A new record for <i><scp>B</scp>emisia tabaci</i> (Gennadius) (Hemiptera: Aleyrodidae) species complex of Turkey

Karut, Kamil; Kaydan, Mehmet Bora; Tok, Başak; Döker, Ismail; Kazak, Cengiz

doi:10.1111/jen.12169

Cited by 16 publications

(15 citation statements)

References 15 publications

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“…The MEAM2 sequence AJ550177, originally referred to as ‘Ms’ biotype 35 , and all subsequent MEAM2-related sequences in GenBank, i.e., (AB308110) 39 ; sequences KK103B, KK104A, KK104B by Karut et al 40 ; KY951453, KY951454, KX234912, KX234913, KX234914 11 ; KX679576 (GenBank unpublished sequence from Iraq); FJ939600, FJ939602 (GenBank unpublished sequence from Egypt)) have been shown 11 to be NUMTs. The original AJ550177 MEAM2 should be differentiated from the ‘MEAM2’ from Africa (KX570778 – KX570784), so named because Mugerwa et al 3 determined a nucleotide distance of <3.5% when compared with the pseudogene MEAM2 AJ550177 instead of first excluding the MEAM2 pseudogene-misidentified species status prior to comparisons being carried out.…”

Section: Resultsmentioning

confidence: 99%

Take out the rubbish – Removing NUMTs and pseudogenes from theBemisia tabacicryptic species mtCOI database

Kunz

Tay

Elfékih

et al. 2019

Preprint

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Identification ofBemisia tabacicryptic whitefly species complex currently relies on molecular characterisation of the mitochondrial DNA cytochrome oxidase subunit I (mtCOI) partial gene, however, nuclear mitochondrial sequences (NUMTs), PCR-derived pseudogenes and/or poor sequence editing have hindered this effort. To-date,ca.5,175 partial (≥ 300bp) mtCOI sequences for species identification purposes have been reported. We reviewedca.10% of sequences representing the standardB. tabacispecies complex mtCOI dataset. We found that 333 sequences (64.9%) were NUMTs, pseudogenes and/or affected by poor sequence quality. Amino acid pattern analyses of high throughput sequencing-derived mtCOI gene from 24 ‘tabaci’ and ‘non-tabaci’ species enabled differentiation between NUMTs/pseudogene-affected and likely real mtCOI sequences, and that the SSA4, SSA5/SSA8, AsiaII-2 and AsiaII_4 species were NUMTs/pseudogenes artefacts. Intra-specific uncorrected nucleotide distances (p-dist) from our up-dated dataset ranged from 0-1.98%, inter-specificp-dist within phylogenetic clades ranged betweenca.2.5 and 8%, and 8 and >19% for species between phylogenetic clades. Differentiating between closely related species could therefore utilise an ‘average’p-dist of 2.5%. Despite the smallerB. tabacimtCOI dataset, six putative new species were identified. Adoption of our standardised workflow and up-dated mtCOI clean dataset could facilitate better diagnostics ofB. tabaciand ‘non-tabaci’ cryptic species.

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Section: Resultsmentioning

confidence: 99%

Take out the rubbish – Removing NUMTs and pseudogenes from theBemisia tabacicryptic species mtCOI database

Kunz

Tay

Elfékih

et al. 2019

Preprint

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“…Despite this, NUMTs can be overlooked (e.g., Boykin etal. 2007 ; Karut etal. 2015 ) when stop codons are found outside the target gene region and this is a particular challenge when the target sequences are short.…”

Section: Introductionmentioning

confidence: 99%

The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex

Tay

Elfékih

Court

et al. 2017

Genome Biology and Evolution

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Molecular species identification using suboptimal PCR primers can over-estimate species diversity due to coamplification of nuclear mitochondrial (NUMT) DNA/pseudogenes. For the agriculturally important whitefly Bemisia tabaci cryptic pest species complex, species identification depends primarily on characterization of the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene. The lack of robust PCR primers for the mtDNA COI gene can undermine correct species identification which in turn compromises management strategies. This problem is identified in the B. tabaci Africa/Middle East/Asia Minor clade which comprises the globally invasive Mediterranean (MED) and Middle East Asia Minor I (MEAM1) species, Middle East Asia Minor 2 (MEAM2), and the Indian Ocean (IO) species. Initially identified from the Indian Ocean island of Réunion, MEAM2 has since been reported from Japan, Peru, Turkey and Iraq. We identified MEAM2 individuals from a Peruvian population via Sanger sequencing of the mtDNA COI gene. In attempting to characterize the MEAM2 mitogenome, we instead characterized mitogenomes of MEAM1. We also report on the mitogenomes of MED, AUS, and IO thereby increasing genomic resources for members of this complex. Gene synteny (i.e., same gene composition and orientation) was observed with published B. tabaci cryptic species mitogenomes. Pseudogene fragments matching MEAM2 partial mtDNA COI gene exhibited low frequency single nucleotide polymorphisms that matched low copy number DNA fragments (<3%) of MEAM1 genomes, whereas presence of internal stop codons, loss of expected stop codons and poor primer annealing sites, all suggested MEAM2 as a pseudogene artifact and so not a real species.

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“…Med, MEAM1, MEAM2, SSA-2 (formerly referred to as biotype S), Italy (formerly referred to as biotype T) and Asia I (formerly referred to as biotype M)] of the complex have been reported (De la Rúa et al 2006;Sartor et al 2008;Bielza et al 2013;Karut et al 2015), but currently Med and MEAM1 species are the most prevalent. In recent years, MEAM1 was reported to have been displaced or even totally supplanted by Med (the western Mediterranean populations also called Q1 Med) B. tabaci species in many Mediterranean countries including Spain, Greece, France, Italy and Morocco (Simón et al 2007;Tsagkarakou et al 2007;Parrella et al 2012;Tahiri et al 2013;Gauthier et al 2014).…”

Section: Introductionmentioning

confidence: 96%

First report of the Sub-Saharan Africa 2 species of the Bemisia tabaci complex in the Southern France

Hadjistylli¹,

Roderick²,

Gauthier³

2015

Phytoparasitica

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A new record for Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) species complex of Turkey

Cited by 16 publications

References 15 publications

Take out the rubbish – Removing NUMTs and pseudogenes from theBemisia tabacicryptic species mtCOI database

Take out the rubbish – Removing NUMTs and pseudogenes from theBemisia tabacicryptic species mtCOI database

The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex

First report of the Sub-Saharan Africa 2 species of the Bemisia tabaci complex in the Southern France

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