Gasser RB

References (7)

Title : The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range - Thia_2022_J.Evol.Biol__
Author(s) : Thia JA , Korhonen PK , Young ND , Gasser RB , Umina PA , Yang Q , Edwards O , Walsh T , Hoffmann AA
Ref : J Evol Biol , : , 2022
Abstract : Genomic data provide valuable insights into pest management issues such as resistance evolution, historical patterns of pest invasions and ongoing population dynamics. We assembled the first reference genome for the redlegged earth mite, Halotydeus destructor (Tucker, 1925), to investigate adaptation to pesticide pressures and demography in its invasive Australian range using whole-genome pool-seq data from regionally distributed populations. Our reference genome comprises 132 autosomal contigs, with a total length of 48.90 Mb. We observed a large complex of ace genes, which has presumably evolved from a long history of organophosphate selection in H. destructor and may contribute towards organophosphate resistance through copy number variation, target-site mutations and structural variants. In the putative ancestral H. destructor ace gene, we identified three target-site mutations (G119S, A201S and F331Y) segregating in organophosphate-resistant populations. Additionally, we identified two new para sodium channel gene mutations (L925I and F1020Y) that may contribute to pyrethroid resistance. Regional structuring observed in population genomic analyses indicates that gene flow in H. destructor does not homogenize populations across large geographic distances. However, our demographic analyses were equivocal on the magnitude of gene flow; the short invasion history of H. destructor makes it difficult to distinguish scenarios of complete isolation vs. ongoing migration. Nonetheless, we identified clear signatures of reduced genetic diversity and smaller inferred effective population sizes in eastern vs. western populations, which is consistent with the stepping-stone invasion pathway of this pest in Australia. These new insights will inform development of diagnostic genetic markers of resistance, further investigation into the multifaceted organophosphate resistance mechanism and predictive modelling of resistance evolution and spread.
ESTHER : Thia_2022_J.Evol.Biol__
PubMedSearch : Thia_2022_J.Evol.Biol__
PubMedID: 36573922
Gene_locus related to this paper: halde-ACHE1

Title : High-quality reference genome for Clonorchis sinensis - Young_2021_Genomics_113_1605
Author(s) : Young ND , Stroehlein AJ , Kinkar L , Wang T , Sohn WM , Chang BCH , Kaur P , Weisz D , Dudchenko O , Aiden EL , Korhonen PK , Gasser RB
Ref : Genomics , 113 :1605 , 2021
Abstract : The Chinese liver fluke, Clonorchis sinensis, causes the disease clonorchiasis, affecting ~35 million people in regions of China, Vietnam, Korea and the Russian Far East. Chronic clonorchiasis causes cholangitis and can induce a malignant cancer, called cholangiocarcinoma, in the biliary system. Control in endemic regions is challenging, and often relies largely on chemotherapy with one anthelmintic, called praziquantel. Routine treatment carries a significant risk of inducing resistance to this anthelmintic in the fluke, such that the discovery of new interventions is considered important. It is hoped that the use of molecular technologies will assist this endeavour by enabling the identification of drug or vaccine targets involved in crucial biological processes and/or pathways in the parasite. Although draft genomes of C. sinensis have been published, their assemblies are fragmented. In the present study, we tackle this genome fragmentation issue by utilising, in an integrated way, advanced (second- and third-generation) DNA sequencing and informatic approaches to build a high-quality reference genome for C. sinensis, with chromosome-level contiguity and curated gene models. This substantially-enhanced genome provides a resource that could accelerate fundamental and applied molecular investigations of C. sinensis, clonorchiasis and/or cholangiocarcinoma, and assist in the discovery of new interventions against what is a highly significant, but neglected disease-complex.
ESTHER : Young_2021_Genomics_113_1605
PubMedSearch : Young_2021_Genomics_113_1605
PubMedID: 33677057
Gene_locus related to this paper: closi-h2krw6

Title : Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications - Wang_2018_Biotechnol.Adv_36_894
Author(s) : Wang D , Korhonen PK , Gasser RB , Young ND
Ref : Biotechnol Adv , 36 :894 , 2018
Abstract : Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations.
ESTHER : Wang_2018_Biotechnol.Adv_36_894
PubMedSearch : Wang_2018_Biotechnol.Adv_36_894
PubMedID: 29454982
Gene_locus related to this paper: closi-h2krw6

Title : Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions - Anstead_2015_Nat.Commun_6_7344
Author(s) : Anstead CA , Korhonen PK , Young ND , Hall RS , Jex AR , Murali SC , Hughes DS , Lee SF , Perry T , Stroehlein AJ , Ansell BR , Breugelmans B , Hofmann A , Qu J , Dugan S , Lee SL , Chao H , Dinh H , Han Y , Doddapaneni HV , Worley KC , Muzny DM , Ioannidis P , Waterhouse RM , Zdobnov EM , James PJ , Bagnall NH , Kotze AC , Gibbs RA , Richards S , Batterham P , Gasser RB
Ref : Nat Commun , 6 :7344 , 2015
Abstract : Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.
ESTHER : Anstead_2015_Nat.Commun_6_7344
PubMedSearch : Anstead_2015_Nat.Commun_6_7344
PubMedID: 26108605
Gene_locus related to this paper: luccu-a0a0l0bn77 , luccu-a0a0l0clk8 , luccu-a0a0l0bxv5 , luccu-a0a0l0bvt1 , luccu-a0a0l0bw31

Title : Genome and transcriptome of the porcine whipworm Trichuris suis - Jex_2014_Nat.Genet_46_701
Author(s) : Jex AR , Nejsum P , Schwarz EM , Hu L , Young ND , Hall RS , Korhonen PK , Liao S , Thamsborg S , Xia J , Xu P , Wang S , Scheerlinck JP , Hofmann A , Sternberg PW , Wang J , Gasser RB
Ref : Nat Genet , 46 :701 , 2014
Abstract : Trichuris (whipworm) infects 1 billion people worldwide and causes a disease (trichuriasis) that results in major socioeconomic losses in both humans and pigs. Trichuriasis relates to an inflammation of the large intestine manifested in bloody diarrhea, and chronic disease can cause malnourishment and stunting in children. Paradoxically, Trichuris of pigs has shown substantial promise as a treatment for human autoimmune disorders, including inflammatory bowel disease (IBD) and multiple sclerosis. Here we report whole-genome sequencing at approximately 140-fold coverage of adult male and female T. suis and approximately 80-Mb draft assemblies. We explore stage-, sex- and tissue-specific transcription of mRNAs and small noncoding RNAs.
ESTHER : Jex_2014_Nat.Genet_46_701
PubMedSearch : Jex_2014_Nat.Genet_46_701
PubMedID: 24929829
Gene_locus related to this paper: 9bila-a0a085nui3 , 9bila-a0a085mx66 , 9bila-a0a085lsb8 , 9bila-a0a085mja7 , 9bila-a0a085ly55 , 9bila-a0a085nlc5 , 9bila-a0a085nb82 , 9bila-a0a085n057 , 9bila-a0a085mjs6

Title : Genome of the human hookworm Necator americanus - Tang_2014_Nat.Genet_46_261
Author(s) : Tang YT , Gao X , Rosa BA , Abubucker S , Hallsworth-Pepin K , Martin J , Tyagi R , Heizer E , Zhang X , Bhonagiri-Palsikar V , Minx P , Warren WC , Wang Q , Zhan B , Hotez PJ , Sternberg PW , Dougall A , Gaze ST , Mulvenna J , Sotillo J , Ranganathan S , Rabelo EM , Wilson RK , Felgner PL , Bethony J , Hawdon JM , Gasser RB , Loukas A , Mitreva M
Ref : Nat Genet , 46 :261 , 2014
Abstract : The hookworm Necator americanus is the predominant soil-transmitted human parasite. Adult worms feed on blood in the small intestine, causing iron-deficiency anemia, malnutrition, growth and development stunting in children, and severe morbidity and mortality during pregnancy in women. We report sequencing and assembly of the N. americanus genome (244 Mb, 19,151 genes). Characterization of this first hookworm genome sequence identified genes orchestrating the hookworm's invasion of the human host, genes involved in blood feeding and development, and genes encoding proteins that represent new potential drug targets against hookworms. N. americanus has undergone a considerable and unique expansion of immunomodulator proteins, some of which we highlight as potential treatments against inflammatory diseases. We also used a protein microarray to demonstrate a postgenomic application of the hookworm genome sequence. This genome provides an invaluable resource to boost ongoing efforts toward fundamental and applied postgenomic research, including the development of new methods to control hookworm and human immunological diseases.
ESTHER : Tang_2014_Nat.Genet_46_261
PubMedSearch : Tang_2014_Nat.Genet_46_261
PubMedID: 24441737
Gene_locus related to this paper: necam-w2tsu7

Title : Whole-genome sequence of Schistosoma haematobium - Young_2012_Nat.Genet_44_221
Author(s) : Young ND , Jex AR , Li B , Liu S , Yang L , Xiong Z , Li Y , Cantacessi C , Hall RS , Xu X , Chen F , Wu X , Zerlotini A , Oliveira G , Hofmann A , Zhang G , Fang X , Kang Y , Campbell BE , Loukas A , Ranganathan S , Rollinson D , Rinaldi G , Brindley PJ , Yang H , Wang J , Gasser RB
Ref : Nat Genet , 44 :221 , 2012
Abstract : Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide. No vaccines are available, and treatment relies on one drug, praziquantel. Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer and as a predisposing factor for HIV/AIDS. The parasite is transmitted to humans from freshwater snails. Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease and induce squamous cell carcinoma. Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites. We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.
ESTHER : Young_2012_Nat.Genet_44_221
PubMedSearch : Young_2012_Nat.Genet_44_221
PubMedID: 22246508
Gene_locus related to this paper: schha-ACHE , schha-a0a094zs51 , schha-a0a095agr4 , schha-a0a095ai61 , schha-a0a095ayl3 , schha-a0a095c2i3 , schha-a0a095ce64