichthys bidens)比較後發現，24條染色體中有15條經歷了染色體斷裂(chromosome fission)。我們進一步檢測了重複序列在染色體上的分布，發現在這些斷裂區間中，LINE-2和LTR-Gypsy轉座子有明顯的增加，這在近期的轉座子上尤其明顯。斷裂後的染色體若缺乏著絲點可能導致染色體丟失(chromosome loss)，進而影響個體的存活，因此我辨認了平頷鱲染色體中節的位置，並發現中節全都落在斷裂區間之間。此外，也發現重組率與近期的LINE-2和LTR-Gypsy轉座子間呈現負相關，顯示中節的低重組率可能也是導致轉座子能夠持續累積在相同區域的原因。 透過基因家族分析，我們發現與基因轉位或重組相關的功能在馬口魚族的擴張基因家族中呈現高度富集，可能與馬口魚族內的物種間有大量的染色體倒位和斷裂有關。此外，亦發現許多與細胞分裂過程染色體正確分離或DNA修復相關的關鍵基因(如smc4、smc5、kif2c、kif22及atm)可能受到正向選擇或選擇性清除，顯示染色體結構維持與穩定可能為平頷鱲演化過程中重要的選擇壓力。 我們也比較了來自中國、韓國、日本與臺灣的平頷鱲，並發現中國與韓國的平頷鱲具有較高的相似度，臺灣的族群則與日本的個體更為接近，本研究以全基因體的角度再次說明了臺灣平頷鱲族群的起源。

Zacco platypus, a freshwater fish of the family Xenocyprididae, is native to eastern China, Korea, and Japan, and was later introduced into the Tamsui River basin in Taiwan. In this study, we present a chromosome-level genome assembly of Z. platypus, comprising 24 chromosomes with a total length of 847 Mb and repetitive elements constitute 55.02% of it. A total of 27,249 genes were annotated, with a BUSCO completeness of 96.7%. Comparative analysis with Opsariichthys bidens, a related species with 39 chromosomes, revealed that 15 out of the 24 chromosomes in Z. platypus have undergone chromosome fission events. Distribution of repetitive elements showed a notable enrichment of LINE-2 and LTR-Gypsy retrotransposon in the breaking regions, particularly among recently active transposons. Since chromosome fission may lead to chromosome lost, potentially affecting viability, we identified the positions of centromeres in Z. platypus and found that all centromeres are located within breaking regions. In addition, we observed a negative correlation between recombination rate and the abundance of recently active LINE-2 and LTR-Gypsy elements, suggesting that low recombination rates around centromeres may facilitate the accumulation of transposons in these regions. Gene family analysis revealed that functions related to transposition and recombination are enriched in expanded gene families within the Opsariichthyini lineage, potentially explaining the extensive chromosomal inversions and fissions observed in this group. We also identified several key genes involved in chromosome segregation and DNA repair (e.g., smc4, smc5, kif2c, kif22, and atm) as likely targets of positive selection or selective sweep, indicating that the maintenance and stability of chromosomal structures may represent important selective pressures during the evolution of Z. platypus.