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Deyell RJ, Shen Y, Titmuss E, Dixon K, Williamson LM, Pleasance E, Nelson JMT, Abbasi S, Krzywinski M, Armstrong L, Bonakdar M, Ch'ng C, Chuah E, Dunham C, Fok A, Jones M, Lee AF, Ma Y, Moore RA, Mungall AJ, Mungall KL, Rogers PC, Schrader KA, Virani A, Wee K, Young SS, Zhao Y, Jones SJM, Laskin J, Marra MA, Rassekh SR. Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers. Nat Commun 2024; 15:4165. [PMID: 38755180 PMCID: PMC11099106 DOI: 10.1038/s41467-024-48363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers.
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Affiliation(s)
- Rebecca J Deyell
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Katherine Dixon
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Jessica M T Nelson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sanna Abbasi
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alexandra Fok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Paul C Rogers
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sean S Young
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Shahrad R Rassekh
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
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Modahl CM, Han SX, van Thiel J, Vaz C, Dunstan NL, Frietze S, Jackson TNW, Mackessy SP, Kini RM. Distinct regulatory networks control toxin gene expression in elapid and viperid snakes. BMC Genomics 2024; 25:186. [PMID: 38365592 PMCID: PMC10874052 DOI: 10.1186/s12864-024-10090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Venom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to share a common origin, but there are major distinctions between venom toxins from the medically significant snake families Elapidae and Viperidae, and toxin gene regulatory investigations in elapid snakes have been limited. Here, we used high-throughput RNA-sequencing to profile gene expression and microRNAs between active (milked) and resting (unmilked) venom glands in an elapid (Eastern Brown Snake, Pseudonaja textilis), in addition to comparative genomics, to identify cis- and trans-acting regulation of venom production in an elapid in comparison to viperids (Crotalus viridis and C. tigris). RESULTS Although there is conservation in high-level mechanistic pathways regulating venom production (unfolded protein response, Notch signaling and cholesterol homeostasis), there are differences in the regulation of histone methylation enzymes, transcription factors, and microRNAs in venom glands from these two snake families. Histone methyltransferases and transcription factor (TF) specificity protein 1 (Sp1) were highly upregulated in the milked elapid venom gland in comparison to the viperids, whereas nuclear factor I (NFI) TFs were upregulated after viperid venom milking. Sp1 and NFI cis-regulatory elements were common to toxin gene promoter regions, but many unique elements were also present between elapid and viperid toxins. The presence of Sp1 binding sites across multiple elapid toxin gene promoter regions that have been experimentally determined to regulate expression, in addition to upregulation of Sp1 after venom milking, suggests this transcription factor is involved in elapid toxin expression. microRNA profiles were distinctive between milked and unmilked venom glands for both snake families, and microRNAs were predicted to target a diversity of toxin transcripts in the elapid P. textilis venom gland, but only snake venom metalloproteinase transcripts in the viperid C. viridis venom gland. These results suggest differences in toxin gene posttranscriptional regulation between the elapid P. textilis and viperid C. viridis. CONCLUSIONS Our comparative transcriptomic and genomic analyses between toxin genes and isoforms in elapid and viperid snakes suggests independent toxin regulation between these two snake families, demonstrating multiple different regulatory mechanisms underpin a venomous phenotype.
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Affiliation(s)
- Cassandra M Modahl
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, U.K..
| | - Summer Xia Han
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- Fulcrum Therapeutics, Cambridge, MA, U.S.A
| | - Jory van Thiel
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, U.K
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Candida Vaz
- Human Development, Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, U.S.A
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, U.S.A
| | - R Manjunatha Kini
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Singapore Eye Research Institute, Singapore, Singapore.
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, U.S.A..
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Shabbir M, Mithani A. Roast: a tool for reference-free optimization of supertranscriptome assemblies. BMC Bioinformatics 2024; 25:2. [PMID: 38166712 PMCID: PMC10763045 DOI: 10.1186/s12859-023-05614-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Transcriptomic studies involving organisms for which reference genomes are not available typically start by generating de novo transcriptome or supertranscriptome assembly from the raw RNA-seq reads. Assembling a supertranscriptome is, however, a challenging task due to significantly varying abundance of mRNA transcripts, alternative splicing, and sequencing errors. As a result, popular de novo supertranscriptome assembly tools generate assemblies containing contigs that are partially-assembled, fragmented, false chimeras or have local mis-assemblies leading to decreased assembly accuracy. Commonly available tools for assembly improvement rely primarily on running BLAST using closely related species making their accuracy and reliability conditioned on the availability of the data for closely related organisms. RESULTS We present ROAST, a tool for optimization of supertranscriptome assemblies that uses paired-end RNA-seq data from Illumina sequencing platform to iteratively identify and fix assembly errors solely using the error signatures generated by RNA-seq alignment tools including soft-clips, unexpected expression coverage, and reads with mates unmapped or mapped on a different contig to identify and fix various supertranscriptome assembly errors without performing BLAST searches against other organisms. Evaluation results using simulated as well as real datasets show that ROAST significantly improves assembly quality by identifying and fixing various assembly errors. CONCLUSION ROAST provides a reference-free approach to optimizing supertranscriptome assemblies highlighting its utility in refining de novo supertranscriptome assemblies of non-model organisms.
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Affiliation(s)
- Madiha Shabbir
- Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore, 54792, Pakistan
| | - Aziz Mithani
- Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore, 54792, Pakistan.
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Campbell LK, Peery RM, Magor KE. Evolution and expression of the duck TRIM gene repertoire. Front Immunol 2023; 14:1220081. [PMID: 37622121 PMCID: PMC10445537 DOI: 10.3389/fimmu.2023.1220081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023] Open
Abstract
Tripartite motif (TRIM) proteins are involved in development, innate immunity, and viral restriction. TRIM gene repertoires vary between species, likely due to diversification caused by selective pressures from pathogens; however, this has not been explored in birds. We mined a de novo assembled transcriptome for the TRIM gene repertoire of the domestic mallard duck (Anas platyrhynchos), a reservoir host of influenza A viruses. We found 57 TRIM genes in the duck, which represent all 12 subfamilies based on their C-terminal domains. Members of the C-IV subfamily with C-terminal PRY-SPRY domains are known to augment immune responses in mammals. We compared C-IV TRIM proteins between reptiles, birds, and mammals and show that many C-IV subfamily members have arisen independently in these lineages. A comparison of the MHC-linked C-IV TRIM genes reveals expansions in birds and reptiles. The TRIM25 locus with related innate receptor modifiers is adjacent to the MHC in reptile and marsupial genomes, suggesting the ancestral organization. Within the avian lineage, both the MHC and TRIM25 loci have undergone significant TRIM gene reorganizations and divergence, both hallmarks of pathogen-driven selection. To assess the expression of TRIM genes, we aligned RNA-seq reads from duck tissues. C-IV TRIMs had high relative expression in immune relevant sites such as the lung, spleen, kidney, and intestine, and low expression in immune privileged sites such as in the brain or gonads. Gene loss and gain in the evolution of the TRIM repertoire in birds suggests candidate immune genes and potential targets of viral subversion.
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Affiliation(s)
- Lee K. Campbell
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Rhiannon M. Peery
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Katharine E. Magor
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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Modahl CM, Chowdhury A, Low DHW, Manuel MC, Missé D, Kini RM, Mendenhall IH, Pompon J. Midgut transcriptomic responses to dengue and chikungunya viruses in the vectors Aedes albopictus and Aedes malayensis. Sci Rep 2023; 13:11271. [PMID: 37438463 DOI: 10.1038/s41598-023-38354-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/06/2023] [Indexed: 07/14/2023] Open
Abstract
Dengue (DENV) and chikungunya (CHIKV) viruses are among the most preponderant arboviruses. Although primarily transmitted through the bite of Aedes aegypti mosquitoes, Aedes albopictus and Aedes malayensis are competent vectors and have an impact on arbovirus epidemiology. Here, to fill the gap in our understanding of the molecular interactions between secondary vectors and arboviruses, we used transcriptomics to profile the whole-genome responses of A. albopictus to CHIKV and of A. malayensis to CHIKV and DENV at 1 and 4 days post-infection (dpi) in midguts. In A. albopictus, 1793 and 339 genes were significantly regulated by CHIKV at 1 and 4 dpi, respectively. In A. malayensis, 943 and 222 genes upon CHIKV infection, and 74 and 69 genes upon DENV infection were significantly regulated at 1 and 4 dpi, respectively. We reported 81 genes that were consistently differentially regulated in all the CHIKV-infected conditions, identifying a CHIKV-induced signature. We identified expressed immune genes in both mosquito species, using a de novo assembled midgut transcriptome for A. malayensis, and described the immune architectures. We found the JNK pathway activated in all conditions, generalizing its antiviral function to Aedines. Our comprehensive study provides insight into arbovirus transmission by multiple Aedes vectors.
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Affiliation(s)
- Cassandra M Modahl
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Liverpool School of Tropical Medicine, Liverpool, U.K
| | - Avisha Chowdhury
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Toronto Centre for Liver Disease, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada
| | - Dolyce H W Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Menchie C Manuel
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Julien Pompon
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France.
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Ribeiro JM, Hartmann D, Bartošová-Sojková P, Debat H, Moos M, Šimek P, Fara J, Palus M, Kučera M, Hajdušek O, Sojka D, Kopáček P, Perner J. Blood-feeding adaptations and virome assessment of the poultry red mite Dermanyssus gallinae guided by RNA-seq. Commun Biol 2023; 6:517. [PMID: 37179447 PMCID: PMC10183022 DOI: 10.1038/s42003-023-04907-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Dermanyssus gallinae is a blood-feeding mite that parasitises wild birds and farmed poultry. Its remarkably swift processing of blood, together with the capacity to blood-feed during most developmental stages, makes this mite a highly debilitating pest. To identify specific adaptations to digestion of a haemoglobin-rich diet, we constructed and compared transcriptomes from starved and blood-fed stages of the parasite and identified midgut-enriched transcripts. We noted that midgut transcripts encoding cysteine proteases were upregulated with a blood meal. Mapping the full proteolytic apparatus, we noted a reduction in the suite of cysteine proteases, missing homologues for Cathepsin B and C. We have further identified and phylogenetically analysed three distinct transcripts encoding vitellogenins that facilitate the reproductive capacity of the mites. We also fully mapped transcripts for haem biosynthesis and the ferritin-based system of iron storage and inter-tissue trafficking. Additionally, we identified transcripts encoding proteins implicated in immune signalling (Toll and IMD pathways) and activity (defensins and thioester-containing proteins), RNAi, and ion channelling (with targets for commercial acaricides such as Fluralaner, Fipronil, and Ivermectin). Viral sequences were filtered from the Illumina reads and we described, in part, the RNA-virome of D. gallinae with identification of a novel virus, Red mite quaranjavirus 1.
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Affiliation(s)
- José M Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - David Hartmann
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Pavla Bartošová-Sojková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Martin Moos
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Petr Šimek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Jiří Fara
- International Poultry Testing Station Ústrašice, Ústrašice, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Matěj Kučera
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Ondřej Hajdušek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Daniel Sojka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Petr Kopáček
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic.
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Tsang ES, Csizmok V, Williamson LM, Pleasance E, Topham JT, Karasinska JM, Titmuss E, Schrader I, Yip S, Tessier-Cloutier B, Mungall K, Ng T, Sun S, Lim HJ, Loree JM, Laskin J, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration. NPJ Precis Oncol 2023; 7:31. [PMID: 36964191 PMCID: PMC10039042 DOI: 10.1038/s41698-023-00368-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
There is emerging evidence about the predictive role of homologous recombination deficiency (HRD), but this is less defined in gastrointestinal (GI) and thoracic malignancies. We reviewed whole genome (WGS) and transcriptomic (RNA-Seq) data from advanced GI and thoracic cancers in the Personalized OncoGenomics trial (NCT02155621) to evaluate HRD scores and single base substitution (SBS)3, which is associated with BRCA1/2 mutations and potentially predictive of defective HRD. HRD scores were calculated by sum of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions scores. Regression analyses examined the association between HRD and time to progression on platinum (TTPp). We included 223 patients with GI (n = 154) or thoracic (n = 69) malignancies. TTPp was associated with SBS3 (p < 0.01) but not HRD score in patients with GI malignancies, whereas neither was associated with TTPp in thoracic malignancies. Tumors with gBRCA1/2 mutations and a somatic second alteration exhibited high SBS3 and HRD scores, but these signatures were also present in several tumors with germline but no somatic second alterations, suggesting silencing of the wild-type allele or BRCA1/2 haploinsufficiency. Biallelic inactivation of an HR gene, including loss of XRCC2 and BARD1, was identified in BRCA1/2 wild-type HRD tumors and these patients had prolonged response to platinum. Thoracic cases with high HRD score were associated with high RECQL5 expression (p ≤ 0.025), indicating another potential mechanism of HRD. SBS3 was more strongly associated with TTPp in patients with GI malignancies and may be complementary to using HRD and BRCA status in identifying patients who benefit from platinum therapy.
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Affiliation(s)
- Erica S Tsang
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
- Pancreas Centre BC, Vancouver, BC, Canada
| | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | | | | | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Intan Schrader
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sophie Sun
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Jonathan M Loree
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada.
- Pancreas Centre BC, Vancouver, BC, Canada.
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8
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Cho N, Joo J, Choi S, Kang BG, Lee AJ, Youn SY, Park SH, Kim EM, Masliah E, Ko Y, Cha SS, Jung I, Kim KK. A novel splicing variant of DJ-1 in Parkinson's disease induces mitochondrial dysfunction. Heliyon 2023; 9:e14039. [PMID: 36915530 DOI: 10.1016/j.heliyon.2023.e14039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
Several studies have identified mutations in neuroprotective genes in a few cases of Parkinson's disease (PD); however, the role of alternative splicing changes in PD remains unelucidated. Based on the transcriptome analysis of substantia nigra (SN) tissues obtained from PD cases and age-matched healthy controls, we identified a novel alternative splicing variant of DJ-1, lacking exon 6 (DJ-1 ΔE6), frequently detected in the SN of patients with PD. We found that the exon 6 skipping of DJ-1 induces mitochondrial dysfunction and impaired antioxidant capability. According to an in silico modeling study, the exon 6 skipping of DJ-1 disrupts the structural state suitable for the oxidation of the cysteine 106 residue that is a prerequisite for activating its neuroprotective roles. Our results suggest that change in DJ-1 alternative splicing may contribute to PD progression and provide an insight for studying PD etiology and its potential therapeutic targets.
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9
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Arumugam T, Hatta MAM. Improving Coconut Using Modern Breeding Technologies: Challenges and Opportunities. Plants (Basel) 2022; 11:3414. [PMID: 36559524 PMCID: PMC9784122 DOI: 10.3390/plants11243414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Coconut (Cocos nucifera L.) is a perennial palm with a wide range of distribution across tropical islands and coastlines. Multitude use of coconut by nature is important in the socio-economic fabric framework among rural smallholders in producing countries. It is a major source of income for 30 million farmers, while 60 million households rely on the coconut industry directly as farm workers and indirectly through the distribution, marketing, and processing of coconut and coconut-based products. Stagnant production, inadequate planting materials, the effects of climate change, as well as pests and diseases are among the key issues that need to be urgently addressed in the global coconut industry. Biotechnology has revolutionized conventional breeding approaches in creating genetic variation for trait improvement in a shorter period of time. In this review, we highlighted the challenges of current breeding strategies and the potential of biotechnological approaches, such as genomic-assisted breeding, next-generation sequencing (NGS)-based genotyping and genome editing tools in improving the coconut. Also, combining these technologies with high-throughput phenotyping approaches and speed breeding could speed up the rate of genetic gain in coconut breeding to solve problems that have been plaguing the industry for decades.
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10
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Yu IS, Wee K, Williamson L, Titmuss E, An J, Naderi-Azad S, Metcalf C, Yip S, Horst B, Jones SJM, Paton K, Nelson BH, Marra M, Laskin JJ, Savage KJ. Exceptional response to combination ipilimumab and nivolumab in metastatic uveal melanoma: Insights from genomic analysis. Melanoma Res 2022; 32:278-285. [PMID: 35726793 DOI: 10.1097/cmr.0000000000000810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Uveal melanoma is the most common intraocular malignancy and has a poor prognosis compared to other melanoma subtypes with a median overall survival of 6-10 months. With immune checkpoint inhibitor therapy, either PD-1 inhibitor alone or combination ipilimumab/nivolumab (anti-CTLA-4/anti-PD-1), responses are rare and often not durable. We present a case report of a now 66-year-old woman with diffuse metastatic uveal melanoma previously treated with a combination of ipilimumab/nivolumab, followed by maintenance nivolumab. Almost complete resolution of all sites of metastatic disease was observed except for one liver metastasis which regressed partially on immunotherapy. Notably, the patient had a significantly elevated BMI and developed widespread vitiligo on treatment. Whole-genome and transcriptome analysis was performed on the residual liver biopsy and molecular markers that may have contributed to the exceptional response were investigated. Several alterations were observed in genes involved in T-cell responses. Estimates of tumour infiltrating immune cells indicated a high level of plasma cells compared to other uveal melanoma cases, a finding previously associated with indolent disease. The patient also carried several germline SNPs that may have contributed to her treatment response as well as widespread vitiligo. Whole-genome and transcriptome sequencing have provided insight into potential molecular underpinnings of an exceptional treatment response in a tumour type typically associated with poor prognosis. Immunological findings suggest a role for plasma cells in the tumour microenvironment. Elevated BMI and the development of vitiligo may be clinically relevant factors for predicting response to immune checkpoint inhibitor therapy, warranting further studies in patients with uveal melanoma.
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Affiliation(s)
- Irene S Yu
- Department of Medical Oncology, BC Cancer
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia
| | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia
| | - Jianghong An
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia
| | - Sheida Naderi-Azad
- Faculty of Medicine, University of Toronto, 1 King's College Cir, Toronto, Ontario
| | | | - Stephen Yip
- Department of Pathology and Laboratory Medicine
| | - Basil Horst
- Department of Pathology and Laboratory Medicine
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia
- Department of Medical Genetics
| | - Katherine Paton
- Department of Ophthalmology and Visual Sciences, University of British Columbia
| | - Brad H Nelson
- Department of Medical Genetics
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Marco Marra
- Department of Medical Oncology, BC Cancer
- Department of Medical Genetics
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11
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Tessier-Cloutier B, Grewal JK, Jones MR, Pleasance E, Shen Y, Cai E, Dunham C, Hoang L, Horst B, Huntsman DG, Ionescu D, Karnezis AN, Lee AF, Lee CH, Lee TH, Twa DD, Mungall AJ, Mungall K, Naso JR, Ng T, Schaeffer DF, Sheffield BS, Skinnider B, Smith T, Williamson L, Zhong E, Regier DA, Laskin J, Marra MA, Gilks CB, Jones SJ, Yip S. The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies. J Pathol Clin Res 2022; 8:395-407. [PMID: 35257510 PMCID: PMC9161328 DOI: 10.1002/cjp2.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/15/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022]
Abstract
In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. WGTA was used to generate reports including molecular alterations and site/tissue of origin prediction. Two reviewers analyzed genomic reports, clinical history, and tumor pathology. We used National Comprehensive Cancer Network (NCCN) consensus guidelines, Food and Drug Administration (FDA) approvals, and provincially reimbursed treatments to define genomic biomarkers associated with approved targeted therapeutic options (TTOs). Tumor tissue/site of origin was reassessed for most cases using genomic analysis, including a machine learning algorithm (Supervised Cancer Origin Prediction Using Expression [SCOPE]) trained on The Cancer Genome Atlas data. WGTA was performed on 652 cases, including a range of primary tumor types/tumor sites and 15 malignant tumors of uncertain histogenesis (MTUH). At the time WGTA was performed, alterations associated with an approved TTO were identified in 39 (6%) cases; 3 of these were not identified through routine pathology workup. In seven (1%) cases, the pathology workup either failed, was not performed, or gave a different result from the WGTA. Approved TTOs identified by WGTA increased to 103 (16%) when applying 2021 guidelines. The histopathologic diagnosis was reviewed in 389 cases and agreed with the diagnostic consensus after WGTA in 94% of non‐MTUH cases (n = 374). The remainder included situations where the morphologic diagnosis was changed based on WGTA and clinical data (0.5%), or where the WGTA was non‐contributory (5%). The 15 MTUH were all diagnosed as specific tumor types by WGTA. Tumor board reviews including WGTA agreed with almost all initial predictive molecular profile and histopathologic diagnoses. WGTA was a powerful tool to assign site/tissue of origin in MTUH. Current efforts focus on improving therapeutic predictive power and decreasing cost to enhance use of WGTA data as a routine clinical test.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jasleen K Grewal
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ellen Cai
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Lynn Hoang
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Basil Horst
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Diana Ionescu
- Department of Anatomical Pathology, BC Cancer, Vancouver, BC, Canada
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, UC Davis, Sacramento, CA, USA
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Cheng Han Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Tae Hoon Lee
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David Dw Twa
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Julia R Naso
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Brandon S Sheffield
- Department of Pathology and Laboratory Medicine, William Osler Health System, Brampton, ON, Canada
| | - Brian Skinnider
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Tyler Smith
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ellia Zhong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dean A Regier
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
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12
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Luo H, Hallen-Adams HE, Lüli Y, Sgambelluri RM, Li X, Smith M, Yang ZL, Martin FM. Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms. Proc Natl Acad Sci U S A 2022; 119:e2201113119. [PMID: 35533275 DOI: 10.1073/pnas.2201113119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Why do unrelated poisonous mushrooms (Amanita, Galerina, and Lepiota) make the same deadly toxin, α-amanitin? One of the most effective and fast strategies for organisms to acquire new abilities is through horizontal gene transfer (HGT). With the help of genome sequencing and the finding of two genes for the amanitin biosynthetic pathway, we demonstrate that the pathway distribution resulted from HGT probably through an unknown ancestral fungal donor. In Amanita mushrooms, the pathway evolved, through a series of gene manipulations, to produce very high levels of toxins, generating “the deadliest mushroom known to mankind.” The deadly toxin α-amanitin is a bicyclic octapeptide biosynthesized on ribosomes. A phylogenetically disjunct group of mushrooms in Agaricales (Amanita, Lepiota, and Galerina) synthesizes α-amanitin. This distribution of the toxin biosynthetic pathway is possibly related to the horizontal transfer of metabolic gene clusters among taxonomically unrelated mushrooms with overlapping habitats. Here, our work confirms that two biosynthetic genes, P450-29 and FMO1, are oxygenases important for amanitin biosynthesis. Phylogenetic and genetic analyses of these genes strongly support their origin through horizontal transfer, as is the case for the previously characterized biosynthetic genes MSDIN and POPB. Our analysis of multiple genomes showed that the evolution of the α-amanitin biosynthetic pathways in the poisonous agarics in the Amanita, Lepiota, and Galerina clades entailed distinct evolutionary pathways including gene family expansion, biosynthetic genes, and genomic rearrangements. Unrelated poisonous fungi produce the same deadly amanitin toxins using variations of the same pathway. Furthermore, the evolution of the amanitin biosynthetic pathway(s) in Amanita species generates a much wider range of toxic cyclic peptides. The results reported here expand our understanding of the genetics, diversity, and evolution of the toxin biosynthetic pathway in fungi.
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13
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Reisle C, Williamson LM, Pleasance E, Davies A, Pellegrini B, Bleile DW, Mungall KL, Chuah E, Jones MR, Ma Y, Lewis E, Beckie I, Pham D, Matiello Pletz R, Muhammadzadeh A, Pierce BM, Li J, Stevenson R, Wong H, Bailey L, Reisle A, Douglas M, Bonakdar M, Nelson JMT, Grisdale CJ, Krzywinski M, Fisic A, Mitchell T, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJM. A platform for oncogenomic reporting and interpretation. Nat Commun 2022; 13:756. [PMID: 35140225 PMCID: PMC8828759 DOI: 10.1038/s41467-022-28348-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
Manual interpretation of variants remains rate limiting in precision oncology. The increasing scale and complexity of molecular data generated from comprehensive sequencing of cancer samples requires advanced interpretative platforms as precision oncology expands beyond individual patients to entire populations. To address this unmet need, we introduce a Platform for Oncogenomic Reporting and Interpretation (PORI), comprising an analytic framework that facilitates the interpretation and reporting of somatic variants in cancer. PORI integrates reporting and graph knowledge base tools combined with support for manual curation at the reporting stage. PORI represents an open-source platform alternative to commercial reporting solutions suitable for comprehensive genomic data sets in precision oncology. We demonstrate the utility of PORI by matching 9,961 pan-cancer genome atlas tumours to the graph knowledge base, calculating therapeutically informative alterations, and making available reports describing select individual samples. The interpretation of somatic variants in cancer is challenging due to the scale and complexity of sequencing data. Here, the authors present PORI, an open-source framework for interpreting somatic variants in cancer using graph knowledge base tools, automated reporting, and manual curation.
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Affiliation(s)
- Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Bioinformatics Graduate Program, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
| | | | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Anna Davies
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Dustin W Bleile
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Eleanor Lewis
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Isaac Beckie
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - David Pham
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | - Brandon M Pierce
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Jacky Li
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ross Stevenson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Hansen Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Lance Bailey
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Abbey Reisle
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Matthew Douglas
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ana Fisic
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Teresa Mitchell
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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14
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Zhao J, Feng H, Zhu D, Lin Y. MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly. IEEE/ACM Trans Comput Biol Bioinform 2022; 19:48-56. [PMID: 34033544 DOI: 10.1109/tcbb.2021.3083277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent advances in RNA-seq technology have made identification of expressed genes affordable, and thus boosting repaid development of transcriptomic studies. Transcriptome assembly, reconstructing all expressed transcripts from RNA-seq reads, is an essential step to understand genes, proteins, and cell functions. Transcriptome assembly remains a challenging problem due to complications in splicing variants, expression levels, uneven coverage and sequencing errors. Here, we formulate the transcriptome assembly problem as path extraction on splicing graphs (or assembly graphs), and propose a novel algorithm MultiTrans for path extraction using mixed integer linear programming. MultiTrans is able to take into consideration coverage constraints on vertices and edges, the number of paths and the paired-end information simultaneously. We benchmarked MultiTrans against two state-of-the-art transcriptome assemblers, TransLiG and rnaSPAdes. Experimental results show that MultiTrans generates more accurate transcripts compared to TransLiG (using the same splicing graphs) and rnaSPAdes (using the same assembly graphs). MultiTrans is freely available at https://github.com/jzbio/MultiTrans.
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15
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Williamson LM, Rive CM, Di Francesco D, Titmuss E, Chun HJE, Brown SD, Milne K, Pleasance E, Lee AF, Yip S, Rosenbaum DG, Hasselblatt M, Johann PD, Kool M, Harvey M, Dix D, Renouf DJ, Holt RA, Nelson BH, Hirst M, Jones SJM, Laskin J, Rassekh SR, Deyell RJ, Marra MA. Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury. NPJ Precis Oncol 2021; 5:103. [PMID: 34931022 PMCID: PMC8688516 DOI: 10.1038/s41698-021-00238-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/22/2021] [Indexed: 01/01/2023] Open
Abstract
Poorly differentiated chordoma (PDC) is a recently recognized subtype of chordoma characterized by expression of the embryonic transcription factor, brachyury, and loss of INI1. PDC primarily affects children and is associated with a poor prognosis and limited treatment options. Here we describe the molecular and immune tumour microenvironment profiles of two paediatric PDCs produced using whole-genome, transcriptome and whole-genome bisulfite sequencing (WGBS) and multiplex immunohistochemistry. Our analyses revealed the presence of tumour-associated immune cells, including CD8+ T cells, and expression of the immune checkpoint protein, PD-L1, in both patient samples. Molecular profiling provided the rationale for immune checkpoint inhibitor (ICI) therapy, which resulted in a clinical and radiographic response. A dominant T cell receptor (TCR) clone specific for a brachyury peptide-MHC complex was identified from bulk RNA sequencing, suggesting that targeting of the brachyury tumour antigen by tumour-associated T cells may underlie this clinical response to ICI. Correlative analysis with rhabdoid tumours, another INI1-deficient paediatric malignancy, suggests that a subset of tumours may share common immune phenotypes, indicating the potential for a therapeutically targetable subgroup of challenging paediatric cancers.
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Affiliation(s)
- Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Craig M Rive
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Daniela Di Francesco
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Hye-Jung E Chun
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, BC, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Daniel G Rosenbaum
- Department of Radiology, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Pascal D Johann
- Hopp Children's Cancer Center (KITZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Core Center, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KITZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Core Center, Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Melissa Harvey
- Division of Pediatric Hematology Oncology BMT, University of British Columbia, Vancouver, BC, Canada
| | - David Dix
- Division of Pediatric Hematology Oncology BMT, University of British Columbia, Vancouver, BC, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer, Victoria, BC, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Shahrad R Rassekh
- Division of Pediatric Hematology Oncology BMT, University of British Columbia, Vancouver, BC, Canada
| | - Rebecca J Deyell
- Division of Pediatric Hematology Oncology BMT, University of British Columbia, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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16
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Liu X, Li Y, Zheng X, Zhang L, Lyu H, Huang H, Fan Z. Anti-oxidant mechanisms of Chlorella pyrenoidosa under acute GenX exposure. Sci Total Environ 2021; 797:149005. [PMID: 34311359 DOI: 10.1016/j.scitotenv.2021.149005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
GenX, a substitute for perfluorooctanoic acid, has been widely detected in surface water. Due to its bioaccumulation, toxicity and persistence, GenX can cause adverse effects such as oxidative damage on aquatic organisms. To investigate the toxicity of GenX and the anti-oxidant mechanism of algae under acute exposure, the growth, photosynthetic activity and gene expression of Chlorella pyrenoidosa (C. pyrenoidosa) were tested. Results showed that the growth of C. pyrenoidosa was inhibited under acute GenX exposure. The toxicity of GenX increased with time and concentration but was lower than that of the traditional perfluoroalkyl and polyfluoroalkyl substances (PFASs). Furthermore, with the increase of GenX concentration, the production of reactive oxygen species increased, while the level of the anti-oxidant enzyme first increased and then decreased. Changes in photosynthetic parameters also indicated that the photosynthetic system of C. pyrenoidosa was negatively affected by GenX exposure. Transcription analysis revealed that the up-regulation of genes related to the glutathione-ascorbate cycle and photosynthesis is a positive strategy to cope with the oxidative stress caused by acute GenX exposure. Our findings provide new insights into the interactions between emerging PFASs and aquatic organisms at the molecular level.
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Affiliation(s)
- Xianglin Liu
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Yanyao Li
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Xiaowei Zheng
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Liangliang Zhang
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Haoxuan Lyu
- ANU College of Engineering & Computer Science, The Australian National University, Canberra, ACT, 2600, Australia
| | - Honghui Huang
- Guangdong Provincial Key Lab of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Zhengqiu Fan
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China.
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17
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Mulder KP, Alarcón-Ríos L, Nicieza AG, Fleischer RC, Bell RC, Velo-Antón G. Independent evolutionary transitions to pueriparity across multiple timescales in the viviparous genus Salamandra. Mol Phylogenet Evol 2021; 167:107347. [PMID: 34763070 DOI: 10.1016/j.ympev.2021.107347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/21/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023]
Abstract
The ability to bear live offspring, viviparity, has evolved multiple times across the tree of life and is a remarkable adaptation with profound life-history and ecological implications. Within amphibians the ancestral reproductive mode is oviparity followed by a larval life stage, but viviparity has evolved independently in all three amphibian orders. Two types of viviparous reproduction can be distinguished in amphibians; larviparity and pueriparity. Larviparous amphibians deliver larvae into nearby ponds and streams, while pueriparous amphibians deliver fully developed juveniles and thus do not require waterbodies for reproduction. Among amphibians, the salamander genus Salamandra is remarkable as it exhibits both inter- and intraspecific variation in the occurrence of larviparity and pueriparity. While the evolutionary relationships among Salamandra lineages have been the focus of several recent studies, our understanding of how often and when transitions between modes occurred is still incomplete. Furthermore, in species with intraspecific variation, the reproductive mode of a given population can only be confirmed by direct observation of births and thus the prevalence of pueriparous populations is also incompletely documented. We used sequence capture to obtain 1,326 loci from 94 individuals from across the geographic range of the genus, focusing on potential reproductive mode transition zones. We also report additional direct observations of pueriparous births for 20 new locations and multiple lineages. We identify at least five independent transitions from the ancestral mode of larviparity to pueriparity among and within species, occurring at different evolutionary timescales ranging from the Pliocene to the Holocene. Four of these transitions occurred within species. Based on a distinct set of markers and analyses, we also confirm previous findings of introgression between species and the need for taxonomic revisions in the genus. We discuss the implications of our findings with respect to the evolution of this complex trait, and the potential of using five independent convergent transitions for further studies on the ecological context in which pueriparity evolves and the genetic architecture of this specialized reproductive mode.
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Affiliation(s)
- Kevin P Mulder
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC 20560, USA; Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
| | - Lucía Alarcón-Ríos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo UO, Oviedo, Spain
| | - Alfredo G Nicieza
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo UO, Oviedo, Spain; Biodiversity Research Institute (IMIB), University of Oviedo-Principality of Asturias-CSIC, 33600 Mieres, Spain
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC 20560, USA; Herpetology Department, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Guillermo Velo-Antón
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Universidade de Vigo, Grupo GEA, Departamento de Ecoloxía e Bioloxía Animal, Vigo, Spain.
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18
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Duarte MA, Campos FS, Araújo Neto OF, Silva LA, Silva AB, Aguiar TC, Santos RN, Souza UJB, Alves GB, Melo FL, Ardisson-Araujo DMP, Aguiar RWS, Ribeiro BM. Identification of potential new mosquito-associated viruses of adult Aedes aegypti mosquitoes from Tocantins state, Brazil. Braz J Microbiol 2021; 53:51-62. [PMID: 34727360 DOI: 10.1007/s42770-021-00632-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/07/2021] [Indexed: 11/29/2022] Open
Abstract
Medically important arboviruses such as dengue virus (DENV), Zika virus (ZIKV), and chikungunya virus (CHIKV) are primarily transmitted by the globally distributed mosquito Aedes aegypti. Increasing evidence suggests that the transmission of some viruses can be influenced by mosquito-specific and mosquito-borne viruses. Advancements in high-throughput sequencing (HTS) and bioinformatics have expanded our knowledge on the richness of viruses harbored by mosquitoes. HTS was used to characterize the presence of virus sequences in wild-caught adult Ae. aegypti from Tocantins (TO) state, Brazil. Samples of mosquitoes were collected in four cities of Tocantins state and submitted to RNA isolation, followed by sequencing at an Illumina HiSeq platform. Our results showed initially by Krona the presence of 3% of the sequenced reads belonging to the viral database. After further analysis, the virus sequences were found to have homology to two viral families found in insects Phenuiviridae and Metaviridae. Three possible viral strains including putative new viruses were detected and named Phasi Charoen-like phasivirus isolate To-1 (PCLV To-1), Aedes aegypti To virus 1 (AAToV1), and Aedes aegypti To virus 2 (AAToV2). The results presented in this work contribute to the growing knowledge about the diversity of viruses in mosquitoes and might be useful for future studies on the interaction between insect-specific viruses and arboviruses.
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Affiliation(s)
- Matheus A Duarte
- Faculdade de Agronomia E Veterinária, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Fabrício S Campos
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil.
| | - Osvaldo F Araújo Neto
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Leonardo A Silva
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Arthur B Silva
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Thalita C Aguiar
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Raissa N Santos
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Ueric J B Souza
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Giselly B Alves
- Laboratório de Biologia Molecular, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Daniel M P Ardisson-Araujo
- Laboratório de Virologia de Insetos, Universidade Federal de Santa Maria, Santa Maria, RS, 97.105-900, Brazil
| | - Raimundo W S Aguiar
- Laboratório de Biologia Molecular, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
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19
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Ponce GE, Fuse M, Chan A, Connor EF. The Localization of Phytohormones within the Gall-inducing Insect Eurosta solidaginis (Diptera: Tephritidae). Arthropod Plant Interact 2021; 15:375-385. [PMID: 34149963 PMCID: PMC8211092 DOI: 10.1007/s11829-021-09817-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
The phytohormone production hypothesis suggests that organisms, including insects, induce galls by producing and secreting plant growth hormones. Auxins and cytokinins are classes of phytohormones that induce cell growth and cell division, which could contribute to the plant tissue proliferation which constitutes the covering gall. Bacteria, symbiotic with insects, may also play a part in gall induction by insects through the synthesis of phytohormones or other effectors. Past studies have shown that concentrations of cytokinins and auxins in gall-inducing insects are higher than in their host plants. However, these analyses have involved whole-body extractions. Using immunolocalization of cytokinin and auxin, in the gall inducing stage of Eurosta solidaginis, we found both phytohormones to localize almost exclusively to the salivary glands. Co-localization of phytohormone label with a nucleic acid stain in the salivary glands revealed the absence of Wolbachia sp., the bacterial symbiont of E. solidaginis, which suggests that phytohormone production is symbiont independent. Our findings are consistent with the hypothesis that phytohormones are synthesized in and secreted from the salivary glands of E. solidaginis into host-plant tissues for the purpose of manipulating the host plant.
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Affiliation(s)
- Gabriela E Ponce
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA USA 94132
| | - Megumi Fuse
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA USA 94132
| | - Annette Chan
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA USA 94132
| | - Edward F Connor
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA USA 94132
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20
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Abstract
Background:
Transcriptome annotation is the basis for understanding gene structures
and analysing gene expression. The transcriptome annotation of many organisms such as humans
is far from incomplete, due partly to the challenge in the identification of isoforms that are
produced from the same gene through alternative splicing. Third generation sequencing (TGS)
reads provide unprecedented opportunity for detecting isoforms due to their long length that
exceeds the length of most isoforms. One limitation of current TGS reads-based isoform detection
methods is that they are exclusively based on sequence reads, without incorporating the sequence
information of annotated isoforms.
Objective:
We aim to develop a method to detect isoforms by incorporating annotated isoforms.
Methods:
Based on annotated isoforms, we propose a splice isoform detection method called
IsoDetect. First, the sequence at exon-exon junctions is extracted from annotated isoforms as
“short feature sequences”, which is used to distinguish splice isoforms. Second, we align these
feature sequences to long reads and partition long reads into groups that contain the same set of
feature sequences, thereby avoiding the pair-wise comparison among the large number of long
reads. Third, clustering and consensus generation are carried out based on sequence similarity. For
the long reads that do not contain any short feature sequence, clustering analysis based on
sequence similarity is performed to identify isoforms. Therefore, our method can detect not only
known but also novel isoforms.
Result:
Tested on two datasets from Calypte anna and Zebra Finch, IsoDetect shows higher speed
and good accuracies compared with four existing methods.
Conclusion:
IsoDetect may become a promising method for isoform detection.
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Affiliation(s)
- Hong-Dong Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Wenjing Zhang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Yuwen Luo
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
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21
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Perner J, Helm D, Haberkant P, Hatalova T, Kropackova S, Ribeiro JM, Kopacek P. The Central Role of Salivary Metalloproteases in Host Acquired Resistance to Tick Feeding. Front Cell Infect Microbiol 2020; 10:563349. [PMID: 33312963 PMCID: PMC7708348 DOI: 10.3389/fcimb.2020.563349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/20/2020] [Indexed: 01/07/2023] Open
Abstract
During feeding on vertebrate hosts, ticks secrete saliva composed of a rich cocktail of bioactive molecules modulating host immune responses. Although most of the proteinaceous fraction of tick saliva is of little immunogenicity, repeated feeding of ticks on mammalian hosts may lead to impairment of tick feeding, preventing full engorgement. Here, we challenged rabbits with repeated feeding of both Ixodes ricinus nymphs and adults and observed the formation of specific antibodies against several tick salivary proteins. Repeated feeding of both I. ricinus stages led to a gradual decrease in engorged weights. To identify the salivary antigens, isolated immunoglobulins from repeatedly infested rabbits were utilized for a protein pull-down from the saliva of pilocarpine-treated ticks. Eluted antigens were first identified by peptide mass fingerprinting with the aid of available I. ricinus salivary gland transcriptomes originating from early phases of tick feeding. To increase the authenticity of immunogens identified, we also performed, for the first time, de novo assembly of the sialome from I. ricinus females fed for six days, a timepoint used for pilocarpine-salivation. The most dominant I. ricinus salivary immunogens identified in our study were zinc-dependent metalloproteases of three different families. To corroborate the role of metalloproteases at the tick/host interface, we fed ticks micro-injected with a zinc metalloprotease inhibitor, phosphoramidon, on a rabbit. These ticks clearly failed to initiate feeding and to engorge. However, neither feeding to ticks immune blood of repeatedly infested rabbits, nor phosphoramidon injection into ticks, prevented their engorgement when fed in vitro on an artificial membrane system. These data show that Zn metalloproteases play a decisive role in the success of tick feeding, mediated by complex molecular interactions between the host immune, inflammatory, and hemostatic processes, which are absent in in vitro feeding. This basic concept warrants further investigation and reconsideration of the current strategies towards the development of an effective “anti-tick” vaccine.
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Affiliation(s)
- Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Dominic Helm
- Proteomics Core Facility, The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tereza Hatalova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Sara Kropackova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Jose M Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Petr Kopacek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
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22
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Tsang ES, Grisdale CJ, Pleasance E, Topham JT, Mungall K, Reisle C, Choo C, Carreira M, Bowlby R, Karasinska JM, MacMillan D, Williamson LM, Chuah E, Moore RA, Mungall AJ, Zhao Y, Tessier-Cloutier B, Ng T, Sun S, Lim HJ, Schaeffer DF, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJM, Loree JM. Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers. Clin Cancer Res 2020; 27:522-531. [PMID: 33148671 DOI: 10.1158/1078-0432.ccr-20-1900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/11/2020] [Accepted: 10/29/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions. EXPERIMENTAL DESIGN Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches. RESULTS In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1). CONCLUSIONS Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.
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Affiliation(s)
- Erica S Tsang
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Caleb Choo
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Marcus Carreira
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Daniel MacMillan
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Sophie Sun
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, Canada.,Pancreas Centre BC, Vancouver, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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23
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Abstract
A decade ago, de novo transcriptome assembly evolved as a versatile and powerful approach to make evolutionary assumptions, analyse gene expression, and annotate novel transcripts, in particular, for non-model organisms lacking an appropriate reference genome. Various tools have been developed to generate a transcriptome assembly, and even more computational methods depend on the results of these tools for further downstream analyses. In this issue of Molecular Ecology Resources, Freedman et al. (Mol Ecol Resourc 2020) present a comprehensive analysis of errors in de novo transcriptome assemblies across public data sets and different assembly methods. They focus on two implicit assumptions that are often violated: First, the assembly presents an unbiased view of the transcriptome. Second, the expression estimates derived from the assembly are reasonable, albeit noisy, approximations of the relative frequency of expressed transcripts. They show that appropriate filtering can reduce this bias but can also lead to the loss of a reasonable number of highly expressed transcripts. Thus, to partly alleviate the noise in expression estimates, they propose a new normalization method called length-rescaled CPM. Remarkably, the authors found considerable distortions at the nucleotide level, which leads to an underestimation of diversity in transcriptome assemblies. The study by Freedman et al. (Mol Ecol Resourc 2020) clearly shows that we have not yet reached "high-quality" in the field of transcriptome assembly. Above all, it helps researchers be aware of these problems and filter and interpret their transcriptome assembly data appropriately and with caution.
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Affiliation(s)
- Martin Hölzer
- MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany.,RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, Germany.,European Virus Bioinformatics Center, Friedrich Schiller University, Jena, Germany
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24
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Vernal S, Oliveira F, Oliveira WHC, Goulart TM, Oristian J, Calvo E, Pinto MC, Roselino AM, Ribeiro JMC. RNA-sequencing of the Nyssomyia neivai sialome: a sand fly-vector from a Brazilian endemic area for tegumentary leishmaniasis and pemphigus foliaceus. Sci Rep 2020; 10:17664. [PMID: 33077743 DOI: 10.1038/s41598-020-74343-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Leishmaniasis encompasses a spectrum of diseases caused by a protozoan belonging to the genus Leishmania. The parasite is transmitted by the bite of sand flies, which inoculate the promastigote forms into the host’s skin while acquiring a blood meal. Nyssomyia neivai is one of the main vectors of tegumentary leishmaniasis (TL) in Brazil. Southeastern Brazil is an endemic region for TL but also overlaps with an endemic focus for pemphigus foliaceus (PF), also known as Fogo Selvagem. Salivary proteins of sand flies, specifically maxadilan and LJM11, have been related to pemphigus etiopathogenesis in the New World, being proposed as an environmental trigger for autoimmunity. We present a comprehensive description of the salivary transcriptome of the N. neivai, using deep sequencing achieved by the Illumina protocol. In addition, we highlight the abundances of several N. neivai salivary proteins and use phylogenetic analysis to compare with Old- and New-World sand fly salivary proteins. The collection of protein sequences associated with the salivary glands of N. neivai can be useful for monitoring vector control strategies as biomarkers of N. neivai, as well as driving vector-vaccine design for leishmaniasis. Additionally, this catalog will serve as reference to screen for possible antigenic peptide candidates triggering anti-Desmoglein-1 autoantibodies.
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25
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Yu T, Liu J, Gao X, Li G. iPAC: a genome-guided assembler of isoforms via phasing and combing paths. Bioinformatics 2020; 36:2712-2717. [PMID: 31985799 DOI: 10.1093/bioinformatics/btaa052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/14/2019] [Accepted: 01/20/2020] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Full-length transcript reconstruction is very important and quite challenging for the widely used RNA-seq data analysis. Currently, available RNA-seq assemblers generally suffered from serious limitations in practical applications, such as low assembly accuracy and incompatibility with latest alignment tools. RESULTS We introduce iPAC, a new genome-guided assembler for reconstruction of isoforms, which revolutionizes the usage of paired-end and sequencing depth information via phasing and combing paths over a newly designed phasing graph. Tested on both simulated and real datasets, it is to some extent superior to all the salient assemblers of the same kind. Especially, iPAC is significantly powerful in recovery of lowly expressed transcripts while others are not. AVAILABILITY AND IMPLEMENTATION iPAC is freely available at http://sourceforge.net/projects/transassembly/files. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ting Yu
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Juntao Liu
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan 250100, China.,Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
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26
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Karim S, Kumar D, Adamson S, Ennen JR, Qualls CP, Ribeiro JMC. The sialotranscriptome of the gopher-tortoise tick, Amblyomma tuberculatum. Ticks Tick Borne Dis 2020; 12:101560. [PMID: 33007669 DOI: 10.1016/j.ttbdis.2020.101560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/07/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
The gopher tortoise tick, Amblyomma tuberculatum, is known to parasitize keystone ectotherm reptile species. The biological success of ticks requires precise mechanisms to evade host hemostatic and immune responses. Acquisition of a full blood meal requires attachment, establishment of the blood pool, and engorgement of the tick. Tick saliva contains molecules which counter the host responses to allow uninterrupted feeding on the host. RNASeq of the salivary glands of Amblyomma tuberculatum ticks were sequenced resulting in 138,030 pyrosequencing reads which were assembled into 29,991 contigs. A total of 1875 coding sequences were deduced from the transcriptome assembly, including 602 putative secretory and 982 putative housekeeping proteins. The annotated data sets are available as a hyperlinked spreadsheet. The sialotranscriptome assembled for this tick species made available a valuable resource for mining novel pharmacological activities and comparative analysis.
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Affiliation(s)
- Shahid Karim
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Deepak Kumar
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Steve Adamson
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Joshua R Ennen
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Carl P Qualls
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - José M C Ribeiro
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12732 Twinbrook Parkway, Room 3E28, Rockville MD 20852, USA.
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27
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Tirloni L, Lu S, Calvo E, Sabadin G, Di Maggio LS, Suzuki M, Nardone G, da Silva Vaz I Jr, Ribeiro JMC. Integrated analysis of sialotranscriptome and sialoproteome of the brown dog tick Rhipicephalus sanguineus (s.l.): Insights into gene expression during blood feeding. J Proteomics 2020; 229:103899. [PMID: 32673754 DOI: 10.1016/j.jprot.2020.103899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 02/08/2023]
Abstract
Tick salivary glands secrete a complex saliva into their hosts which modulates vertebrate hemostasis, immunity and tissue repair mechanisms. Transcriptomic studies revealed a large number of transcripts coding for structural and secreted protein products in a single tick species. These transcripts are organized in several large families according to their products. Not all transcripts are expressed at the same time, transcription profile switches at intervals, characterizing the phenomenon of "sialome switching". In this work, using transcriptomic and proteomic analysis we explored the sialome of Rhipicephalus sanguineus (s.l.) adult female ticks feeding on a rabbit. The correlations between transcriptional and translational results in the different groups were evaluated, confirming the "sialome switching" and validating the idea that the expression switch may serve as a mechanism of escape from the host immunity. Recombination breakpoints were identified in lipocalin and metalloprotease families, indicating this mechanism could be a possible source of diversity in the tick sialome. Another remarkable observation was the identification of host-derived proteins as a component of tick salivary gland content. These results and disclosed sequences contribute to our understanding of tick feeding biology, to the development of novel anti-tick methods, and to the discovery of novel pharmacologically active products. SIGNIFICANCE: Ticks are a burden by themselves to humans and animals, and vectors of viral, bacterial, protozoal and helminthic diseases. Their saliva has anti-clotting, anti-platelet, vasodilatory and immunomodulatory activities that allows successful feeding and pathogen transmission. Previous transcriptomic studies indicate ticks to have over one thousand transcripts coding for secreted salivary proteins. These transcripts code for proteins of diverse families, but not all are transcribed simultaneously, but rather transiently, in a succession. Here we explored the salivary transcriptome and proteome of the brown dog tick, Rhipicephalus sanguineus. A protein database of over 20 thousand sequences was "de novo" assembled from over 600 million nucleotide reads, from where over two thousand polypeptides were identified by mass spectrometry. The proteomic data was shown to vary in time with the transcription profiles, validating the idea that the expression switch may serve as a mechanism of escape from the host immunity. Analysis of the transcripts coding for lipocalin and metalloproteases indicate their genes to contain signals of breakpoint recombination suggesting a new mechanism responsible for the large diversity in tick salivary proteins. These results and the disclosed sequences contribute to our understanding of the success ticks enjoy as ectoparasites, to the development of novel anti-tick methods, and to the discovery of novel pharmacologically active products.
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Tan J, Wang W, Wu F, Li Y, Fan Q. Transcriptome profiling of venom gland from wasp species: de novo assembly, functional annotation, and discovery of molecular markers. BMC Genomics 2020; 21:427. [PMID: 32580761 PMCID: PMC7315503 DOI: 10.1186/s12864-020-06851-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/18/2020] [Indexed: 01/01/2023] Open
Abstract
Background Vespa velutina, one of the most aggressive and fearful wasps in China, can cause grievous allergies and toxic reactions, leading to organ failure and even death. However, there is little evidence on molecular data regarding wasps. Therefore, we aimed to provide an insight into the transcripts expressed in the venom gland of wasps. Results In our study, high-throughput RNA sequencing was performed using the venom glands of four wasp species. First, the mitochondrial cytochrome C oxidase submit I (COI) barcoding and the neighbor joining (NJ) tree were used to validate the unique identity and lineage of each individual species. After sequencing, a total of 127,630 contigs were generated and 98,716 coding domain sequences (CDS) were predicted from the four species. The Gene ontology (GO) enrichment analysis of unigenes revealed their functional role in important biological processes (BP), molecular functions (MF) and cellular components (CC). In addition, c-type, p1 type, p2 type and p3 type were the most commonly found simple sequence repeat (SSR) types in the four species of wasp transcriptome. There were differences in the distribution of SSRs and single nucleotide polymorphisms (SNPs) among the four wasp species. Conclusions The transcriptome data generated in this study will improve our understanding on bioactive proteins and venom-related genes in wasp venom gland and provide a basis for pests control and other applications. To our knowledge, this is the first study on the identification of large-scale genomic data and the discovery of microsatellite markers from V. tropica ducalis and V. analis fabricius.
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Affiliation(s)
- Junjie Tan
- General Hospital of Western Theater Command, Chengdu, 610021, China.,CDC of Western Theater Command, PLA, Chengdu, 610021, China
| | - Wenbo Wang
- CDC of Western Theater Command, PLA, Chengdu, 610021, China
| | - Fan Wu
- General Hospital of Western Theater Command, Chengdu, 610021, China
| | - Yunming Li
- General Hospital of Western Theater Command, Chengdu, 610021, China
| | - Quanshui Fan
- CDC of Western Theater Command, PLA, Chengdu, 610021, China.
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Jennings EC, Korthauer MW, Hendershot JM, Bailey ST, Weirauch MT, Ribeiro JMC, Benoit JB. Molecular mechanisms underlying milk production and viviparity in the cockroach, Diploptera punctata. Insect Biochem Mol Biol 2020; 120:103333. [PMID: 32119906 PMCID: PMC7293887 DOI: 10.1016/j.ibmb.2020.103333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 05/09/2023]
Abstract
Viviparous reproduction is characterized by maternal retention of developing offspring within the reproductive tract during gestation, culminating in live birth. In some cases, a mother will provide nutrition beyond that present in the yolk; this is known as matrotrophic viviparity. While this phenomenon is best associated with mammals, it is observed in insects such as the viviparous cockroach, Diploptera punctata. Female D. punctata carry developing embryos in the brood sac, a reproductive organ that acts as both a uterus and a placenta by protecting and providing a nutritive secretion to the intrauterine developing progeny. While the basic physiology of D. punctata pregnancy has been characterized, little is known about the molecular mechanisms underlying this phenomenon. This study combined RNA-seq analysis, RNA interference, and other assays to characterize molecular and physiological changes associated with D. punctata reproduction. A comparison of four stages of the female reproductive cycle and males revealed unique gene expression profiles corresponding to each stage and between sexes. Differentially regulated transcripts of interest include the previously identified family of milk proteins and transcripts associated with juvenile hormone metabolism. RNA interference and methoprene application experiments established the potential impacts of bothbreakdown and synthesis reduction of juvenile hormone in maintaining pregnancy in D. punctata. These studies provide the comprehensive molecular mechanisms associated with cockroach viviparity, which will be a critical resource for comparative purposes among viviparity in insect systems.
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Affiliation(s)
- Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Matthew W Korthauer
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Jacob M Hendershot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Jose M C Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, Bethesda, MD, 20892, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
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Freedman AH, Clamp M, Sackton TB. Error, noise and bias in de novo transcriptome assemblies. Mol Ecol Resour 2020; 21:18-29. [PMID: 32180366 DOI: 10.1111/1755-0998.13156] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/25/2020] [Accepted: 03/10/2020] [Indexed: 12/21/2022]
Abstract
De novo transcriptome assembly is a powerful tool, and has been widely used over the last decade for making evolutionary inferences. However, it relies on two implicit assumptions: that the assembled transcriptome is an unbiased representation of the underlying expressed transcriptome, and that expression estimates from the assembly are good, if noisy approximations of the relative abundance of expressed transcripts. Using publicly available data for model organisms, we demonstrate that, across assembly algorithms and data sets, these assumptions are consistently violated. Bias exists at the nucleotide level, with genotyping error rates ranging from 30% to 83%. As a result, diversity is underestimated in transcriptome assemblies, with consistent underestimation of heterozygosity in all but the most inbred samples. Even at the gene level, expression estimates show wide deviations from map-to-reference estimates, and positive bias at lower expression levels. Standard filtering of transcriptome assemblies improves the robustness of gene expression estimates but leads to the loss of a meaningful number of protein-coding genes, including many that are highly expressed. We demonstrate a computational method, length-rescaled CPM, to partly alleviate noise and bias in expression estimates. Researchers should consider ways to minimize the impact of bias in transcriptome assemblies.
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Affiliation(s)
- Adam H Freedman
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, MA, USA
| | - Michele Clamp
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, MA, USA
| | - Timothy B Sackton
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, MA, USA
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Pleasance E, Titmuss E, Williamson L, Kwan H, Culibrk L, Zhao EY, Dixon K, Fan K, Bowlby R, Jones MR, Shen Y, Grewal JK, Ashkani J, Wee K, Grisdale CJ, Thibodeau ML, Bozoky Z, Pearson H, Majounie E, Vira T, Shenwai R, Mungall KL, Chuah E, Davies A, Warren M, Reisle C, Bonakdar M, Taylor GA, Csizmok V, Chan SK, Zong Z, Bilobram S, Muhammadzadeh A, D’Souza D, Corbett RD, MacMillan D, Carreira M, Choo C, Bleile D, Sadeghi S, Zhang W, Wong T, Cheng D, Brown SD, Holt RA, Moore RA, Mungall AJ, Zhao Y, Nelson J, Fok A, Ma Y, Lee MKC, Lavoie JM, Mendis S, Karasinska JM, Deol B, Fisic A, Schaeffer DF, Yip S, Schrader K, Regier DA, Weymann D, Chia S, Gelmon K, Tinker A, Sun S, Lim H, Renouf DJ, Laskin J, Jones SJM, Marra MA. Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. ACTA ACUST UNITED AC 2020; 1:452-468. [DOI: 10.1038/s43018-020-0050-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/05/2020] [Indexed: 02/08/2023]
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Hart CE, Ribeiro JM, Kazimirova M, Thangamani S. Tick-Borne Encephalitis Virus Infection Alters the Sialome of Ixodes ricinus Ticks During the Earliest Stages of Feeding. Front Cell Infect Microbiol 2020; 10:41. [PMID: 32133301 PMCID: PMC7041427 DOI: 10.3389/fcimb.2020.00041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/21/2020] [Indexed: 01/14/2023] Open
Abstract
Ticks are hematophagous arthropods that transmit a number of pathogens while feeding. Among these is tick-borne encephalitis virus (TBEV), a flavivirus transmitted by Ixodes ricinus ticks in the temperate zone of Europe. The infection results in febrile illness progressing to encephalitis and meningitis with a possibility of fatality or long-term neurological sequelae. The composition of tick saliva plays an essential role in the initial virus transmission during tick feeding. Ticks secrete a diverse range of salivary proteins to modulate the host response, such as lipocalins to control the itch and inflammatory response, and both proteases and protease inhibitors to prevent blood coagulation. Here, the effect of viral infection of adult females of Ixodes ricinus was studied with the goal of determining how the virus alters the tick sialome to modulate host tissue response at the site of infection. Uninfected ticks or those infected with TBEV were fed on mice and removed and dissected one- and 3-h post-attachment. RNA from the salivary glands of these ticks, as well as from unfed ticks, was extracted and subjected to next-generation sequencing to determine the expression of key secreted proteins at each timepoint. Genes showing statistically significant up- or down-regulation between infected and control ticks were selected and compared to published literature to ascertain their function. From this, the effect of tick viral infection on the modulation of the tick-host interface was determined. Infected ticks were found to differentially express a number of uncategorized genes, proteases, Kunitz-type serine protease inhibitors, cytotoxins, and lipocalins at different timepoints. These virus-induced changes to the tick sialome may play a significant role in facilitating virus transmission during the early stages of tick feeding.
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Affiliation(s)
- Charles E. Hart
- SUNY Center for Environmental Health and Medicine, SUNY Upstate Medical University, Syracuse, NY, United States,Institute for Global Health and Translational Science, SUNY Upstate Medical University, Syracuse, NY, United States,The Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, United States
| | - Jose M. Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Maria Kazimirova
- Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Saravanan Thangamani
- SUNY Center for Environmental Health and Medicine, SUNY Upstate Medical University, Syracuse, NY, United States,Institute for Global Health and Translational Science, SUNY Upstate Medical University, Syracuse, NY, United States,Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, United States,*Correspondence: Saravanan Thangamani
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Razo-Mendivil FG, Martínez O, Hayano-Kanashiro C. Compacta: a fast contig clustering tool for de novo assembled transcriptomes. BMC Genomics 2020; 21:148. [PMID: 32046653 PMCID: PMC7014741 DOI: 10.1186/s12864-020-6528-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/22/2020] [Indexed: 12/25/2022] Open
Abstract
Background RNA-Seq is the preferred method to explore transcriptomes and to estimate differential gene expression. When an organism has a well-characterized and annotated genome, reads obtained from RNA-Seq experiments can be directly mapped to that genome to estimate the number of transcripts present and relative expression levels of these transcripts. However, for unknown genomes, de novo assembly of RNA-Seq reads must be performed to generate a set of contigs that represents the transcriptome. These contig sets contain multiple transcripts, including immature mRNAs, spliced transcripts and allele variants, as well as products of close paralogs or gene families that can be difficult to distinguish. Thus, tools are needed to select a set of less redundant contigs to represent the transcriptome for downstream analyses. Here we describe the development of Compacta to produce contig sets from de novo assemblies. Results Compacta is a fast and flexible computational tool that allows selection of a representative set of contigs from de novo assemblies. Using a graph-based algorithm, Compacta groups contigs into clusters based on the proportion of shared reads. The user can determine the minimum coverage of the contigs to be clustered, as well as a threshold for the proportion of shared reads in the clustered contigs, thus providing a dynamic range of transcriptome compression that can be adapted according to experimental aims. We compared the performance of Compacta against state of the art clustering algorithms on assemblies from Arabidopsis, mouse and mango, and found that Compacta yielded more rapid results and had competitive precision and recall ratios. We describe and demonstrate a pipeline to tailor Compacta parameters to specific experimental aims. Conclusions Compacta is a fast and flexible algorithm for the determination of optimum contig sets that represent the transcriptome for downstream analyses.
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Affiliation(s)
- Fernando G Razo-Mendivil
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Universidad de Sonora, Hermosillo, Mexico
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigacíon y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Gto, Mexico.
| | - Corina Hayano-Kanashiro
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Universidad de Sonora, Hermosillo, Mexico.
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Pascini TV, Ramalho-Ortigão M, Ribeiro JM, Jacobs-Lorena M, Martins GF. Transcriptional profiling and physiological roles of Aedes aegypti spermathecal-related genes. BMC Genomics 2020; 21:143. [PMID: 32041546 PMCID: PMC7011475 DOI: 10.1186/s12864-020-6543-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Successful mating of female mosquitoes typically occurs once, with the male sperm being stored in the female spermatheca for every subsequent oviposition event. The female spermatheca is responsible for the maintenance, nourishment, and protection of the male sperm against damage during storage. Aedes aegypti is a major vector of arboviruses, including Yellow Fever, Dengue, Chikungunya, and Zika. Vector control is difficult due to this mosquito high reproductive capacity. RESULTS Following comparative RNA-seq analyses of spermathecae obtained from virgin and inseminated females, eight transcripts were selected based on their putative roles in sperm maintenance and survival, including energy metabolism, chitin components, transcriptional regulation, hormonal signaling, enzymatic activity, antimicrobial activity, and ionic homeostasis. In situ RNA hybridization confirmed tissue-specific expression of the eight transcripts. Following RNA interference (RNAi), observed outcomes varied between targeted transcripts, affecting mosquito survival, egg morphology, fecundity, and sperm motility within the spermathecae. CONCLUSIONS This study identified spermatheca-specific transcripts associated with sperm storage in Ae. aegypti. Using RNAi we characterized the role of eight spermathecal transcripts on various aspects of female fecundity and offspring survival. RNAi-induced knockdown of transcript AeSigP-66,427, coding for a Na+/Ca2+ protein exchanger, specifically interfered with egg production and reduced sperm motility. Our results bring new insights into the molecular basis of sperm storage and identify potential targets for Ae. aegypti control.
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Affiliation(s)
- Tales Vicari Pascini
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900 Brazil
| | - Marcelo Ramalho-Ortigão
- Division of Tropical Public Health, Department of Preventive Medicine and Biostatistics, Uniformed Services University, 4301 Jones Bridge Road, Rm A-3083, Bethesda, MD 20814 USA
| | - José Marcos Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway, Rm 2E32D, Rockville, MD 20852 USA
| | - Marcelo Jacobs-Lorena
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
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Reynolds DA, Yoo MJ, Dixson DL, Ross C. Exposure to the Florida red tide dinoflagellate, Karenia brevis, and its associated brevetoxins induces ecophysiological and proteomic alterations in Porites astreoides. PLoS One 2020; 15:e0228414. [PMID: 32032360 PMCID: PMC7006924 DOI: 10.1371/journal.pone.0228414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/14/2020] [Indexed: 01/27/2023] Open
Abstract
As reef-building corals are increasingly being exposed to persistent threats that operate on both regional and global scales, there is a pressing need to better understand the complex processes that diminish coral populations. This study investigated the impacts of the Florida red tide dinoflagellate Karenia brevis and associated brevetoxins on selected facets of coral biology using Porites astreoides as a model system. When provided with choice assays, P. astreoides larvae were shown to actively avoid seawater containing red tide (5×105 cells L-1–7.6×106 cells L-1) or purified brevetoxins (0.018 μg mL-1 brevetoxin-2 and 0.0018 μg mL-1 brevetoxin-3). However, forced exposure to similar treatments induced time-dependent physiological and behavioral changes that were captured by PAM fluorometry and settlement and survival assays, respectively. Adult fragments of P. astreoides exposed to red tide or associated brevetoxins displayed signs of proteomic alterations that were characterized by the use of an iTRAQ-based quantitative proteomic analysis. The novel use of this technique with P. astreoides demonstrated that protein regulation was highly contingent upon biological versus chemical treatment (i.e. live K. brevis vs. solely brevetoxin exposure) and that several broad pathways associated with cell stress were affected including redox homeostasis, protein folding, energy metabolism and reactive oxygen species production. The results herein provide new insight into the ecology, behavior and sublethal stress of reef-building corals in response to K. brevis exposure and underscore the importance of recognizing the potential of red tide to act as a regional stressor to these important foundation species.
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Affiliation(s)
- David A. Reynolds
- Department of Biology, University of North Florida, Jacksonville, Florida, United States of America
| | - Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, United States of America
| | - Danielle L. Dixson
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, United States of America
| | - Cliff Ross
- Department of Biology, University of North Florida, Jacksonville, Florida, United States of America
- * E-mail:
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Abstract
Transcriptome assembly plays a critical role in studying biological properties and
examining the expression levels of genomes in specific cells. It is also the basis of many
downstream analyses. With the increase of speed and the decrease in cost, massive sequencing
data continues to accumulate. A large number of assembly strategies based on different
computational methods and experiments have been developed. How to efficiently perform
transcriptome assembly with high sensitivity and accuracy becomes a key issue. In this work, the
issues with transcriptome assembly are explored based on different sequencing technologies.
Specifically, transcriptome assemblies with next-generation sequencing reads are divided into
reference-based assemblies and de novo assemblies. The examples of different species are used to
illustrate that long reads produced by the third-generation sequencing technologies can cover fulllength
transcripts without assemblies. In addition, different transcriptome assemblies using the
Hybrid-seq methods and other tools are also summarized. Finally, we discuss the future directions
of transcriptome assemblies.
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Affiliation(s)
- Yuwen Luo
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Xingyu Liao
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Fang-Xiang Wu
- Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan, Canada
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, China
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Majounie E, Wee K, Williamson LM, Jones MR, Pleasance E, Lim HJ, Ho C, Renouf DJ, Yip S, Jones SJM, Marra MA, Laskin J. Fluorouracil sensitivity in a head and neck squamous cell carcinoma with a somatic DPYD structural variant. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004713. [PMID: 31871216 PMCID: PMC6996515 DOI: 10.1101/mcs.a004713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide and represents a heterogeneous group of tumors, the majority of which are treated with a combination of surgery, radiation, and chemotherapy. Fluoropyrimidine (5-FU) and its oral prodrug, capecitabine, are commonly prescribed treatments for several solid tumor types including HNSCC. 5-FU-associated toxicity is observed in ∼30% of treated patients and is largely caused by germline polymorphisms in DPYD, which encodes dihydropyrimidine dehydrogenase, a key enzyme of 5-FU catabolism and deactivation. Although the association of germline DPYD alterations with toxicity is well-described, the potential contribution of somatic DPYD alterations to 5-FU sensitivity has not been explored. In a patient with metastatic HNSCC, in-depth genomic and transcriptomic integrative analysis on a biopsy from a metastatic neck lesion revealed alterations in genes that are associated with 5-FU uptake and metabolism. These included a novel somatic structural variant resulting in a partial deletion affecting DPYD, a variant of unknown significance affecting SLC29A1, and homozygous deletion of MTAP. There was no evidence of deleterious germline polymorphisms that have been associated with 5-FU toxicity, indicating a potential vulnerability of the tumor to 5-FU therapy. The discovery of the novel DPYD variant led to the initiation of 5-FU treatment that resulted in a rapid response lasting 17 wk, with subsequent relapse due to unknown resistance mechanisms. This suggests that somatic alterations present in this tumor may serve as markers for tumor sensitivity to 5-FU, aiding in the selection of personalized treatment strategies.
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Affiliation(s)
- Elisa Majounie
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Cheryl Ho
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, British Columbia V5A 1S6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
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Dhar R, Seethy A, Pethusamy K, Singh S, Rohil V, Purkayastha K, Mukherjee I, Goswami S, Singh R, Raj A, Srivastava T, Acharya S, Rajashekhar B, Karmakar S. De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing. Gigascience 2019; 8:5488106. [PMID: 31077316 PMCID: PMC6511069 DOI: 10.1093/gigascience/giz038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 09/30/2018] [Accepted: 03/18/2019] [Indexed: 01/23/2023] Open
Abstract
Background The Indian peafowl (Pavo cristanus) is native to South Asia and is the national bird of India. Here we present a draft genome sequence of the male blue peacock using Illumina and Oxford Nanopore technology (ONT). Results ONT sequencing gave ∼2.3-fold sequencing coverage, whereas Illumina generated 150–base pair paired-end sequence data at 284.6-fold coverage from 5 libraries. Subsequently, we generated a 0.915-gigabase pair de novo assembly of the peacock genome with a scaffold N50 of 0.23 megabase pairs (Mb). We predict that the peacock genome contains 23,153 protein-coding genes and 75.3 Mb (7.33%) of repetitive sequences. Conclusions We report a high-quality assembly of the peacock genome using a hybrid approach of sequences generated by both Illumina and ONT. The long-read chemistry generated by ONT was useful for addressing challenges related to de novo assembly, particularly at regions containing repetitive sequences spanning longer than the read length, and which could not be resolved with only short-read–based assembly. Contig assembly of Illumina short reads gave an N50 of 1,639 bases, whereas with ONT, the N50 increased by >9-fold to 14,749 bases. The initial contig assembly based on Illumina sequencing reads alone gave 685,241 contigs. Further scaffolding on assembled contigs using both Illumina and ONT sequencing reads resulted in a final assembly of 15,025 super-scaffolds, with an N50 of ∼0.23 Mb. Ninety-five percent of proteins predicted by homology matched with those in a public repository, verifying the completeness of our assembly. Like other phylogenetic studies of avian conserved genes, we found P. cristatus to be most closely related to Gallus gallus, followed by Meleagris gallopavo and Anas platyrhynchos. Compared with the recently published peacock genome assembly, the current, superior, hybrid assembly has greater sequencing depth, fewer non-ATGC sequences, and fewer scaffolds.
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Affiliation(s)
- Ruby Dhar
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ashikh Seethy
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sunil Singh
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Vishwajeet Rohil
- Vallabhbhai Patel Chest Institute (VPCI), Delhi University, New Delhi 110007, India
| | - Kakali Purkayastha
- Vallabhbhai Patel Chest Institute (VPCI), Delhi University, New Delhi 110007, India
| | - Indrani Mukherjee
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sandeep Goswami
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Rakesh Singh
- Kanpur Zoo, Hastings Ave, Azad Nagar, Nawabganj, Kanpur, Uttar Pradesh 208002, India
| | - Ankita Raj
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Tryambak Srivastava
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sovon Acharya
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Balaji Rajashekhar
- Institute of Computer Science, University of Tartu, J. Liivi, Tartu 50409, Estonia.,Celixa, 19/1 Sankey Road, Bangalore 560020, India
| | - Subhradip Karmakar
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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Caicedo-Montoya C, Pinilla L, Toro LF, Yepes-García J, Ríos-Estepa R. Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study. High Throughput 2019; 8:E20. [PMID: 31801255 DOI: 10.3390/ht8040020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 12/15/2022] Open
Abstract
The performance of software tools for de novo transcriptome assembly greatly depends on the selection of software parameters. Up to now, the development of de novo transcriptome assembly for prokaryotes has not been as remarkable as that for eukaryotes. In this contribution, Rockhopper2 was used to perform a comparative transcriptome analysis of Streptomyces clavuligerus exposed to diverse environmental conditions. The study focused on assessing the incidence of software parameters on software performance for the identification of differentially expressed genes as a final goal. For this, a statistical optimization was performed using the Transrate Assembly Score (TAS). TAS was also used for evaluating the software performance and for comparing it with related tools, e.g., Trinity. Transcriptome redundancy and completeness were also considered for this analysis. Rockhopper2 and Trinity reached a TAS value of 0.55092 and 0.58337, respectively. Trinity assembles transcriptomes with high redundancy, with 55.6% of transcripts having some duplicates. Additionally, we observed that the total number of differentially expressed genes (DEG) and their annotation greatly depends on the method used for removing redundancy and the tools used for transcript quantification. To our knowledge, this is the first work aimed at assessing de novo assembly software for prokaryotic organisms.
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Shen Y, Grisdale CJ, Islam SA, Bose P, Lever J, Zhao EY, Grinshtein N, Ma Y, Mungall AJ, Moore RA, Lun X, Senger DL, Robbins SM, Wang AY, MacIsaac JL, Kobor MS, Luchman HA, Weiss S, Chan JA, Blough MD, Kaplan DR, Cairncross JG, Marra MA, Jones SJM. Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments. Proc Natl Acad Sci U S A 2019; 116:19098-108. [PMID: 31471491 DOI: 10.1073/pnas.1813495116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most deadly brain tumor, and currently lacks effective treatment options. Brain tumor-initiating cells (BTICs) and orthotopic xenografts are widely used in investigating GBM biology and new therapies for this aggressive disease. However, the genomic characteristics and molecular resemblance of these models to GBM tumors remain undetermined. We used massively parallel sequencing technology to decode the genomes and transcriptomes of BTICs and xenografts and their matched tumors in order to delineate the potential impacts of the distinct growth environments. Using data generated from whole-genome sequencing of 201 samples and RNA sequencing of 118 samples, we show that BTICs and xenografts resemble their parental tumor at the genomic level but differ at the mRNA expression and epigenomic levels, likely due to the different growth environment for each sample type. These findings suggest that a comprehensive genomic understanding of in vitro and in vivo GBM model systems is crucial for interpreting data from drug screens, and can help control for biases introduced by cell-culture conditions and the microenvironment in mouse models. We also found that lack of MGMT expression in pretreated GBM is linked to hypermutation, which in turn contributes to increased genomic heterogeneity and requires new strategies for GBM treatment.
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Ribeiro JM, Debat HJ, Boiani M, Ures X, Rocha S, Breijo M. An insight into the sialome, mialome and virome of the horn fly, Haematobia irritans. BMC Genomics 2019; 20:616. [PMID: 31357943 PMCID: PMC6664567 DOI: 10.1186/s12864-019-5984-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/19/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The horn fly (Haematobia irritans) is an obligate blood feeder that causes considerable economic losses in livestock industries worldwide. The control of this cattle pest is mainly based on insecticides; unfortunately, in many regions, horn flies have developed resistance. Vaccines or biological control have been proposed as alternative control methods, but the available information about the biology or physiology of this parasite is rather scarce. RESULTS We present a comprehensive description of the salivary and midgut transcriptomes of the horn fly (Haematobia irritans), using deep sequencing achieved by the Illumina protocol, as well as exploring the virome of this fly. Comparison of the two transcriptomes allow for identification of uniquely salivary or uniquely midgut transcripts, as identified by statistically differential transcript expression at a level of 16 x or more. In addition, we provide genomic highlights and phylogenetic insights of Haematobia irritans Nora virus and present evidence of a novel densovirus, both associated to midgut libraries of H. irritans. CONCLUSIONS We provide a catalog of protein sequences associated with the salivary glands and midgut of the horn fly that will be useful for vaccine design. Additionally, we discover two midgut-associated viruses that infect these flies in nature. Future studies should address the prevalence, biological effects and life cycles of these viruses, which could eventually lead to translational work oriented to the control of this economically important cattle pest.
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Affiliation(s)
- J. M. Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, 12735 Twinbrook Parkway Room 3E28, Rockville, MD 20852 USA
| | - Humberto Julio Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - M. Boiani
- Unidad de Reactivos y Biomodelos de Experimentación, Facultad de Medicina, Universidad de la República, Gral. Flores, 2125 Montevideo, Uruguay
| | - X. Ures
- Unidad de Reactivos y Biomodelos de Experimentación, Facultad de Medicina, Universidad de la República, Gral. Flores, 2125 Montevideo, Uruguay
| | - S. Rocha
- Unidad de Reactivos y Biomodelos de Experimentación, Facultad de Medicina, Universidad de la República, Gral. Flores, 2125 Montevideo, Uruguay
| | - M. Breijo
- Unidad de Reactivos y Biomodelos de Experimentación, Facultad de Medicina, Universidad de la República, Gral. Flores, 2125 Montevideo, Uruguay
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Abstract
Large-scale genomics demands computational methods that scale sublinearly with the growth of data. We review several data structures and sketching techniques that have been used in genomic analysis methods. Specifically, we focus on four key ideas that take different approaches to achieve sublinear space usage and processing time: compressed full-text indices, approximate membership query data structures, locality-sensitive hashing, and minimizers schemes. We describe these techniques at a high level and give several representative applications of each.
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Affiliation(s)
- Guillaume Marçais
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA;,
| | - Brad Solomon
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rob Patro
- Department of Computer Science, Stony Brook University, Stony Brook, New York 11794, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA;,
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Magi A, Semeraro R, Mingrino A, Giusti B, D'Aurizio R. Nanopore sequencing data analysis: state of the art, applications and challenges. Brief Bioinform 2019. [PMID: 28637243 DOI: 10.1093/bib/bbx062] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data. Despite the short period of time from the release of the MinION, a large number of algorithms and tools have been developed for base calling, data handling, read mapping, de novo assembly and variant discovery. Here, we face the main computational challenges related to the analysis of nanopore data, and we carry out a comprehensive and up-to-date survey of the algorithmic solutions adopted by the bioinformatic community comparing performance and reporting limits and advantages of using this new generation of sequences for genomic analyses. Our analyses demonstrate that the use of nanopore data dramatically improves the de novo assembly of genomes and allows for the exploration of structural variants with an unprecedented accuracy and resolution. However, despite the impressive improvements reached by ONT in the past 2 years, the use of these data for small-variant calling is still challenging, and at present, it needs to be coupled with complementary short sequences for mitigating the intrinsic biases of nanopore sequencing technology.
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Affiliation(s)
- Alberto Magi
- Department of Statistics, National Cheng Kung University in Taiwan
| | - Roberto Semeraro
- Department of Molecular Physiology and Biophysics, Vanderbilt University, USA
| | | | - Betti Giusti
- Department of Biostatistics, Vanderbilt University, USA
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Kong J, Huh S, Won JI, Yoon J, Kim B, Kim K. GAAP: A Genome Assembly + Annotation Pipeline. Biomed Res Int 2019; 2019:4767354. [PMID: 31346518 DOI: 10.1155/2019/4767354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 12/24/2022]
Abstract
Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method.
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Fu S, Chang PL, Friesen ML, Teakle NL, Tarone AM, Sze SH. Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus. BMC Genomics 2019; 20:425. [PMID: 31167652 PMCID: PMC6551239 DOI: 10.1186/s12864-019-5702-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background A popular strategy to study alternative splicing in non-model organisms starts from sequencing the entire transcriptome, then assembling the reads by using de novo transcriptome assembly algorithms to obtain predicted transcripts. A similarity search algorithm is then applied to a related organism to infer possible function of these predicted transcripts. While some of these predictions may be inaccurate and transcripts with low coverage are often missed, we observe that it is possible to obtain a more complete set of transcripts to facilitate possible functional assignments by starting the search from the intermediate de Bruijn graph that contains all branching possibilities. Results We develop an algorithm to extract similar transcripts in a related organism by starting the search from the de Bruijn graph that represents the transcriptome instead of from predicted transcripts. We show that our algorithm is able to recover more similar transcripts than existing algorithms, with large improvements in obtaining longer transcripts and a finer resolution of isoforms. We apply our algorithm to study salt and waterlogging tolerance in two Melilotus species by constructing new RNA-Seq libraries. Conclusions We have developed an algorithm to identify paths in the de Bruijn graph that correspond to similar transcripts in a related organism directly. Our strategy bypasses the transcript prediction step in RNA-Seq data and makes use of support from evolutionary information. Electronic supplementary material The online version of this article (10.1186/s12864-019-5702-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuhua Fu
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, 77843, TX, USA
| | - Peter L Chang
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, 90089, CA, USA
| | - Maren L Friesen
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, 90089, CA, USA.,Department of Crop and Soil Sciences, Washington State University, Pullman, 99164, WA, USA.,Department of Plant Pathology, Washington State University, Pullman, 99164, WA, USA
| | - Natasha L Teakle
- Centre for Ecohydrology, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia.,School of Plant Biology (M084), Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | - Aaron M Tarone
- Department of Entomology, Texas A&M University, College Station, 77843, TX, USA
| | - Sing-Hoi Sze
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, 77843, TX, USA. .,Department of Computer Science and Engineering, Texas A&M University, College Station, 77843, TX, USA.
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Williamson LM, Steel M, Grewal JK, Thibodeau ML, Zhao EY, Loree JM, Yang KC, Gorski SM, Mungall AJ, Mungall KL, Moore RA, Marra MA, Laskin J, Renouf DJ, Schaeffer DF, Jones SJM. Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor. Cold Spring Harb Mol Case Stud 2019; 5:a003814. [PMID: 31160355 DOI: 10.1101/mcs.a003814] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/06/2019] [Indexed: 01/05/2023] Open
Abstract
Pancreatic neuroendocrine neoplasms (PanNENs) represent a minority of pancreatic neoplasms that exhibit variability in prognosis. Ongoing mutational analyses of PanNENs have found recurrent abnormalities in chromatin remodeling genes (e.g., DAXX and ATRX), and mTOR pathway genes (e.g., TSC2, PTEN PIK3CA, and MEN1), some of which have relevance to patients with related familial syndromes. Most recently, grade 3 PanNENs have been divided into two groups based on differentiation, creating a new group of well-differentiated grade 3 neuroendocrine tumors (PanNETs) that have had a limited whole-genome level characterization to date. In a patient with a metastatic well-differentiated grade 3 PanNET, our study utilized whole-genome sequencing of liver metastases for the comparative analysis and detection of single-nucleotide variants, insertions and deletions, structural variants, and copy-number variants, with their biologic relevance confirmed by RNA sequencing. We found that this tumor most notably exhibited a TSC1-disrupting fusion, showed a novel CHD7–BEND2 fusion, and lacked any somatic variants in ATRX, DAXX, and MEN1.
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Araujo RN, Silva NCS, Mendes-Sousa A, Paim R, Costa GCA, Dias LR, Oliveira K, Sant'Anna MRV, Gontijo NF, Pereira MH, Pessoa GD, Valenzuela JG, Koerich LB, Oliveira F. RNA-seq analysis of the salivary glands and midgut of the Argasid tick Ornithodoros rostratus. Sci Rep 2019; 9:6764. [PMID: 31043627 DOI: 10.1038/s41598-019-42899-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/21/2019] [Indexed: 01/28/2023] Open
Abstract
Ornithodoros rostratus is a South American argasid tick which importance relies on its itchy bite and potential as disease vector. They feed on a wide variety of hosts and secrete different molecules in their saliva and intestinal content that counteract host defences and help to accommodate and metabolize the relatively large quantity of blood upon feeding. The present work describes the transcriptome profile of salivary gland (SG) and midgut (MG) of O. rostratus using Illumina sequencing. A total of 8,031 contigs were assembled and assigned to different functional classes. Secreted proteins were the most abundant in the SG and accounted for ~67% of all expressed transcripts with contigs with identity to lipocalins and acid tail proteins being the most representative. On the other hand, immunity genes were upregulated in MG with a predominance of defensins and lysozymes. Only 10 transcripts in SG and 8 in MG represented ~30% of all RNA expressed in each tissue and one single contig (the acid tail protein ORN-9707) represented ~7% of all expressed contigs in SG. Results highlight the functional difference of each organ and identified the most expressed classes and contigs of O. rostratus SG and MG.
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Scarpassa VM, Debat HJ, Alencar RB, Saraiva JF, Calvo E, Arcà B, Ribeiro JMC. An insight into the sialotranscriptome and virome of Amazonian anophelines. BMC Genomics 2019; 20:166. [PMID: 30832587 PMCID: PMC6399984 DOI: 10.1186/s12864-019-5545-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/18/2019] [Indexed: 01/17/2023] Open
Abstract
Background Saliva of mosquitoes contains anti-platelet, anti-clotting, vasodilatory, anti-complement and anti-inflammatory substances that help the blood feeding process. The salivary polypeptides are at a fast pace of evolution possibly due to their relative lack of structural constraint and possibly also by positive selection on their genes leading to evasion of host immune pressure. Results In this study, we used deep mRNA sequence to uncover for the first time the sialomes of four Amazonian anophelines species (Anopheles braziliensis, A. marajorara, A. nuneztovari and A. triannulatus) and extend the knowledge of the A. darlingi sialome. Two libraries were generated from A. darlingi mosquitoes, sampled from two localities separated ~ 1100 km apart. A total of 60,016 sequences were submitted to GenBank, which will help discovery of novel pharmacologically active polypeptides and the design of specific immunological markers of mosquito exposure. Additionally, in these analyses we identified and characterized novel phasmaviruses and anpheviruses associated to the sialomes of A. triannulatus, A. marajorara and A. darlingi species. Conclusions Besides their pharmacological properties, which may be exploited for the development of new drugs (e.g. anti-thrombotics), salivary proteins of blood feeding arthropods may be turned into tools to prevent and/or better control vector borne diseases; for example, through the development of vaccines or biomarkers to evaluate human exposure to vector bites. The sialotranscriptome study reported here provided novel data on four New World anopheline species and allowed to extend our knowledge on the salivary repertoire of A. darlingi. Additionally, we discovered novel viruses following analysis of the transcriptomes, a procedure that should become standard within future RNAseq studies. Electronic supplementary material The online version of this article (10.1186/s12864-019-5545-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vera Margarete Scarpassa
- Laboratório de Genética de Populações e Evolução de Mosquitos Vetores de Malária e Dengue, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Humbeto Julio Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Ronildo Baiatone Alencar
- Laboratório de Genética de Populações e Evolução de Mosquitos Vetores de Malária e Dengue, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - José Ferreira Saraiva
- Laboratório de Genética de Populações e Evolução de Mosquitos Vetores de Malária e Dengue, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Eric Calvo
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Bruno Arcà
- Department of Public Health and Infectious Diseases, Division of Parasitology, Sapienza University of Rome, Rome, Italy
| | - José M C Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
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Abstract
BACKGROUND Tree species in the genus Cedrela P. Browne are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several 'omic resources including a leaf transcriptome, organelle genome (cpDNA), and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin and enable future research on this widespread Neotropical tree genus. RESULTS We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaf tissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptome for C. odorata, and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript models successfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probes worked effectively for five Cedrela species, with each species showing similar mean on-target sequence yield and depth. The probes showed greater enrichment efficiency for Cedrela species relative to the other three distantly related Meliaceae species. We provide a set of candidate SNPs for species identification of four of the Cedrela species included in this analysis, and present draft chloroplast genomes for multiple individuals of eight species from four genera in the Meliaceae. CONCLUSIONS Deforestation and illegal logging threaten forest biodiversity globally, and wood screening tools offer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources described here provide the foundation required to develop genetic screening methods for Cedrela species identification and source validation. Due to their transferability across the genus and family as well as demonstrated applicability for both fresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studies examining the ecology and evolutionary history of Cedrela and related species in the Meliaceae.
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Affiliation(s)
- Kristen N. Finch
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - F. Andrew Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Richard C. Cronn
- USDA Forest Service Pacific Northwest Research Station, Corvallis, Oregon 97331 USA
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Bourret TJ, Boyle WK, Zalud AK, Valenzuela JG, Oliveira F, Lopez JE. The relapsing fever spirochete Borrelia turicatae persists in the highly oxidative environment of its soft-bodied tick vector. Cell Microbiol 2019; 21:e12987. [PMID: 30489694 PMCID: PMC6454574 DOI: 10.1111/cmi.12987] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 12/17/2022]
Abstract
The relapsing fever spirochete Borrelia turicatae possesses a complex life cycle in its soft-bodied tick vector, Ornithodoros turicata. Spirochetes enter the tick midgut during a blood meal, and, during the following weeks, spirochetes disseminate throughout O. turicata. A population persists in the salivary glands allowing for rapid transmission to the mammalian hosts during tick feeding. Little is known about the physiological environment within the salivary glands acini in which B. turicatae persists. In this study, we examined the salivary gland transcriptome of O. turicata ticks and detected the expression of 57 genes involved in oxidant metabolism or antioxidant defences. We confirmed the expression of five of the most highly expressed genes, including glutathione peroxidase (gpx), thioredoxin peroxidase (tpx), manganese superoxide dismutase (sod-1), copper-zinc superoxide dismutase (sod-2), and catalase (cat) by reverse-transcriptase droplet digital polymerase chain reaction (RT-ddPCR). We also found distinct differences in the expression of these genes when comparing the salivary glands and midguts of unfed O. turicata ticks. Our results indicate that the salivary glands of unfed O. turicata nymphs are highly oxidative environments where reactive oxygen species (ROS) predominate, whereas midgut tissues comprise a primarily nitrosative environment where nitric oxide synthase is highly expressed. Additionally, B. turicatae was found to be hyperresistant to ROS compared with the Lyme disease spirochete Borrelia burgdorferi, suggesting it is uniquely adapted to the highly oxidative environment of O. turicata salivary gland acini.
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Affiliation(s)
- Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska
| | - William K Boyle
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska
| | - Amanda K Zalud
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska
| | - Jesus G Valenzuela
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Fabiano Oliveira
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Job E Lopez
- Departments of Pediatrics and Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
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