scholarly journals Whole-genome assembly of Culex tarsalis

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Bradley J Main ◽  
Matteo Marcantonio ◽  
J Spencer Johnston ◽  
Jason L Rasgon ◽  
C Titus Brown ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Vector Competence ◽  
Mosquito Species ◽  
Single Copy ◽  
Whole Genome ◽  
Culex Tarsalis ◽  
Single Male ◽  
High Molecular Weight Dna ◽  
Genetic Studies ◽  
Genetic Clusters

Abstract The mosquito, Culex tarsalis, is a key vector in the western United States due to its role in transmission of zoonotic arboviruses that affect human health. Extensive research has been conducted on Cx. tarsalis ecology, feeding behavior, vector competence, autogeny, diapause, genetics, and insecticide resistance. Population genetic analyses in the western U.S. have identified at least three genetic clusters that are geographically distinct. However, in-depth genetic studies have been hindered by the lack of a reference genome. In this study, we present the first whole-genome assembly of this mosquito species (CtarK1) based on PacBio HiFi reads from high-molecular-weight DNA extracted from a single male. The CtarK1 assembly is 790 Mb with an N50 of 58 kb, which is 27% larger than Culex quinquefasciatus (578 Mb). This difference appears to be mostly composed of transposable elements. To annotate CtarK1, we used a previously assembled Cx. tarsalis transcriptome and approximately 17,456 protein genes from Cx. quinquefasciatus (N = 17,456). Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 84.8% of the 2799 Dipteran BUSCO genes. Using a Bayesian phylogeny based on mitochondrial genomes, we place Cx. tarsalis in the context of other mosquito species and estimate the divergence between Cx. tarsalis and Cx. quinquefasciatus to be between 15.8 and 22.2 million years ago (MYA). Important next steps from this work include characterizing the genetic basis of diapause and sex determination in Culex mosquitoes.

scholarly journals Whole genome assembly of Culex tarsalis

2020 ◽  
Author(s):  
Bradley J. Main ◽  
Matteo Marcantonio ◽  
J. Spencer Johnston ◽  
Jason L. Rasgon ◽  
C. Titus Brown ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Culex Quinquefasciatus ◽  
Reference Genome ◽  
Vector Competence ◽  
Mosquito Species ◽  
Single Copy ◽  
Specific Gene ◽  
Culex Tarsalis ◽  
Single Male ◽  
A Genome

AbstractThe mosquito, Culex tarsalis, is a key vector in the western United States due to its role in transmission of zoonotic arboviruses that affect human health. Extensive research has been conducted on Cx. tarsalis ecology, feeding behavior, vector competence, autogeny, diapause, genetics, and insecticide resistance. Population genetic analyses in the western U.S. have identified at least three genetic clusters that are geographically distinct. Salivary gland-specific gene expression has also revealed genes involved in blood feeding. However, genetic studies of this mosquito have been hindered by the lack of a reference genome. To facilitate genomic studies in Cx. tarsalis, we have assembled and annotated a reference genome (CtarK1) based on PacBio HiFi reads from a single male. Using the Cx. tarsalis transcriptome and protein sequences from Culex quinquefasciatus, approximately 17,456 protein-coding genes, including the para insecticide resistance gene, were annotated in the CtarK1 genome. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 84.8% of the 2799 Dipteran BUSCO genes. The CtarK1 assembly is 790Mb with an N50 of 58kb. Using full mitochondrial genome alignments with other sequenced mosquito genomes we present a Bayesian phylogeny, which estimates that the divergence of Cx. tarsalis from Culex quinquefasciatus, the most closely related mosquito species with a genome, occurred 15.8-22.2 million years ago.

scholarly journals Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China

2021 ◽  
Author(s):  
Yuanchao Liu ◽  
Longhua Huang ◽  
Huiping Hu ◽  
Manjun Cai ◽  
Xiaowei Liang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Southwest China ◽  
Reference Genome ◽  
Biological Activities ◽  
Single Copy ◽  
The Tibetan Plateau ◽  
Whole Genome ◽  
High Quality ◽  
Pharmacological Activities ◽  
Genetic Studies

Abstract Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. G. leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with a N50 scaffold size of 3.06 Mb, 78,206 coding sequences and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and G. lucidum. G. leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.

scholarly journals Whole genome amplification (WGA) for archiving and genotyping of clinical isolates ofCryptosporidiumspecies

Parasitology ◽  
2009 ◽  
Vol 137 (1) ◽  
pp. 27-36 ◽  
Author(s):  
MAHA BOUZID ◽  
DARREN HEAVENS ◽  
KRISTIN ELWIN ◽  
RACHEL M. CHALMERS ◽  
STEPHEN J. HADFIELD ◽  
...  
Keyword(s):  
Whole Genome Amplification ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Whole Genome ◽  
High Molecular Weight Dna ◽  
Genetic Studies ◽  
Genome Amplification ◽  
Pcr Products ◽  
Varying Length ◽  
Commercial Kits

SUMMARYClinical and environmental isolates of pathogens are often unique and may be unculturable, yielding a very limited amount of DNA for genetic studies.Cryptosporidiumin particular are difficult to propagate. Whole genome amplification (WGA) is a valuable technique for amplifying genomic material. In this study, we tested 5 WGA commercial kits usingCryptosporidiumclinical isolates. DNA of 5C. hominisand 5C. parvumclinical isolates andC. parvumIOWA reference strain were used. The majority of the samples were amplified by all of the kits tested. The integrity and fidelity of the amplified genomic DNA were assessed by sequence analysis of several PCR products of varying length. We found evidence that one kit in particular may be more error prone while another seemed the more suitable kit forCryptosporidiumclinical samples, generating high molecular weight DNA from all the samples with high fidelity. Thus WGA was found to be a useful technique for producing amplified DNA suitable for downstream genotyping techniques and archiving ofCryptosporidiumclinical isolates.

scholarly journals Vector competence of selected North AmericanAnophelesandCulexmosquitoes for Zika virus

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4324 ◽  
Author(s):  
Brittany L. Dodson ◽  
Sujit Pujhari ◽  
Jason L. Rasgon
Keyword(s):  
North America ◽  
Aedes Aegypti ◽  
Zika Virus ◽  
Vector Competence ◽  
Mosquito Species ◽  
Culex Tarsalis ◽  
Anopheles Quadrimaculatus ◽  
Vector Borne ◽  
Serious Disease ◽  
Blood Meals

Zika virus (ZIKV) is a vector-borne flavivirus that has caused recent outbreaks associated with serious disease in infants and newborns in the Americas.Aedesmosquitoes are the primary vectors for ZIKV, but little is known about the diversity of mosquitoes that can transmit ZIKV in North America. We chose three abundant North American mosquito species (Anopheles freeborni,Anopheles quadrimaculatus, andCulex tarsalis) and one known vector species (Aedes aegypti), fed them blood meals supplemented with a recent outbreak ZIKV strain, and tested bodies, legs, and saliva for infectious ZIKV. ZIKV was able to infect, disseminate, and be transmitted byAedes aegypti. However,Anopheles freeborni,Anopheles quadrimaculatus, andCulex tarsaliswere unable to be infected. We conclude that these species are unlikely to be involved in ZIKV transmission in North America. However, we should continue to examine the ability for other mosquito species to potentially act as ZIKV vectors in North America.

scholarly journals Microbiota identified from preserved Anopheles

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Bianca E Silva ◽  
Zvifadzo Matsena Zingoni ◽  
Lizette L. Koekemoer ◽  
Yael L. Dahan-Moss
Keyword(s):  
Microbial Diversity ◽  
Vector Competence ◽  
Mosquito Species ◽  
Anopheles Funestus ◽  
Cost Effective ◽  
Diversity Indices ◽  
Malaria Vectors ◽  
Microbial Composition ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background Mosquito species from the Anopheles gambiae complex and the Anopheles funestus group are dominant African malaria vectors. Mosquito microbiota play vital roles in physiology and vector competence. Recent research has focused on investigating the mosquito microbiota, especially in wild populations. Wild mosquitoes are preserved and transported to a laboratory for analyses. Thus far, microbial characterization post-preservation has been investigated in only Aedes vexans and Culex pipiens. Investigating the efficacy of cost-effective preservatives has also been limited to AllProtect reagent, ethanol and nucleic acid preservation buffer. This study characterized the microbiota of African Anopheles vectors: Anopheles arabiensis (member of the An. gambiae complex) and An. funestus (member of the An. funestus group), preserved on silica desiccant and RNAlater® solution. Methods Microbial composition and diversity were characterized using culture-dependent (midgut dissections, culturomics, MALDI-TOF MS) and culture-independent techniques (abdominal dissections, DNA extraction, next-generation sequencing) from laboratory (colonized) and field-collected mosquitoes. Colonized mosquitoes were either fresh (non-preserved) or preserved for 4 and 12 weeks on silica or in RNAlater®. Microbiota were also characterized from field-collected An. arabiensis preserved on silica for 8, 12 and 16 weeks. Results Elizabethkingia anophelis and Serratia oryzae were common between both vector species, while Enterobacter cloacae and Staphylococcus epidermidis were specific to females and males, respectively. Microbial diversity was not influenced by sex, condition (fresh or preserved), preservative, or preservation time-period; however, the type of bacterial identification technique affected all microbial diversity indices. Conclusions This study broadly characterized the microbiota of An. arabiensis and An. funestus. Silica- and RNAlater®-preservation were appropriate when paired with culture-dependent and culture-independent techniques, respectively. These results broaden the selection of cost-effective methods available for handling vector samples for downstream microbial analyses.

scholarly journals A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

2021 ◽  
Author(s):  
Seyoung Mun ◽  
Songmi Kim ◽  
Wooseok Lee ◽  
Keunsoo Kang ◽  
Thomas J. Meyer ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Personal Genome ◽  
Human Populations ◽  
Whole Genome ◽  
Structural Variations ◽  
Insert Size ◽  
Human Genomes ◽  
Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

scholarly journals Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amit Rai ◽  
Hideki Hirakawa ◽  
Ryo Nakabayashi ◽  
Shinji Kikuchi ◽  
Koki Hayashi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Experimental Validation ◽  
Genome Duplication ◽  
Indole Alkaloids ◽  
Whole Genome ◽  
Comparative Genome Analysis ◽  
Plant Genomes ◽  
Genome Triplication ◽  
Chromosome Level

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

scholarly journals Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guilherme B. Dias ◽  
Musaad A. Altammami ◽  
Hamadttu A. F. El-Shafie ◽  
Fahad M. Alhoshani ◽  
Mohamed B. Al-Fageeh ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Control Strategies ◽  
Insect Pest ◽  
Single Copy ◽  
Gene Content ◽  
Rhynchophorus Ferrugineus ◽  
Red Palm Weevil ◽  
Transcriptomic Data ◽  
Palm Trees ◽  
Palm Weevil

AbstractThe red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage ($$\sim$$ ∼ 62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.

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