Unravelling the Genetic Diversity among Cassava Bemisia tabaci Whiteflies Using NextRAD Sequencing

Abstract

Bemisia tabaci threatens production of cassava in Africa through vectoring viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). B. tabaci sampled from cassava in eight countries in Africa were genotyped using NextRAD sequencing, and their phylogeny and population genetics were investigated using the resultant single nucleotide polymorphism (SNP) markers. SNP marker data and short sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) obtained from the same insect were compared. Eight genetically distinct groups were identified based on mtCOI, whereas phylogenetic analysis using SNPs identified six major groups, which were further confirmed by PCA and multidimensional analyses. STRUCTURE analysis identified four ancestral B. tabaci populations that have contributed alleles to the six SNP-based groups. Significant gene flows were detected between several of the six SNP-based groups. Evidence of gene flow was strongest for SNP-based groups occurring in central Africa. Comparison of the mtCOI and SNP identities of sampled insects provided a strong indication that hybrid populations are emerging in parts of Africa recently affected by the severe CMD pandemic. This study reveals that mtCOI is not an effective marker at distinguishing cassava-colonizing B. tabaci haplogroups, and that more robust SNP-based multilocus markers should be developed. Significant gene flows between populations could lead to the emergence of haplogroups that might alter the dynamics of cassava virus spread and disease severity in Africa. Continuous monitoring of genetic compositions of whitefly populations should be an essential component in efforts to combat cassava viruses in Africa.

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

“…For example, NUMTs (nuclear mitochondrial sequences) have been misidentified and published in high frequencies 9 which resulted in conflicting estimates of inter-species nucleotide distances 2,10 and erroneous molecular species diagnosis (e.g., MEAM2, see Dinsdale et al 10 cf . Tay et al 11 ; SSA4 see Berry et al 12 and Wosula et al 13 cf . Elfekih et al 14 ).…”

“…Difficulties to identify NUTMs and pseudogenes have significantly and negatively impacted research efforts to better manage the Bemisia cryptic species pest complex 25 , leading to misinterpretations of genome-wide SNP data 13 and understanding of evolutionary genomics involving whole genome sequencing 26 . Although the recently published mtCOI dataset with 513 B. tabaci sequences 8 aimed to address molecular diagnostic needs and species identification with efforts to remove insertion-deletion (indel)-affected sequences from the original dataset 8 , indel-affected sequences nevertheless remained present, while amino acid substitution patterns in sequences unaffected by indels were not examined.…”

Minimum sample sizes for invasion genomics: Empirical investigation in an invasive whitefly

“…The techniques based on RADseq include original RAD, double‐digest RAD (ddRAD), type IIB endonucleases restriction site‐associated DNA (2b‐RAD), and ezRAD (Andrews, Good, Miller, Luikart, & Hohenlohe, ; Davey et al, ). In recent years, the RADseq technique has been widely used in the study of population genomics (Blanco‐Bercial & Bucklin, ; Wosula, Chen, Fei, & Legg, ), with the minimum sample size for population genomics being evaluated based on simulation (Willing et al, ) or empirical analysis (Nazareno et al, ). For example, by estimating the genetic differentiation ( F ST ) a simulation analysis has shown that sample size can be reduced to four to six individuals when using a large number of SNPs (Willing et al, ).…”

High-density genetic linkage map construction and white rot resistance QTL mapping for Vitis based on restriction site-associated DNA sequencing

“…With the development of high-throughput sequencing technology, SNP markers have been widely used in genetic diversity and evolutionary analysis, high-density genetic linkage map construction, genomic association analysis, and QTL mapping (Brookes 1999, Fujii et al 2013). Simplified genome sequencing was proposed by Miller et al in 2007, and the corresponding technology of restriction endonuclease-related DNA sequencing (RAD-seq) was developed and became widely used in plant research including tea (Hua et al 2016), cassava (Wosula et al 2017), eggplant (Barchi et al 2011), sesame (Wang et al 2016), and barley (Chutimanitsakun et al 2011). It has also been used for fruit tree research such as apple (Sun et al 2015), pummelo (Guy et al 2015), and pear (Wu et al 2014).…”