Draft genome sequence of Cicuta witches' broom phytoplasma, subgroup 16SrIII-J: a subgroup with phytopathological relevance in South America

IF 2.5 3区农林科学 Q2 Agricultural and Biological Sciences

Tropical Plant Pathology Pub Date : 2024-05-28 DOI:10.1007/s40858-024-00658-0

Franco Daniel Fernández, Fabiana Aída Guzmán, Luis Rogelio Conci

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Abstract

Phytoplasmas are uncultivable wall-less bacteria causing plant diseases worldwide. Phytoplasmas from X-disease are one of the most diverse and economically important in South America. The Cicuta witches' broom Phytoplasma (CicWB) was described in association to cicuta or hemlock (Conium maculatum L.) exhibiting witches' broom and phyllody symptoms in surrounding potato fields in Los Cerrillos (Córdoba- Argentina). The partial genome of CicWB phytoplasma was obtained using a hybrid approach combining Illumina and Oxford Nanopore Technologies. Final draft genome consists of 16 contigs totaling 758.187 bp of length, with 400X of coverage and 96.70% of the estimated completeness. Comparative genomics, based on Average Nucleotide Identity (ANI), digital DNA-DNA hybridization (dDDH), and phylogenomic analyses, revealed its close relationship to subgroup 16SrIII-J phytoplasmas. Furthermore, the study identified 37 putative effectors, including orthologs for SAP11, SAP54, SAP05, as well as immunodominant membrane proteins Imp and IdpA. This comprehensive genome analysis provides crucial insights into the genomic landscape of phytoplasmas in the region, contributing to our understanding of their diversity and pathogenicity.

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Cicuta 女巫扫帚植物支原体 16SrIII-J 亚群基因组序列草案：南美洲植物病理学相关亚群

植物病原菌是一种不可培养的无壁细菌，可在全球范围内引起植物病害。在南美洲，来自 X 病菌的植原体是种类最多、经济价值最高的植原体之一。在洛斯塞里略斯（阿根廷科尔多瓦省）的马铃薯田中，马铃薯或铁杉（Conium maculatum L.）表现出马铃薯帚病和植物病害症状，与之相关的西葫芦巫帚病植物支原体（CicWB）也被描述出来。CicWB 植原体的部分基因组是利用 Illumina 和 Oxford Nanopore 技术相结合的混合方法获得的。最终基因组草案由 16 个等位基因组成，总长度为 758.187 bp，覆盖率为 400 倍，估计完整度为 96.70%。基于平均核苷酸同一性（ANI）、数字 DNA-DNA 杂交（dDDH）和系统发生组分析的比较基因组学发现，它与 16SrIII-J 亚群植物病原菌关系密切。此外，该研究还发现了 37 种推测的效应物，包括 SAP11、SAP54、SAP05 的直向同源物，以及免疫显性膜蛋白 Imp 和 IdpA。这项全面的基因组分析提供了对该地区植物病原菌基因组状况的重要见解，有助于我们了解它们的多样性和致病性。

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来源期刊

Tropical Plant Pathology PLANT SCIENCES-

CiteScore

4.50

自引率

4.00%

发文量

审稿时长

6-12 weeks

期刊介绍： Tropical Plant Pathology is an international journal devoted to publishing a wide range of research on fundamental and applied aspects of plant diseases of concern to agricultural, forest and ornamental crops from tropical and subtropical environments.  Submissions must report original research that provides new insights into the etiology and epidemiology of plant disease as well as population biology of plant pathogens, host-pathogen interactions, physiological and molecular plant pathology, and strategies to promote crop protection. The journal considers for publication: original articles, short communications, reviews and letters to the editor. For more details please check the submission guidelines. Founded in 1976, the journal is the official publication of the Brazilian Phytopathology Society.