扎科鸭嘴兽基因组的注释和特征描述

Diversity Pub Date : 2024-09-01 DOI:10.3390/d16090529
Sang-Eun Nam, Dae-Yeul Bae, Jae-Sung Rhee
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引用次数: 0

摘要

鸭嘴鱼(鲤形目;Xenocyprididae;Jordan & Evermann,1902 年)广泛分布于东亚的淡水生态系统中,被认为是生态毒理学和环境监测的潜在模式鱼种。在这里,通过整合太平洋生物科学公司(PacBio)的长读数测序、Illumina的短读数测序和Hi-C测序技术,构建了鸭嘴兽的高质量全新基因组。与鲤形目其他物种相比,鸭嘴兽的基因组最小。组装的基因组包含 41.45% 的重复序列。正如在其他鱼类中观察到的那样,基因组大小与基因组中转座元素(TE)的组成呈正相关。在转座元件中,DNA转座子的比例相对较高,这也是鲤形目成员的常见模式。利用四个具有代表性的数据库进行了功能注释,确定了由 12,907 个基因组成的核心基因组。同源基因家族分析表明,与其他鲤形目物种相比,鸭嘴兽经历了更多的基因家族收缩而非扩张。在鸭嘴兽独特的扩展基因家族中,发现了与解毒和应激相关的基因家族,这表明该物种可以作为生态毒理学和环境监测的一个有前途的模型。总之,鸭嘴兽基因组的组装将为水生生态系统中基于omics的健康评估提供宝贵的数据,为进一步了解该物种的环境和生态面貌提供依据。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Annotation and Characterization of the Zacco platypus Genome
The pale chub Zacco platypus (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of Z. platypus was constructed through the integration of a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. Z. platypus has the smallest genome size compared to other species belonging to the order Cypriniformes. The assembled genome encompasses 41.45% repeat sequences. As shown in other fish, a positive correlation was observed between genome size and the composition of transposable elements (TE) in the genome. Among TEs, a relatively higher rate of DNA transposon was observed, which is a common pattern in the members of the order Cypriniformes. Functional annotation was processed using four representative databases, identifying a core set of 12,907 genes shared among them. Orthologous gene family analysis revealed that Z. platypus has experienced more gene family contraction rather than expansion compared to other Cypriniformes species. Among the uniquely expanded gene families in Z. platypus, detoxification and stress-related gene families were identified, suggesting that this species could represent a promising model for ecotoxicology and environmental monitoring. Taken together, the Z. platypus genome assembly will provide valuable data for omics-based health assessments in aquatic ecosystems, offering further insights into the environmental and ecological facets within this species.
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