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A polyphasic approach to delineate species in Bipolaris

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Abstract

Bipolaris species are important plant pathogens with a worldwide distribution in tropical and temperate environments. Species recognition in Bipolaris has been problematic due to a lack of molecular data from ex-type cultures, the use of few gene regions for species resolution and overlapping morphological characters. In this study, we evaluate the efficiency of different DNA barcodes in species delimitation in Bipolaris by phylogenetic analyses, Automatic Barcode Gap Discovery and Objective Clustering. GAPDH is determined to be the best single marker for the genus. These approaches are used to clarify the taxonomic placement of all sequences currently named as Bipolaris in GenBank based on ITS and GAPDH gene sequence data. In checking various publications, we found that the majority of new host records of fungal species published in the Plant Disease journal from 2010 to 2019 were based on BLAST searches of the ITS sequences and up to 82% of those records could be erroneous. Therefore, relying on BLAST searches from GenBank to name species is not recommended. Editorial boards of journals and reviewers of new record papers should be aware of this problem. In naming Bipolaris species, whether new or known, it is recommended to perform phylogenetic analyses based on GAPDH using the correct taxon sampling for accurate results and the species relationship should have reliable statistical support. At least two new species are represented by molecular data in GenBank and we provide an updated taxonomic revision of Bipolaris. We accept 45 species in Bipolaris and notes are provided for all the species including hosts and geographic distribution.

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Acknowledgements

The authors would like to thank Yunnan Provincial Key Programs of Yunnan Eco-friendly Food International Cooperation Research Center Project under Grant 2019ZG00908. KD Hyde would like to thank the Thailand Research Fund, grant RDG6130001 entitled “Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion”. We would like to thank Dr Sophie Brouillet (Systematique, Adaptation et Evolution, Sorbonne University Pierre and Marie Curie Campus (UPMC), France) for providing critical insight and expertise to the manuscript.

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Author notes

  1. Kevin D. Hyde and Jun Sheng have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, People’s Republic of China

    Chitrabhanu S. Bhunjun, Kevin D. Hyde & Jun Sheng

  2. Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand

    Chitrabhanu S. Bhunjun, Ruvishika S. Jayawardena, Chayanard Phukhamsakda & Digvijayini Bundhun

  3. School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand

    Chitrabhanu S. Bhunjun

  4. Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, People’s Republic of China

    Yang Dong & Jun Sheng

  5. Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius

    Rajesh Jeewon

  6. Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50002, Thailand

    Digvijayini Bundhun

  7. Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou, 510225, People’s Republic of China

    Kevin D. Hyde

  8. Centre for Mountain Futures, Kunming Institute of Botany, Kunming, 650201, Yunnan, People’s Republic of China

    Kevin D. Hyde

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  1. Chitrabhanu S. Bhunjun
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Corresponding authors

Correspondence to Kevin D. Hyde or Jun Sheng.

Electronic supplementary material

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Supplementary file3 (DOCX 15 kb)

Sequences deleted from the bulk ITS dataset. These sequences are not currently classified under Bipolaris

Supplementary file1 (PDF 14353 kb)

Phylogenetic tree generated by maximum likelihood analysis of all ITS sequences of Bipolaris from GenBank. RAxML bootstrap support values ≥ 60% (BT) are shown respectively near the nodes. All separate clusters with statistical support are shown (13 separate clusters to the accepted type species). The scale bar indicates 0.02 changes per site and the tree is rooted with C. buchloes and C. subpapendorfii

Supplementary file4 (DOCX 25 kb)

List of all the sequences (66 in total) which did not cluster with their respective type sequences based on phylogenetic analyses of the ITS regions ((≥60% BT)

Supplementary file5 (DOCX 20 kb)

List of 57 sequences which did not cluster with any type sequences based on phylogenetic analyses of the ITS regions (≥ 60% BT)

Supplementary file2 (PDF 460 kb)

Phylogenetic tree generated by maximum likelihood analysis of GAPDH sequence data of Bipolaris type sequences. RAxML bootstrap support values ≥ 60% (BT) are shown respectively near the nodes. The scale bar indicates 0.02 changes per site and the tree is rooted with C. buchloes and C. subpapendorfii. Clade 1 and 2 represents the sequences that formed separate clades to the accepted type species of Bipolaris

Supplementary file6 (DOCX 18 kb)

List of GAPDH sequences which did not cluster with their respective type sequences (≥ 60% BT) and 3 sequences which formed separate clusters

Supplementary file7 (XLS 46 kb)

Estimates of evolutionary divergence between sequences in the ITS type dataset. Pairwise distance between 45 nucleotide sequences based on the K2P model. The analysis included all codon positions and pairwise deletion of gaps for each sequence pair

Supplementary file8 (XLS 45 kb)

Estimates of evolutionary divergence between sequences in the GAPDH type dataset. Pairwise distance between 44 nucleotide sequences based on the K2P model. The analysis included all codon positions and pairwise deletion of gaps for each sequence pair

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Bhunjun, C.S., Dong, Y., Jayawardena, R.S. et al. A polyphasic approach to delineate species in Bipolaris. Fungal Diversity 102, 225–256 (2020). https://doi.org/10.1007/s13225-020-00446-6

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