Biology subjects

Boykin, L. M.

Publications and source records attributed to Boykin, L. M..

3 recordsLinked to original sources

bioRxiv2018

Real time portable genome sequencing for global food security

The United Nations has listed Zero Hunger as one of the 17 global sustainable development goals to end extreme poverty by 2030. Plant viruses are a major constraint to crop production globally causing an estimated $30 billion in damage 1 leaving millions of people food insecure 2. In Africa, agriculture employs up to 50% of the workforce, yet only contributes 15% to the GDP on average 3, suggesting that there is low productivity and limited value addition. This can be addressed through continued innovation in the fields of science and technology as suggested in the Science Agenda for Agriculture in Africa (S3A) 4. Sustainable management of plant viruses and their associated vectors must include efficient diagnostics for surveillance, detection and identification to inform disease management, including the development and strategic deployment of virus resistant varieties. To date, researchers have been utilizing conventional methods such as; PCR, qPCR, high throughput sequencing (RNA-Seq, DNA-Seq) and Sanger sequencing for pathogen identification. However, these methods are both costly and time consuming, delaying timely control actions. The emergence of new tools for real-time diagnostics, such as the Oxford Nanopore MinION, have recently proven useful for early detection of Ebola 6 and Zika 7,8, even in low resourced laboratories. For the first time globally, the MinION portable pocket DNA sequencer was used to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating CMD which is ravaging smallholder farmers crops in sub-Saharan Africa. Cassava, a carbohydrate crop from which tapioca originates, is a major source of calories for over eight hundred (800) million people worldwide. With this technology, farmers struggling with diseased crops can take immediate, restorative action to improve their livelihoods based on information about the health of their plants, generated using a portable, real-time DNA sequencing device.

plant biology↗

bioRxiv2018

Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

Plant viral diseases are one of the major limitations in legume production within sub Saharan Africa (SSA), as they account for up to 100 % in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out. The main aim was to gain insights into the selection pressure and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV), within symptomatic common beans and cowpeas. Eleven near complete genomes of BCMNV and two for CABMV sequences were obtained from SSA. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes was carried out. Three distinct well-supported clades were identified across the whole genome tree, and were in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. These results will contribute greatly to the knowledge gap surrounding the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and support the current breeding efforts towards resistance for BCMNV and CABMV.

evolutionary biology↗

bioRxiv2017

A novel method for single whitefly (Bemisia tabaci) transcriptomes reveals an eleven amino acid deletion in the NusG protein in the bacterial endosymbiont Portiera aleyrodidarum

BackgroundBemisia tabaci species (whiteflies) are the worlds most devastating insect pests within crops in the tropics. They cause billions of dollars (US) of damage each year and are leaving farmers in the developing world food insecure. Understanding the genetic and transcriptomic composition of these insect pests, the viruses they transmit and the microbiota is crucial to sustainable insect and virus management solutions for farmers. Currently, publically available transcriptome data for B. tabaci has been generated from pooled samples (mainly inbred lab colonies) consisting of several individuals because whiteflies are small (approximately 0.2 mm wide and 0.1 mm in height). Pooling individuals can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technology limitations. Therefore, the understanding of whitefly-microbiotad-viral species composition of an individual field-collected whitefly has also remained unknown. In this study, we developed a single whitefly RNA extraction procedure and subsequently successfully sequenced the transcriptome of four individual adult SubdSaharan Africa (SSA1) B. tabaci.\n\nResultsTranscriptome sequencing on individual whiteflies resulted in between 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 transcripts across all four B. tabaci transcriptomes. In addition, Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLAST searches on assembled transcripts within the four individual transcriptomes identified five endosymbionts; the primary endosymbiont Portiera,aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. These five endosymbionts were predominant across all four SSA1 B. tabaci study samples with prevalence levels of between 54.1d75%. Nucleotide and amino acid sequence alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Although NusG is key in regulating of transcription elongation, it is believed that the shortening of the loop region in the N-terminal domain is unlikely to affect transcription termination. Therefore, the effect of variability in this region across species is unknown.\n\nConclusionIn this study, we optimised a single whitefly high quality RNA extraction procedure and successfully carried out individual whitefly transcriptome sequencing on adult B. tabaci whiteflies. This enabled the detection of unique genetic differences in the NusG genes of the primary endosymbiont P. aleyrodidarum in four field-collected SSA1 whiteflies that may not have been detected using lab-pooled B. tabaci isolines. The use of field-collected specimens means that both time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. In addition, the methods we have developed here are applicable to any small organism where RNA quantity has limited transcriptome studies.

genetics↗