Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
Records 1-8 (of 8 Records) |
Query Trace: Howell PI [original query] |
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Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies (preprint)
Waterhouse RM , Aganezov S , Anselmetti Y , Lee J , Ruzzante L , Reijnders Mjmf , Feron R , Berard S , George P , Hahn MW , Howell PI , Kamali M , Koren S , Lawson D , Maslen G , Peery A , Phillippy AM , Sharakhova MV , Tannier E , Unger MF , Zhang SV , Alekseyev MA , Besansky NJ , Chauve C , Emrich SJ , Sharakhov IV . bioRxiv 2019 434670 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 employed three 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: six with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and three with new assemblies based on re-scaffolding or Pacific Biosciences long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: seven for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further seven 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 comparisons 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.ADADSEQAGOAGOUTI-basedAGOUTIannotated genome optimization using transcriptome information toolALNalignment-basedCAMSAcomparative analysis and merging of scaffold assemblies toolDPdynamic programmingFISHfluorescence in situ hybridizationGAGOS-ASMGOS-ASMGene order scaffold assemblerKbpkilobasepairsMbpmegabasepairsOSORTHOSTITCHPacBioPacific BiosciencesPBPacBio-basedPHYphysical-mapping-basedRNAseqRNA sequencingQTLquantitative trait lociSYNsynteny-based. |
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.
Waterhouse RM , Aganezov S , Anselmetti Y , Lee J , Ruzzante L , Reijnders Mjmf , Feron R , Berard S , George P , Hahn MW , Howell PI , Kamali M , Koren S , Lawson D , Maslen G , Peery A , Phillippy AM , Sharakhova MV , Tannier E , Unger MF , Zhang SV , Alekseyev MA , Besansky NJ , Chauve C , Emrich SJ , Sharakhov IV . BMC Biol 2020 18 (1) 1 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.
Mitchell SN , Kakani EG , South A , Howell PI , Waterhouse RM , Catteruccia F . Science 2015 347 (6225) 985-8 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. |
Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
Neafsey DE , Waterhouse RM , Abai MR , Aganezov SS , Alekseyev MA , Allen JE , Amon J , Arca B , Arensburger P , Artemov G , Assour LA , Basseri H , Berlin A , Birren BW , Blandin SA , Brockman AI , Burkot TR , Burt A , Chan CS , Chauve C , Chiu JC , Christensen M , Costantini C , Davidson VL , Deligianni E , Dottorini T , Dritsou V , Gabriel SB , Guelbeogo WM , Hall AB , Han MV , Hlaing T , Hughes DS , Jenkins AM , Jiang X , Jungreis I , Kakani EG , Kamali M , Kemppainen P , Kennedy RC , Kirmitzoglou IK , Koekemoer LL , Laban N , Langridge N , Lawniczak MK , Lirakis M , Lobo NF , Lowy E , MacCallum RM , Mao C , Maslen G , Mbogo C , McCarthy J , Michel K , Mitchell SN , Moore W , Murphy KA , Naumenko AN , Nolan T , Novoa EM , O'Loughlin S , Oringanje C , Oshaghi MA , Pakpour N , Papathanos PA , Peery AN , Povelones M , Prakash A , Price DP , Rajaraman A , Reimer LJ , Rinker DC , Rokas A , Russell TL , Sagnon N , Sharakhova MV , Shea T , Simao FA , Simard F , Slotman MA , Somboon P , Stegniy V , Struchiner CJ , Thomas GW , Tojo M , Topalis P , Tubio JM , Unger MF , Vontas J , Walton C , Wilding CS , Willis JH , Wu YC , Yan G , Zdobnov EM , Zhou X , Catteruccia F , Christophides GK , Collins FH , Cornman RS , Crisanti A , Donnelly MJ , Emrich SJ , Fontaine MC , Gelbart W , Hahn MW , Hansen IA , Howell PI , Kafatos FC , Kellis M , Lawson D , Louis C , Luckhart S , Muskavitch MA , Ribeiro JM , Riehle MA , Sharakhov IV , Tu Z , Zwiebel LJ , Besansky NJ . Science 2015 347 (6217) 1258522 Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts. |
Colonisation and mass rearing: learning from others
Benedict MQ , Knols BG , Bossin HC , Howell PI , Mialhe E , Caceres C , Robinson AS . Malar J 2009 8 Suppl 2 S4 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
Howell PI , Knols BG . Malar J 2009 8 Suppl 2 S8 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. |
Mating competitiveness of Anopheles arabiensis males as a function of transgenic state and genetic similarity to females
Howell PI , Benedict MQ . J Insect Behav 2009 22 (6) 477-491 We conducted mating competitions between wild-type and heterozygous transgenic Anopheles arabiensis males that were produced by repeated backcrosses of a transposable element expressing the β2-tubulin eGFP marker into two genetic backgrounds. These competed for genetically similar or dissimilar females in ratios of 1:1:3. We analyzed the effect of genetic similarity, transgenic state and stock on mating frequency. We observed no differences in the competitiveness of the wild and transgenic heterozygotes, no effect of genetic relatedness, nor a clear benefit of the out-crossing strategy to increase competitiveness. A decrease in the development rate of all phenotypic classes was observed among progeny of transgenic males but the rate of adult emergence of transgenic individuals was in most cases slightly faster than wild-type siblings. |
Authentication scheme for routine verification of genetically similar laboratory colonies: a trial with Anopheles gambiae
Wilkins EE , Marcet PL , Sutcliffe AC , Howell PI . BMC Biotechnol 2009 9 91 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. |
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