Draft genome of pin nematode Paratylenchus projectus recovered from rhizosphere of blueberry.

IF 3 2区 医学 Q1 PARASITOLOGY
Liang-Qin Liu, Wei-Qi Fu, Yuan-Yuan Ma, Zhi-Yin Liu, Chun-Feng Ge, Yi-Ru Yang, Xue Qing, Qi-Long Zeng
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Abstract

Background: The pin nematode, belonging to the genus Paratylenchus, parasitizes higher plants, often causing reduced or inhibited root tip development.

Methods: Pin nematodes were isolated from the roots and rhizosphere of blueberry plants and subsequently identified as representatives of Paratylenchus projectus based on morphological characteristics and molecular barcoding. The P. projectus draft genome was sequenced using the Illumina platform.

Results: Phylogenetic analysis based on 18S, 28S and ITS rRNA placed this species in highly supported clades alongside other P. projectus specimens. The draft genome of P. projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae. The assembled genome, though fragmented, had a total length of 191.36 Mb and an estimated genome size of 64.9 Mb. Protein-coding genes were predicted using four different databases, with particular focus on carbohydrate-active enzymes from the GH5 and GH18 families. The recovered GH5 genes were distributed among three distinct clades: one forming a basal group relative to other nematodes, one as a sister clade to the fungivorous nematode Aphelenchus avenae and one nested within a fungal clade. The GH18 chitinase genes were grouped into two clades: one closely related to sedentary plant-parasitic nematodes of the genera Heterodera and Globodera and the other closely related to the fungivorous nematode Ditylenchus.

Conclusions: The draft genome of Paratylenchus projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae to our knowledge.

从蓝莓根际提取针线虫基因组草图。
背景:针状线虫属于副针状线虫属,寄生于高等植物,经常导致根尖发育减少或抑制。方法:从蓝莓根系和根际分离出针线虫,根据形态特征和分子条形码鉴定为项目副叶柄线虫的代表。利用Illumina平台对P. projectus草图基因组进行测序。结果:基于18S, 28S和ITS rRNA的系统发育分析将该物种与其他投影种标本一起置于高度支持的支系中。结果表明,该植物的基因组初稿首次获得了副叶蝉属和叶蝉科的基因组数据。组装的基因组虽然是碎片化的,但总长度为191.36 Mb,估计基因组大小为64.9 Mb。蛋白质编码基因使用四个不同的数据库进行预测,特别关注来自GH5和GH18家族的碳水化合物活性酶。回收的GH5基因分布在三个不同的分支中:一个与其他线虫形成基础群,一个作为食真菌线虫的姐妹分支,一个嵌套在真菌分支中。GH18几丁质酶基因被分为两个分支:一个与定居植物寄生线虫(Heterodera属和Globodera属)密切相关,另一个与食真菌线虫(diylenchus)密切相关。结论:基因组草案Paratylenchus projectus测序和组装,代表第一个基因组数据属Paratylenchus和家庭Tylenchulidae我们的知识。
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来源期刊
Parasites & Vectors
Parasites & Vectors 医学-寄生虫学
CiteScore
6.30
自引率
9.40%
发文量
433
审稿时长
1.4 months
期刊介绍: Parasites & Vectors is an open access, peer-reviewed online journal dealing with the biology of parasites, parasitic diseases, intermediate hosts, vectors and vector-borne pathogens. Manuscripts published in this journal will be available to all worldwide, with no barriers to access, immediately following acceptance. However, authors retain the copyright of their material and may use it, or distribute it, as they wish. Manuscripts on all aspects of the basic and applied biology of parasites, intermediate hosts, vectors and vector-borne pathogens will be considered. In addition to the traditional and well-established areas of science in these fields, we also aim to provide a vehicle for publication of the rapidly developing resources and technology in parasite, intermediate host and vector genomics and their impacts on biological research. We are able to publish large datasets and extensive results, frequently associated with genomic and post-genomic technologies, which are not readily accommodated in traditional journals. Manuscripts addressing broader issues, for example economics, social sciences and global climate change in relation to parasites, vectors and disease control, are also welcomed.
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