Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae

BMC Plant Biology

Research

Namkhang Leeratsuwan¹  Intawat Nookaew²  Chutima Kuhakarn³  Vichai Reutrakul³  Narong Nuntasaen⁴  Piroon Jenjaroenpun⁵  Thidathip Wongsurawat⁵  Pravech Ajawatanawong⁵  Phongthana Pasookhush⁵  Wonnop Visessanguan⁶  Kwanjeera Wanichthanarak⁷  Sakda Khoomrung⁸  Songsak Wattanachaisaereekul⁹  Yongyut Sirivatanauksorn^1,10 

[1] Department of Biology, Faculty of Science, Mahidol University, 10400, Bangkok, Thailand;Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, 72205, Little Rock, AR, USA;Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, 10400, Bangkok, Thailand;Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, 10400, Bangkok, Thailand;Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, 10900, Bangkok, Thailand;Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, 10700, Bangkok, Thailand;Functional Ingredients and Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 12120, Phathumthani, Thailand;Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, 10700, Bangkok, Thailand;Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, 10700, Bangkok, Thailand;Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, 10700, Bangkok, Thailand;Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, 10700, Bangkok, Thailand;Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, 10400, Bangkok, Thailand;School of Food industry, King Mongkut’s Institute of Technology Ladkrabang, 10520, Bangkok, Thailand;Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, 10700, Bangkok, Thailand;

关键词: Ventilago harmandiana;    Rhamnaceae;    Chloroplast genome;    Plant genomics;    Natural product;    Genome assembly;    Genome annotation;    Oxford Nanopore technologies;   

DOI  :  10.1186/s12870-023-04074-5

 received in 2022-09-12, accepted in 2023-01-18,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundMassive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed.ResultsThe complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis.ConclusionsIn summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.

【 授权许可】

CC BY   
© The Author(s) 2023

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