Literature DB >> 35462955

Draft genome sequence of 'Candidatus Phytoplasma australasia', strain SS02 associated with sesame phyllody disease.

Hemavati Ranebennur1, Kiran Kirdat2, Bhavesh Tiwarekar2, Kirti Rawat1, V Celia Chalam3, Amolkumar U Solanke4, Rashmi Yadav3, Kuldeep Singh3, Shivaji Sathe5, Amit Yadav2, G P Rao1.   

Abstract

'Candidatus Phytoplasma' is an uncultivated, intracellular bacterial plant pathogen transmitted by phloem-feeding insect vectors. Among the group of phytoplasmas, the Peanut Witches' Broom or 16SrII group of phytoplasmas associated with various diseases cause severe crop losses every year in India. The 'Ca. Phytoplasma sp.' strain SS02 was associated with phyllody disease of sesame plants collected from New Delhi. The genome sequence of strain SS02 was obtained using its genomic DNA enrichment and hybrid assembly of sequences generated on Illumina and Oxford Nanopore Technologies MinION platforms. The hybrid assembly strategy generated a draft genome with 60 contigs totaling 553,228 bp of length with more than 400 × depth coverage and 95.21% of the estimated completeness. The SS02 genome draft sequence contains 465 protein-coding genes, 17 tRNA genes, and 3 rRNA genes. The availability of this draft genome also provided a foundation for genome-scale genotypic analyses. © King Abdulaziz City for Science and Technology 2022.

Entities:  

Year:  2022        PMID: 35462955      PMCID: PMC8989914          DOI: 10.1007/s13205-022-03163-w

Source DB:  PubMed          Journal:  3 Biotech        ISSN: 2190-5738            Impact factor:   2.893


  22 in total

1.  Draft Genome Sequences of Two Phytoplasma Strains Associated with Sugarcane Grassy Shoot (SCGS) and Bermuda Grass White Leaf (BGWL) Diseases.

Authors:  Kiran Kirdat; Bhavesh Tiwarekar; Vipool Thorat; Nitin Narawade; Dhiraj Dhotre; Shivaji Sathe; Yogesh Shouche; Amit Yadav
Journal:  Mol Plant Microbe Interact       Date:  2020-03-10       Impact factor: 4.171

2.  First Report of a New Subgroup 16Sr II-M 'Candidatus Phytoplasma aurantifolia' Associated with Witches'-Broom Disease of Tephrosia purpurea in India.

Authors:  A Yadav; U Bhale; V Thorat; Y Shouche
Journal:  Plant Dis       Date:  2014-07       Impact factor: 4.438

3.  PGAP: pan-genomes analysis pipeline.

Authors:  Yongbing Zhao; Jiayan Wu; Junhui Yang; Shixiang Sun; Jingfa Xiao; Jun Yu
Journal:  Bioinformatics       Date:  2011-11-29       Impact factor: 6.937

4.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Authors:  Donovan H Parks; Michael Imelfort; Connor T Skennerton; Philip Hugenholtz; Gene W Tyson
Journal:  Genome Res       Date:  2015-05-14       Impact factor: 9.043

5.  Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.

Authors:  Bruce J Walker; Thomas Abeel; Terrance Shea; Margaret Priest; Amr Abouelliel; Sharadha Sakthikumar; Christina A Cuomo; Qiandong Zeng; Jennifer Wortman; Sarah K Young; Ashlee M Earl
Journal:  PLoS One       Date:  2014-11-19       Impact factor: 3.240

6.  Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.

Authors:  Seok-Hwan Yoon; Sung-Min Ha; Soonjae Kwon; Jeongmin Lim; Yeseul Kim; Hyungseok Seo; Jongsik Chun
Journal:  Int J Syst Evol Microbiol       Date:  2017-05-30       Impact factor: 2.747

7.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.

Authors:  Ryan R Wick; Louise M Judd; Claire L Gorrie; Kathryn E Holt
Journal:  PLoS Comput Biol       Date:  2017-06-08       Impact factor: 4.475

8.  FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool.

Authors:  Joseph Brown; Meg Pirrung; Lee Ann McCue
Journal:  Bioinformatics       Date:  2017-06-09       Impact factor: 6.937

9.  eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.

Authors:  Carlos P Cantalapiedra; Ana Hernández-Plaza; Ivica Letunic; Peer Bork; Jaime Huerta-Cepas
Journal:  Mol Biol Evol       Date:  2021-12-09       Impact factor: 16.240

10.  Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (Echinacea purpurea) Witches' Broom Disease in Taiwan.

Authors:  Shu-Heng Chang; Shu-Ting Cho; Chung-Li Chen; Jun-Yi Yang; Chih-Horng Kuo
Journal:  Genome Announc       Date:  2015-11-25
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  1 in total

Review 1.  Phytoplasma Taxonomy: Nomenclature, Classification, and Identification.

Authors:  Wei Wei; Yan Zhao
Journal:  Biology (Basel)       Date:  2022-07-26
  1 in total

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