Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.

BACKGROUND: New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. RESULTS: We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. CONCLUSIONS: Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

Mosquito biology. Evolution of sexual traits influencing vectorial capacity in anopheline mosquitoes.

The availability of genome sequences from 16 anopheline species provides unprecedented opportunities to study the evolution of reproductive traits relevant for malaria transmission. In Anopheles gambiae, a likely candidate for sexual selection is male 20-hydroxyecdysone (20E). Sexual transfer of this steroid hormone as part of a mating plug dramatically changes female physiological processes intimately tied to vectorial capacity. By combining phenotypic studies with ancestral state reconstructions and phylogenetic analyses, we show that mating plug transfer and male 20E synthesis are both derived characters that have coevolved in anophelines, driving the adaptation of a female 20E-interacting protein that promotes oogenesis via mechanisms also favoring Plasmodium survival. Our data reveal coevolutionary dynamics of reproductive traits between the sexes likely to have shaped the ability of anophelines to transmit malaria.

The evolution of the Anopheles 16 genomes project.

We report the imminent completion of a set of reference genome assemblies for 16 species of Anopheles mosquitoes. In addition to providing a generally useful resource for comparative genomic analyses, these genome sequences will greatly facilitate exploration of the capacity exhibited by some Anopheline mosquito species to serve as vectors for malaria parasites. A community analysis project will commence soon to perform a thorough comparative genomic investigation of these newly sequenced genomes. Completion of this project via the use of short next-generation sequence reads required innovation in both the bioinformatic and laboratory realms, and the resulting knowledge gained could prove useful for genome sequencing projects targeting other unconventional genomes.

Colonisation and mass rearing: learning from others.

Mosquitoes, just as other insects produced for the sterile insect technique (SIT), are subjected to several unnatural processes including laboratory colonisation and large-scale factory production. After these processes, sterile male mosquitoes must perform the natural task of locating and mating with wild females. Therefore, the colonisation and production processes must preserve characters necessary for these functions. Fortunately, in contrast to natural selection which favours a suite of characteristics that improve overall fitness, colonisation and production practices for SIT strive to maximize only the few qualities that are necessary to effectively control populations. However, there is considerable uncertainty about some of the appropriate characteristics due to the lack of data. Development of biological products for other applications suggest that it is possible to identify and modify competitiveness characteristics in order to produce competitive mass produced sterile mosquitoes. This goal has been pursued--and sometimes achieved--by mosquito colonisation, production, and studies that have linked these characteristics to field performance. Parallels are drawn to studies in other insect SIT programmes and aquaculture which serve as vital technical reference points for mass-production of mosquitoes, most of whose development occurs--and characteristics of which are determined--in an aquatic environment. Poorly understood areas that require further study are numerous: diet, mass handling and genetic and physiological factors that influence mating competitiveness. Compromises in such traits due to demands to increase numbers or reduce costs, should be carefully considered in light of the desired field performance.

Male mating biology.

Before sterile mass-reared mosquitoes are released in an attempt to control local populations, many facets of male mating biology need to be elucidated. Large knowledge gaps exist in how both sexes meet in space and time, the correlation of male size and mating success and in which arenas matings are successful. Previous failures in mosquito sterile insect technique (SIT) projects have been linked to poor knowledge of local mating behaviours or the selection of deleterious phenotypes during colonisation and long-term mass rearing. Careful selection of mating characteristics must be combined with intensive field trials to ensure phenotypic characters are not antagonistic to longevity, dispersal, or mating behaviours in released males. Success has been achieved, even when colonised vectors were less competitive, due in part to extensive field trials to ensure mating compatibility and effective dispersal. The study of male mating biology in other dipterans has improved the success of operational SIT programmes. Contributing factors include inter-sexual selection, pheromone based attraction, the ability to detect alterations in local mating behaviours, and the effects of long-term colonisation on mating competitiveness. Although great strides have been made in other SIT programmes, this knowledge may not be germane to anophelines, and this has led to a recent increase in research in this area.

Authentication scheme for routine verification of genetically similar laboratory colonies: a trial with Anopheles gambiae.

BACKGROUND: When rearing morphologically indistinguishable laboratory strains concurrently, the threat of unintentional genetic contamination is constant. Avoidance of accidental mixing of strains is difficult due to the use of common equipment, technician error, or the possibility of self relocation by adult mosquitoes ("free fliers"). In many cases, laboratory strains are difficult to distinguish because of morphological and genetic similarity, especially when laboratory colonies are isolates of certain traits from the same parental strain, such as eye color mutants, individuals with certain chromosomal arrangements or high levels of insecticide resistance. Thus, proving genetic integrity could seem incredibly time-consuming or impossible. On the other hand, lacking proof of genetically isolated laboratory strains could question the validity of research results. RESULTS: We present a method for establishing authentication matrices to routinely distinguish and confirm that laboratory strains have not become physically or genetically mixed through contamination events in the laboratory. We show a specific example with application to Anopheles gambiae sensu stricto strains at the Malaria Research and Reference Reagent Resource Center. This authentication matrix is essentially a series of tests yielding a strain-specific combination of results. CONCLUSION: These matrix-based methodologies are useful for several mosquito and insect populations but must be specifically tailored and altered for each laboratory based on the potential contaminants available at any given time. The desired resulting authentication plan would utilize the least amount of routine effort possible while ensuring the integrity of the strains.

Methylparaben in Anopheles gambiae s.l. sugar meals increases longevity and malaria oocyst abundance but is not a preferred diet.

The antimicrobial and antifungal chemical methylparaben (methyl-4-hydroxybenzoate) was added to the adult sucrose diet of Anopheles gambiae and Anopheles arabiensis, and its effect on longevity was determined. In all cases, significant increases in longevity were observed when 0.2% (w/v) methylparaben was added to meals that were refreshed weekly. When fresh sugar diet was refreshed daily, no increase in longevity was observed due to methylparaben suggesting that the effect of methylparaben is to preserve the quality of the sugar diet. No longevity effect of providing pure water in addition to sugar- or methylparaben-supplemented meals was observed. Feeding preference tests were performed to determine whether meals containing methylparaben were preferred, and whether, when given no choice but the less-preferred diet, mosquitoes would consume less sugar. Using the stable carbon isotope (13)C in paired tests, we show that the sugar diet containing methylparaben was clearly avoided by A. gambiae but not A. arabiensis. Little effect of methylparaben on the total amount of sugar consumed was observed when mosquitoes were given no diet choice. Methylparaben effects on Plasmodium cynomolgi B oocyst formation and encapsulation were observed in a normal A. gambiae stock and one which encapsulates at a high frequency. Nearly two-fold increases in the number of both normal and encapsulated oocysts were observed as a result of methylparaben in the diet. Because of its longevity effects, we have implemented methylparaben use for all mosquitoes in our holdings and recommend it as a routine sugar meal supplement.

The influence of house construction on the indoor abundance of mosquitoes.

This study examined the potential effects of different house construction features on the indoor abundance of culicine mosquitoes in Trinidad (TT) and the Dominican Republic (DR) using xenomonitoring surveys. To assess these effects, a survey was taken of different homes in both countries alongside concurrent indoor resting mosquito collections to determine which features may be correlated with a greater abundance. Between June 2002 and April 2003 data were collected from 104 homes in TT and 121 homes in the DR. In TT, 61 (58.65%) of the homes were located in urban areas and 43 (41.35%) were located in rural villages, whereas in the DR 40 (33.06%) were located in rural areas, and 81 (66.94%) in the urban area. Overall, a total of 1,630 mosquitoes were collected in TT, of which 77% were Culex quinquefasciatus, whereas 459 mosquitoes were collected from the DR, of which 46% were Cx. quinquefasciatus. It was found that in TT and the DR the mean number of Cx. quinquefasciatus mosquitoes was greater in cement homes than in either wood or other poorer quality homes (TT cement 17.43, others 14.43; DR cement 4.24, others 3.41). In TT it was found that homes that had painted interiors were significantly more likely to have a high abundance of mosquitoes resting indoors compared to homes without painted interiors (OR 2.90, CI 1.09-8.72). Likewise, having a painted exterior was not significant, but only slightly so, in TT as having a detrimental effect (OR 2.14, CI 0.89-6.67). Similarly, having a painted interior or exterior was also found to be a predictor of a high abundance of indoor resting mosquitoes in the DR (interior OR 3.13, CI 1.41-6.92; exterior OR 1.97, CI .91-4.26). Reduced adult abundance in TT was correlated with homes being built on stilts, with more than four people sleeping in the home, and having a painted interior. In the DR, reductions were correlated with homes where residents slept under a bed net and with people who lived in a rural location. Changes in construction patterns in the Caribbean region could help prevent human-mosquito contact potentially reducing the transmission of certain vector-borne diseases in the population.

IMP PCR primers detect single nucleotide polymorphisms for Anopheles gambiae species identification, Mopti and Savanna rDNA types, and resistance to dieldrin in Anopheles arabiensis.

BACKGROUND: Polymerase chain reactions to distinguish single-nucleotide polymorphisms are commonly used for mosquito identification and identifying insecticide resistance alleles. However, the existing methods used for primer design often result in analyses that are not robust or require additional steps. METHODS: Utilizing oligonucleotides that are unique in having an intentional mismatch to both templates three bases from the SNP at the 3-prime end, three new PCR assays that distinguish SNP targets using standard gel electrophoresis of undigested DNA fragments were developed and tested. These were applied to: (1) an alternative ribosomal DNA PCR assay to distinguish five members of the Anopheles gambiae complex; (2) detection of the Mopti and Savanna rDNA types; and (3) an assay to distinguish resistance to dieldrin (Rdl) alleles in Anopheles arabiensis. RESULTS: Reproducible specific amplification of the target alleles was observed in all three assays. The results were consistent with existing analyses but proved simpler and the results more distinct in our hands. CONCLUSION: The simplicity and effectiveness of the method should be utilized in these and other PCR analyses to increase their specificity and simplicity. These results have the potential to be extended not only to mosquito analyses but also to parasite and human polymorphisms.