Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses
Phytoplasmas are uncultivated plant-pathogenic bacteria with agricultural importance. Those belonging to the 16SrII group, represented by ‘Candidatus P. aurantifolia’, have a wide range of plant hosts and cause significant yield losses in valuable crops, such as pear, sweet potato, peanut, and soybe...
Guardado en:
| Autores principales: | , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Frontiers Media S.A.
2021
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/fb3764cc82474ed2b975b8c676a68312 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:fb3764cc82474ed2b975b8c676a68312 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:fb3764cc82474ed2b975b8c676a683122021-11-11T10:02:33ZAccelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses1664-302X10.3389/fmicb.2021.766221https://doaj.org/article/fb3764cc82474ed2b975b8c676a683122021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.766221/fullhttps://doaj.org/toc/1664-302XPhytoplasmas are uncultivated plant-pathogenic bacteria with agricultural importance. Those belonging to the 16SrII group, represented by ‘Candidatus P. aurantifolia’, have a wide range of plant hosts and cause significant yield losses in valuable crops, such as pear, sweet potato, peanut, and soybean. In this study, a method that combines immunoprecipitation-based enrichment and MinION long-read DNA sequencing was developed to solve the challenge of phytoplasma genome studies. This approach produced long reads with high mapping rates and high genomic coverage that can be combined with Illumina reads to produce complete genome assemblies with high accuracy. We applied this method to strain NCHU2014 and determined its complete genome sequence, which consists of one circular chromosome with 635,584 bp and one plasmid with 4,224 bp. Although ‘Ca. P. aurantifolia’ NCHU2014 has a small chromosome with only 471 protein-coding genes, it contains 33 transporter genes and 27 putative effector genes, which may contribute to obtaining nutrients from hosts and manipulating host developments for their survival and multiplication. Two effectors, the homologs of SAP11 and SAP54/PHYL1 identified in ‘Ca. P. aurantifolia’ NCHU2014, have the biochemical activities in destabilizing host transcription factors, which can explain the disease symptoms observed in infected plants. Taken together, this study provides the first complete genome available for the 16SrII phytoplasmas and contributes to the understanding of phytoplasma pathogenicity.Choon Meng TanYu-Chen LinJian-Rong LiYuan-Yu ChienChien-Jui WangLin ChouCheng-Wei WangYi-Ching ChiuYi-Ching ChiuChih-Horng KuoChih-Horng KuoChih-Horng KuoJun-Yi YangJun-Yi YangJun-Yi YangJun-Yi YangFrontiers Media S.A.articlephytoplasmaNanoporeeffectorSAP11genome sequencingpotential mobile unitMicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
phytoplasma Nanopore effector SAP11 genome sequencing potential mobile unit Microbiology QR1-502 |
| spellingShingle |
phytoplasma Nanopore effector SAP11 genome sequencing potential mobile unit Microbiology QR1-502 Choon Meng Tan Yu-Chen Lin Jian-Rong Li Yuan-Yu Chien Chien-Jui Wang Lin Chou Cheng-Wei Wang Yi-Ching Chiu Yi-Ching Chiu Chih-Horng Kuo Chih-Horng Kuo Chih-Horng Kuo Jun-Yi Yang Jun-Yi Yang Jun-Yi Yang Jun-Yi Yang Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses |
| description |
Phytoplasmas are uncultivated plant-pathogenic bacteria with agricultural importance. Those belonging to the 16SrII group, represented by ‘Candidatus P. aurantifolia’, have a wide range of plant hosts and cause significant yield losses in valuable crops, such as pear, sweet potato, peanut, and soybean. In this study, a method that combines immunoprecipitation-based enrichment and MinION long-read DNA sequencing was developed to solve the challenge of phytoplasma genome studies. This approach produced long reads with high mapping rates and high genomic coverage that can be combined with Illumina reads to produce complete genome assemblies with high accuracy. We applied this method to strain NCHU2014 and determined its complete genome sequence, which consists of one circular chromosome with 635,584 bp and one plasmid with 4,224 bp. Although ‘Ca. P. aurantifolia’ NCHU2014 has a small chromosome with only 471 protein-coding genes, it contains 33 transporter genes and 27 putative effector genes, which may contribute to obtaining nutrients from hosts and manipulating host developments for their survival and multiplication. Two effectors, the homologs of SAP11 and SAP54/PHYL1 identified in ‘Ca. P. aurantifolia’ NCHU2014, have the biochemical activities in destabilizing host transcription factors, which can explain the disease symptoms observed in infected plants. Taken together, this study provides the first complete genome available for the 16SrII phytoplasmas and contributes to the understanding of phytoplasma pathogenicity. |
| format |
article |
| author |
Choon Meng Tan Yu-Chen Lin Jian-Rong Li Yuan-Yu Chien Chien-Jui Wang Lin Chou Cheng-Wei Wang Yi-Ching Chiu Yi-Ching Chiu Chih-Horng Kuo Chih-Horng Kuo Chih-Horng Kuo Jun-Yi Yang Jun-Yi Yang Jun-Yi Yang Jun-Yi Yang |
| author_facet |
Choon Meng Tan Yu-Chen Lin Jian-Rong Li Yuan-Yu Chien Chien-Jui Wang Lin Chou Cheng-Wei Wang Yi-Ching Chiu Yi-Ching Chiu Chih-Horng Kuo Chih-Horng Kuo Chih-Horng Kuo Jun-Yi Yang Jun-Yi Yang Jun-Yi Yang Jun-Yi Yang |
| author_sort |
Choon Meng Tan |
| title |
Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses |
| title_short |
Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses |
| title_full |
Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses |
| title_fullStr |
Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses |
| title_full_unstemmed |
Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses |
| title_sort |
accelerating complete phytoplasma genome assembly by immunoprecipitation-based enrichment and minion-based dna sequencing for comparative analyses |
| publisher |
Frontiers Media S.A. |
| publishDate |
2021 |
| url |
https://doaj.org/article/fb3764cc82474ed2b975b8c676a68312 |
| work_keys_str_mv |
AT choonmengtan acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT yuchenlin acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT jianrongli acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT yuanyuchien acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT chienjuiwang acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT linchou acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT chengweiwang acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT yichingchiu acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT yichingchiu acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT chihhorngkuo acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT chihhorngkuo acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT chihhorngkuo acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT junyiyang acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT junyiyang acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT junyiyang acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses AT junyiyang acceleratingcompletephytoplasmagenomeassemblybyimmunoprecipitationbasedenrichmentandminionbaseddnasequencingforcomparativeanalyses |
| _version_ |
1718439276933283840 |