| 摘要: |
| 摘要：【目的】 参环毛蚓（A.aspergillum）是中国广东与广西地区广泛分布的蚯蚓物种，俗称为广地龙，利用高通量测序技术对其基因组大小和特征进行分析，为全基因组精细测序、遗传多样性保护、人工选育等研究奠定基础。【方法】 采用细胞流式与高通量测序方法对A.aspergillum基因组进行分析，测算出其基因组大小、重复序列、杂合率和GC含量等， 利用生物信息学对基因组进行预测、注释和基因家族鉴定。【结果】 估算出A.aspergillum基因组大小约1 Gb，通过从头组装二代数据，我们获得全长为765.69 Mb的Contig，组装成单倍体基因组641 Mb左右，其中重复序列为329 Mb，占全长的51.3%，杂合率约1.68% ，GC含量为40.34%，数据表明A.aspergillum基因组有高重复、高杂合等特征。该基因组共预测到27,864个基因，99.04%基因能在功能数据库中找到注释，较多基因富集于在信号转导（Signal Transduction）、内分泌系统（Endocrine system）与传染相关（Infectious disease）功能上。通过对巨蚓科所属物种的线粒体组的分析，蚯蚓种内的遗传距离（p-distance）有着较宽的分布（0-15.1%），其中Amynthas robustus显示最大的种内差距（15.1%），其次是Duplodicodrilus acinctus（13.6%）、Pheretima kutamaensis（10.9%）、A.aspergillum种内遗传距离为1.9%。进一步对不同物种间的遗传距离进行统计，A.aspergillum与Metaphire colifornica遗传距离（16%）最小，其次是A.masatakae （16.20%）与A.robustus（16.21%），以上四个物种同属于广西区域广泛分布的蚯蚓物种。A.aspergillum与M.vulgaris、A. corticis通过核基因组的数据计算的遗传距离（p-distance）为15.64%、20.03%，而通过线粒体基因组计算的遗传距离为21%与19.8%。以上数据提示无论是基于形态和解剖特征的传统分类学，还是基于线粒体谱系的分类，在单独使用时均有一定的局限性，全面厘清蚯蚓物种间的进化历程依赖更多的核基因组数据。【结论】 初步获得了A.aspergillum基因组大小、基因组特征、功能基因及基因家族等信息，对于研究其遗传多样性，人工选育具有指导意义，为进一步研究该物种的全基因组精细测序提供了参考。
关键词：参环毛蚓；基因组分析；基因组大小；基因组特征 |
| 关键词: 参环毛蚓A.aspergillum survery分析 基因组大小 基因组特征 |
| DOI： |
| 投稿时间：2024-07-24修订日期：2024-11-11 |
| 基金项目:广西重点研发计划项目(桂科AB21238014)资助。**通信作者：刘军,(1980-),男,高级工程师,主要从事森林培育及林下经济研究。E-mail:71068973@qq.com#共同通讯作者：彭立新,1980.10,男,副研究员,主要从事动物遗传方向研究,penglixin@gxas.cn |
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| Genome Sequencing And Characterization Of The Ginseng Annelid Worm (Amynthas aspergillum) |
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ZHANG Jun1, JIANG Shunda1, LI Xiuzhi2, LI Xuesong2, LU Bo2, HUANG Jun2, LIU Jun3,4, PENG Lixin2
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| (1.Guangxi Zhuang Autonomous Region State-owned Qipo Forest Farm;2.Guangxi Academy of Sciences;3.Guangxi Zhuang Autonomous Region State-owned Qipo Forest Farm,Nanning;4.Guangxi Academy of Sciences,Institute of Biological Science and Technology,Nanning) |
| Abstract: |
| Abstract: (Objective) The earthworm A. aspergillum, commonly known as “Guangdi Long,” is a widespread species in Guangdong and Guangxi regions of China. Using high-throughput sequencing technology, this study analyzed its genome size and features, laying the groundwork for whole-genome fine sequencing, genetic diversity protection, and artificial breeding research. (Methods)The A. aspergillum genome was analyzed using flow cytometry and high-throughput sequencing methods. Genome size, repeat sequences, heterozygosity rate, and GC content were estimated. (Results)The A. aspergillum genome was estimated to be approximately 1 Gb. De novo assembly yielded a contig with a total length of 765.69 Mb, which was further assembled into a haploid genome of approximately 641 Mb. Of this, 329 Mb (51.3%) consisted of repeat sequences, with a heterozygosity rate of approximately 1.68% and a GC content of 40.34%. These data suggest that the A. aspergillum genome is characterized by high repeat content and heterozygosity. A total of 27,864 genes were predicted, 99.04% of which were annotated in functional databases. Many genes were enriched in functions related to signal transduction, endocrine systems, and infectious diseases. Mitochondrial genome analysis of species within the family Megascolecidae revealed a wide range of intraspecific genetic distances (p-distance) from 0 to 15.1%, with Amynthas robustus showing the largest intraspecific divergence (15.1%), followed by Duplodicodrilus acinctus (13.6%) and Pheretima kutamaensis (10.9%). The intraspecific genetic distance of A. aspergillum was 1.9%. Further analysis of interspecies genetic distances showed that A. aspergillum had the smallest genetic distance with Metaphire colifornica (16%), followed by A. masatakae (16.20%) and A. robustus (16.21%). These four species are all widely distributed earthworms in the Guangxi region. The p-distances of the nuclear genome between A. aspergillum and M. vulgaris (15.64%) and A. corticis (20.03%) contrast with the corresponding mitochondrial genome values of 21% and 19.8%. The discrepancies between these data indicate that both traditional taxonomy based on morphological and anatomical characteristics and taxonomy based on mitochondrial phylogenies have limitations when used independently. A comprehensive understanding of earthworm evolutionary relationships requires more nuclear genome data.(Conclusion)This study offers preliminary insights into the genome size, characteristics, functional genes, and gene families of A. aspergillum. These findings are valuable for understanding its genetic diversity, guiding artificial breeding efforts, and serving as a reference for future whole-genome sequencing research.
Keywords: Amynthas aspergillum; genome survey; genome size; genome characteristics |
| Key words: ginseng annelid worm A. aspergillum survery analysis genome size genome characterization |
