A DNA extraction protocol for improved DNA yield from individual mosquitoes

Nieman, Catelyn C.; Yamasaki, Youki; Collier, Travis C.; Y, Lee

doi:10.12688/f1000research.7413.1

Cited by 28 publications

(24 citation statements)

References 14 publications

(18 reference statements)

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“…Samples of allopatric populations (Takouti, Tissana, Yorobougoula and Foumbot) were collected for comparison with samples from sympatric ones. DNA was extracted from individual mosquito whole bodies using the QIAGEN Biosprint 96 system and QIAGEN blood tissue kit and protocols described in Nieman, Yamasaki, Collier, and Lee () and Yamasaki et al (). We used the “Divergence Island SNP” (DIS) assay (Lee, Marsden, Nieman, & Lanzaro, ) to genotype A. coluzzii , A. gambiae , F1 hybrids and early and late backcrosses as described in Lee, Marsden, et al () and Lee et al ().…”

Section: Methodsmentioning

confidence: 99%

The fate of genes that cross species boundaries after a major hybridization event in a natural mosquito population

et al. 2018

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Animal species are able to acquire new genetic material via hybridization and subsequent introgression. However, little is known about how foreign genomic material is incorporated into a population over time and what genes are susceptible to introgression. Here, we follow the closely related mosquito sister species Anopheles coluzzii and Anopheles gambiae in a sympatric natural population in Mali at multiple time points spanning a period of 25 years. During this period, we observed the temporary breakdown of mating barriers, which allowed us to explore the fate of alleles that crossed the species boundary in a natural population. Whole genome sequencing of 74 individuals revealed introgression within only 34 genes (0.26% of total genes) from A. gambiae to A. coluzzii, the majority contained within a 4 Mb region on the 2L chromosome which includes the insecticide resistance gene (AGAP004707). We designed a genotyping assay to follow 25 of the 34 introgressed alleles over time and found that all A. gambiae alleles, except four, reached a frequency of 50% in the A. coluzzii population within 4 years (~50 generations) and increased to ~80% within 6 years (~75 generations). However, the frequency of all introgressed alleles, except three, decreased to ~60% in 2016. This suggests an ongoing process of purifying selection in the population against DNA of foreign ancestry, except for alleles that are under positive selection, resulting in a complex genomic landscape. This study shows that stable introgression is limited to only specific genes even within closely related species.

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Section: Methodsmentioning

confidence: 99%

The fate of genes that cross species boundaries after a major hybridization event in a natural mosquito population

et al. 2018

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“…Genomic DNA from K. lycopersicella, P. operculella, and T. absoluta was extracted using the method as described in Nieman et al (2015) Table 1). Primer cocktails for multiplex PCR of 21 loci were prepared as described in Gabriel et al (2009).…”

Section: Massarray System Combined With Iplex Chemistry For Species Imentioning

confidence: 99%

Sequencing of Tuta absoluta genome to develop SNP genotyping assays for species identification

et al. 2019

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Tuta absoluta is one of the most devastating pests of fresh market and processing tomatoes. Native to South America, its detection was confined to that continent until 2006 when it was identified in Spain. It has now spread to almost every continent, threatening countries whose economies rely heavily on tomatoes. This insect causes damage to all developmental stages of its host plant, leading to crop losses as high as 80 to 100%. Although T. absoluta has yet to be found in the U.S. and China, which makes up a large portion of the tomato production in the world, computer models project a high likelihood of invasion. To halt the continued spread of T. absoluta and limit economic loss associated with tomato supply chain, it is necessary to develop accurate and efficient methods to identify T. absoluta and strengthen surveillance programs. Current identification of T. absoluta relies on examination of morphology and assessment of host plant damage, which are difficult to differentiate from that of native tomato pests. To address this need, we sequenced the genomes of T. absoluta and two closely related Gelechiidae, Keiferia lycopersicella, and Phthorimaea operculella, and developed a bioinformatic pipeline to design a panel of 21 SNP markers for species identification. The accuracy of the SNP panel was validated in a multiplex format using the iPLEX chemistry of Agena MassARRAY system. Finally, the new T. absoluta genomic resources we generated can be leveraged to study T. absoluta biology and develop species-specific management strategies. Key Message  Surveillance and identification of Tuta absoluta are challenging because it is morphologically similar to closely related species, e.g. Keiferia lycopersicella and Phthorimaea operculella.  We generated new genomic sequences for these three species and identified single nucleotide polymorphisms (SNPs) to facilitate species identification.  We validated a multiplex genotyping panel of 21 SNPs using the iPLEX MassARRAY platform and confirmed its accuracy for species identification.  We generated new molecular tools and genome resources to aid Tuta absoluta management. leaves, where the larvae will emerge from eggs and begin mining host tissues. Larvae can also enter the stems through the buds, and feed within the tomato fruit, leaving them unmarketable. Its distribution was largely confined to South America until it was first detected in Spain in 2006 (Desneux et al. 2010; Guillemaud et al. 2015). Since then T. absoluta has spread rapidly and is now

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“…DNA was extracted from individual Anopheles mosquitoes using a Qiagen, Biosprint 96 system, with Qiagen blood and tissue kits (Qiagen, Valencia, CA, USA) described in Nieman et al . ().…”

Section: Methodsmentioning

confidence: 97%

High endemism of mosquitoes on São Tomé and Príncipe Islands: evaluating the general dynamic model in a worldwide island comparison

Loiseau

Melo

Y³

et al. 2018

Insect Conserv Diversity

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The archipelago of São Tomé and Príncipe is a major centre of endemism for vertebrates but, to date, arthropods remain poorly studied, with the exception of mosquitoes due to their medical and economic relevance. Previous studies, over 20 years old, recorded 26 species of mosquitoes for São Tomé and 14 for Príncipe, of which six and two were endemic to each island respectively. We collected mosquito larvae and adults on both islands and found three species as a first record, putting the number of mosquito species collected at least once on São Tomé at 29 and 15 for Príncipe. We compared the mosquito richness on São Tomé and Príncipe islands to 71 other oceanic islands represented within 20 archipelagoes worldwide. We used the general dynamic model of oceanic island biogeography and the associated ATT2 (for Area+Time+Time2) model to explain two different metrics: (i) the richness of the single‐island endemics and (ii) the richness of archipelago endemics. We also included other island characteristics in our model, such as isolation and latitude. Our data compilation and comparative analyses revealed an overall low richness of endemic mosquitoes on islands, with the highest number of single‐island endemics found on São Tomé Island. As predicted, we found a positive relationship between our two richness metrics and the general dynamic model ATT2, although the model with the area (A) alone also explained endemic richness. Isolation was also predictor of mosquito diversification.

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A DNA extraction protocol for improved DNA yield from individual mosquitoes

Cited by 28 publications

References 14 publications

The fate of genes that cross species boundaries after a major hybridization event in a natural mosquito population

The fate of genes that cross species boundaries after a major hybridization event in a natural mosquito population

Sequencing of Tuta absoluta genome to develop SNP genotyping assays for species identification

High endemism of mosquitoes on São Tomé and Príncipe Islands: evaluating the general dynamic model in a worldwide island comparison

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