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Updated mtCOI reference dataset for the Bemisia tabaci species complex

[version 1; peer review: 2 approved]
Laura M. Boykin
https://orcid.org/0000-0002-6101-1921
1, Anders Savill1, Paul De Barro2
Laura M. Boykin
https://orcid.org/0000-0002-6101-1921
1, Anders Savill1, Paul De Barro2
PUBLISHED 13 Oct 2017
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OPEN PEER REVIEW
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This article is included in the Agriculture, Food and Nutrition gateway.

Abstract

Members of the whitefly Bemisia tabaci species complex cause millions of dollars of damage globally and are considered one of the world’s most invasive species. They are capable of causing extensive damage to major vegetable, grain legume and fiber crops. All member of the species complex are morphologically identical therefore, data from the partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene sequence has been used to identify the various species. The current reference dataset that is widely used is found on the CSIRO data portal. However, the reference set stored on the CSIRO data does not include newly added sequences (2013-2017), therefore an updated reference dataset is needed.  All mtCOI data for the Bemisia tabaci species complex were downloaded on 22 May 2017 from GenBank and after quality checking, a dataset of 1,071 unique sequences and 696 base pairs was generated (https://doi.org/10.6084/m9.figshare.5437420.v1).

Keywords

species identification, whitefly, insect vector, mitochondrial cytochrome oxidase, DNA barcoding

Corresponding author: Laura M. Boykin
Competing interests: The authors have no competing interests.
Grant information: The author(s) declared that no grants were involved in supporting this work.
Copyright:  © 2017 Boykin LM et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
How to cite: Boykin LM, Savill A and De Barro P. Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved]. F1000Research 2017, 6:1835 (https://doi.org/10.12688/f1000research.12858.1) First published: 13 Oct 2017, 6:1835 (https://doi.org/10.12688/f1000research.12858.1) Latest published: 13 Oct 2017, 6:1835 (https://doi.org/10.12688/f1000research.12858.1)

Introduction

Members of the Bemisia tabaci (whiteflies) species complex are among the world’s most devastating insect pests and cause billions of dollars (US) of damage each year, leaving farmers in the developing world food insecure (De Barro et al., 2011). As a species complex with at least 34 members, identification is based on the use of the 657 bp portion of the 3’ end of the mitochondrial COI (mtCOI) (Boykin et al., 2012, Boykin et al., 2013). In order to identify members of the complex correctly, a curated reference dataset is a useful resource. In 2012, a reference mtCOI dataset was made available on the CSIRO data portal (De Barro & Boykin, 2012). Errors in the dataset were subsequently identified and so the dataset was updated on 15 May 2017 (http://doi.org/10.4225/08/591a4018dfca8) (De Barro & Boykin, 2017), but did not include new additions from GenBank (post 2012). Therefore, the dataset described herein represents the most up-to-date reference resource for members of the complex.

Methods

The CSIRO dataset (http://doi.org/10.4225/08/591a4018dfca8), updated 15 May 2017 was used as the starting point. The existing records were updated to include host plant data. New records post-2012 were then downloaded on 22 May 2017 directly from GenBank. All downloaded data was treated as follows:

1) Data was classified with BLAST using the new CSIRO reference data set

2) Sequences that caused gaps in the alignment were removed

2) Sequences that had stop codons present were removed

3) Clustal Omega (Sievers & Higgins, 2014) was used for preliminary alignment and fine tuning of the alignment was carried out with MAFFT (Katoh & Standley, 2013).

4) Duplicate sequences were then removed using BBMAP Dedupe (Bushnell, 2017).

In addition, all MEAM2 sequences were removed as they have now been confirmed to be pseudogenes (Tay et al., 2017).

Data availability

Figshare: Dataset 1. mtCOI reference data for species ID of Bemisia tabaci. DOI: 10.6084/m9.figshare.5437420 (Boykin et al., 2017)

Competing interests

The authors have no competing interests.

Grant information

The author(s) declared that no grants were involved in supporting this work.

References

  •  Boykin LM, Armstrong KF, Kubatko L, et al.: Species delimitation and global biosecurity. Evol Bioinform Online. 2012; 8: 1–37. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Boykin LM, Bell CD, Evans G, et al.: Is agriculture driving the diversification of the Bemisia tabaci species complex (Hemiptera: Sternorrhyncha: Aleyrodidae)?: Dating, diversification and biogeographic evidence revealed. BMC Evol Biol. 2013; 13: 228. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Boykin L, Savill A, De Barro P: mtCOI reference data for species ID of Bemisia tabaci. figshare. 2017. Data Source
  •  Bushnell B: BBmap. 2017. Reference Source
  •  De Barro P, Boykin LM: Global Bemisia dataset release version 31 Dec 2012. CSIRO. 2012. Publisher Full Text
  •  De Barro P, Boykin LM: Global Bemisia dataset release version 15 May 2017. CSIRO. 2017. Publisher Full Text
  •  De Barro PJ, Liu SS, Boykin LM, et al.: Bemisia tabaci: a statement of species status. Annu Rev Entomol. 2011; 56: 1–19. PubMed Abstract | Publisher Full Text
  •  Katoh K, Standley DM: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4): 772–780. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Sievers F, Higgins DG: Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol. 2014; 1079: 105–116. PubMed Abstract | Publisher Full Text
  •  Tay WT, Elfekih S, Court LN, et al.: The trouble with MEAM2: Implications of pseudogenes on species delimitation in the globally invasive Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species complex. Genome Biol Evol. 2017. PubMed Abstract | Publisher Full Text

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Boykin LM, Savill A and De Barro P. Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved]. F1000Research 2017, 6:1835 (https://doi.org/10.12688/f1000research.12858.1)
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ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 1
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PUBLISHED 13 Oct 2017
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Reviewer Report 08 Nov 2017
Sharad Saurabh, Molecular and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India 
Manisha Mishra, Developmental Toxicology Division, CSIR-Indian Institute of Toxicology Research, Lucknow, India 
Approved
VIEWS 14
https://doi.org/10.5256/f1000research.13935.r26987
Whitefly (Bemisia tabaci) is becoming a global hazard for crop and ornamental plants. Identification of correct species is always better for the implication of best control strategy. In this regard, the effort made by Boykin et al for speedy and ... Continue reading
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Saurabh S and Mishra M. Reviewer Report For: Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved]. F1000Research 2017, 6:1835 (https://doi.org/10.5256/f1000research.13935.r26987)
The direct URL for this report is:
https://f1000research.com/articles/6-1835/v1#referee-response-26987
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Reviewer Report 23 Oct 2017
Renate Krause Sakate, Department of Plant Protection, Faculty of Agronomic Sciences, São Paulo State University (UNESP), Botucatu, Brazil 
Approved
VIEWS 22
https://doi.org/10.5256/f1000research.13935.r26988
The updated mtCOI reference dataset for the Bemisia tabaci species complex will add a valuable contribution to researches for a fast and accurate identification of members from the B. tabaci species complex based on the partial mitochondrial COI gene.
... Continue reading
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Sakate RK. Reviewer Report For: Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved]. F1000Research 2017, 6:1835 (https://doi.org/10.5256/f1000research.13935.r26988)
The direct URL for this report is:
https://f1000research.com/articles/6-1835/v1#referee-response-26988
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Approved
The paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations
A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved
Fundamental flaws in the paper seriously undermine the findings and conclusions

Reviewer Reports

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  1. Renate Krause Sakate, São Paulo State University (UNESP), Botucatu, Brazil
  2. Sharad Saurabh, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
    Manisha Mishra, CSIR-Indian Institute of Toxicology Research, Lucknow, India

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    Alongside their report, reviewers assign a status to the article:
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    Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
    Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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