Take out the rubbish – Removing NUMTs and pseudogenes from the Bemisia tabaci cryptic species mtCOI database

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