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Johnson CJ, Zhang Z, Zhang H, Shang R, Piekarz KM, Bi P, Stolfi A. A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates. Development 2024; 151:dev202968. [PMID: 39114943 PMCID: PMC11441980 DOI: 10.1242/dev.202968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/25/2024] [Indexed: 08/16/2024]
Abstract
Vertebrates and tunicates are sister groups that share a common fusogenic factor, Myomaker (Mymk), that drives myoblast fusion and muscle multinucleation. Yet they are divergent in when and where they express Mymk. In vertebrates, all developing skeletal muscles express Mymk and are obligately multinucleated. In tunicates, Mymk is expressed only in post-metamorphic multinucleated muscles, but is absent from mononucleated larval muscles. In this study, we demonstrate that cis-regulatory sequence differences in the promoter region of Mymk underlie the different spatiotemporal patterns of its transcriptional activation in tunicates and vertebrates. Although in vertebrates myogenic regulatory factors (MRFs) such as MyoD1 alone are required and sufficient for Mymk transcription in all skeletal muscles, we show that transcription of Mymk in post-metamorphic muscles of the tunicate Ciona requires the combinatorial activity of MRF, MyoD and Early B-cell Factor (Ebf). This macroevolutionary difference appears to be encoded in cis, likely due to the presence of a putative Ebf-binding site adjacent to predicted MRF binding sites in the Ciona Mymk promoter. We further discuss how Mymk and myoblast fusion might have been regulated in the last common ancestor of tunicates and vertebrates, for which we propose two models.
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Affiliation(s)
| | - Zheng Zhang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA
| | - Haifeng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA
| | - Renjie Shang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna M. Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pengpeng Bi
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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2
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Johnson CJ, Zhang Z, Zhang H, Shang R, Piekarz KM, Bi P, Stolfi A. A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583753. [PMID: 38559144 PMCID: PMC10979880 DOI: 10.1101/2024.03.06.583753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Vertebrates and tunicates are sister groups that share a common fusogenic factor, Myomaker (Mymk), that drives myoblast fusion and muscle multinucleation. Yet they are divergent in when and where they express Mymk. In vertebrates, all developing skeletal muscles express Mymk and are obligately multinucleated. In tunicates, Mymk is only expressed in post-metamorphic multinucleated muscles, but is absent from mononucleated larval muscles. In this study, we demonstrate that cis-regulatory sequence differences in the promoter region of Mymk underlie the different spatiotemporal patterns of its transcriptional activation in tunicates and vertebrates. While in vertebrates Myogenic Regulatory Factors (MRFs) like MyoD1 alone are required and sufficient for Mymk transcription in all skeletal muscles, we show that transcription of Mymk in post-metamorphic muscles of the tunicate Ciona requires the combinatorial activity of MRF/MyoD and Early B-Cell Factor (Ebf). This macroevolutionary difference appears to be encoded in cis, likely due to the presence of a putative Ebf binding site adjacent to predicted MRF binding sites in the Ciona Mymk promoter. We further discuss how Mymk and myoblast fusion might have been regulated in the last common ancestor of tunicates and vertebrates, for which we propose two models.
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Affiliation(s)
| | - Zheng Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Haifeng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Renjie Shang
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pengpeng Bi
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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3
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Puritz JB, Guo X, Hare M, He Y, Hillier LW, Jin S, Liu M, Lotterhos KE, Minx P, Modak T, Proestou D, Rice ES, Tomlinson C, Warren WC, Witkop E, Zhao H, Gomez-Chiarri M. A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference. Mol Ecol Resour 2024; 24:e13801. [PMID: 37186213 DOI: 10.1111/1755-0998.13801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.
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Affiliation(s)
- Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Matthew Hare
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Yan He
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Shubo Jin
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Ming Liu
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - Pat Minx
- Donald Danforth Plant Science Center, Olivette, Missouri, USA
| | - Tejashree Modak
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Dina Proestou
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, Kingston, Rhode Island, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA
| | - Wesley C Warren
- Departments of Animal Sciences and Surgery, Institute of Informatics and Data Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Erin Witkop
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Honggang Zhao
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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4
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Tobias Z, Solow A, Tepolt C. Geography and developmental plasticity shape post-larval thermal tolerance in the golden star tunicate, Botryllus schlosseri. J Therm Biol 2024; 119:103763. [PMID: 38071896 DOI: 10.1016/j.jtherbio.2023.103763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 11/19/2023] [Indexed: 02/25/2024]
Abstract
Local adaptation and phenotypic plasticity play key roles in mediating organisms' ability to respond to spatiotemporal variation in temperature. These two processes often act together to generate latitudinal or elevational clines in acute temperature tolerance. Phenotypic plasticity is also subject to local adaptation, with the expectation that populations inhabiting more variable environments should exhibit greater phenotypic plasticity of thermal tolerance. Here we examine the potential for local adaptation and developmental plasticity of thermal tolerance in the widespread invasive tunicate Botryllus schlosseri. By comparing five populations across a thermal gradient spanning 4.4° of latitude in the northwest Atlantic, we demonstrate that warmer populations south of the Gulf of Maine exhibit significantly increased (∼0.2 °C) post-larval temperature tolerance relative to the colder populations within it. We also show that B. schlosseri post-larvae possess a high degree of developmental plasticity for this trait, shifting their median temperature of survival (LT50) upwards by as much as 0.18 °C per 1 °C increase in environmental temperature. Lastly, we found that populations vary in their degrees of developmental plasticity, with populations that experience more pronounced short-term temperature variability exhibiting greater developmental plasticity, suggesting the local adaptation of developmental plasticity. By comparing the thermal tolerance of populations across space and through time, we demonstrate how geography and developmental plasticity have shaped thermal tolerance in B. schlosseri. These results help inform our understanding of how species are able to adjust their thermal physiology in new environments, including those encountered during invasion and under increasingly novel climate conditions.
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Affiliation(s)
- Zachary Tobias
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA; Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Andrew Solow
- Marine Policy Center, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Carolyn Tepolt
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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Gryganskyi AP, Golan J, Muszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith ME, Reynolds N, James TY, Grigoriev IV, Spatafora JW, Stajich JE. Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms 2023; 11:1830. [PMID: 37513002 PMCID: PMC10386755 DOI: 10.3390/microorganisms11071830] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.
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Affiliation(s)
- Andrii P. Gryganskyi
- Division of Biological & Nanoscale Technologies, UES, Inc., Dayton, OH 45432, USA
| | - Jacob Golan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Anna Muszewska
- Institute of Biochemistry & Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Somayeh Dolatabadi
- Biology Department, Hakim Sabzevari University, Sabzevar 96179-76487, Iran;
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
| | - Vira B. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | - Volodymyr O. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | | | - Iryna M. Anishchenko
- MG Kholodny Institute of Botany, National Academy of Sciences, 01030 Kyiv, Ukraine;
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological & Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland;
| | - Ngoc Vinh Tran
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Ingo Ebersberger
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Ying Chang
- Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore;
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Joseph Heitman
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, NC 27708, USA;
| | - Gregory Bonito
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA;
| | - Gerald L. Benny
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Matthew E. Smith
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Nicole Reynolds
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Joseph W. Spatafora
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 93106, USA;
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6
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Ko BJ, Lee C, Kim J, Rhie A, Yoo DA, Howe K, Wood J, Cho S, Brown S, Formenti G, Jarvis ED, Kim H. Widespread false gene gains caused by duplication errors in genome assemblies. Genome Biol 2022; 23:205. [PMID: 36167596 PMCID: PMC9516828 DOI: 10.1186/s13059-022-02764-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/02/2022] [Indexed: 12/22/2022] Open
Abstract
Background False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Anna’s Hummingbird, and their new counterparts of the same species generated by the Vertebrate Genomes Project, of which the Vertebrate Genomes Project pipeline attempted to eliminate false duplications through haplotype phasing and purging. These assemblies are among the first generated by the Vertebrate Genomes Project where there was a prior chromosomal level reference assembly to compare with. Results Whole genome alignments revealed that 4 to 16% of the sequences are falsely duplicated in the previous assemblies, impacting hundreds to thousands of genes. These lead to overestimated gene family expansions. The main source of the false duplications is heterotype duplications, where the haplotype sequences were relatively more divergent than other parts of the genome leading the assembly algorithms to classify them as separate genes or genomic regions. A minor source is sequencing errors. Ancient ATP nucleotide binding gene families have a higher prevalence of false duplications compared to other gene families. Although present in a smaller proportion, we observe false duplications remaining in the Vertebrate Genomes Project assemblies that can be identified and purged. Conclusions This study highlights the need for more advanced assembly methods that better separate haplotypes and sequence errors, and the need for cautious analyses on gene gains. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02764-1.
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Affiliation(s)
- Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Dong Ahn Yoo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | | | | | - Seoae Cho
- eGnome, Inc, Seoul, Republic of Korea
| | - Samara Brown
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Giulio Formenti
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,eGnome, Inc, Seoul, Republic of Korea.
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7
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Stahlke AR, Bitume EV, Özsoy ZA, Bean DW, Veillet A, Clark MI, Clark EI, Moran P, Hufbauer RA, Hohenlohe PA. Hybridization and range expansion in tamarisk beetles ( Diorhabda spp.) introduced to North America for classical biological control. Evol Appl 2022; 15:60-77. [PMID: 35126648 PMCID: PMC8792477 DOI: 10.1111/eva.13325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/31/2023] Open
Abstract
With the global rise of human-mediated translocations and invasions, it is critical to understand the genomic consequences of hybridization and mechanisms of range expansion. Conventional wisdom is that high genetic drift and loss of genetic diversity due to repeated founder effects will constrain introduced species. However, reduced genetic variation can be countered by behavioral aspects and admixture with other distinct populations. As planned invasions, classical biological control (biocontrol) agents present important opportunities to understand the mechanisms of establishment and spread in a novel environment. The ability of biocontrol agents to spread and adapt, and their effects on local ecosystems, depends on genomic variation and the consequences of admixture in novel environments. Here, we use a biocontrol system to examine the genome-wide outcomes of introduction, spread, and hybridization in four cryptic species of a biocontrol agent, the tamarisk beetle (Diorhabda carinata, D. carinulata, D. elongata, and D. sublineata), introduced from six localities across Eurasia to control the invasive shrub tamarisk (Tamarix spp.) in western North America. We assembled a de novo draft reference genome and applied RADseq to over 500 individuals across laboratory cultures, the native ranges, and the introduced range. Despite evidence of a substantial genetic bottleneck among D. carinulata in N. America, populations continue to establish and spread, possibly due to aggregation behavior. We found that D. carinata, D. elongata, and D. sublineata hybridize in the field to varying extents, with D. carinata × D. sublineata hybrids being the most abundant. Genetic diversity was greater at sites with hybrids, highlighting potential for increased ability to adapt and expand. Our results demonstrate the complex patterns of genomic variation that can result from introduction of multiple ecotypes or species for biocontrol, and the importance of understanding them to predict and manage the effects of biocontrol agents in novel ecosystems.
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Affiliation(s)
- Amanda R. Stahlke
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS)Beltsville Agricultural Research Center, Bee Research LaboratoryBeltsvilleMarylandUSA
| | - Ellyn V. Bitume
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS), Invasive Species and Pollinator Health Research UnitAlbanyCaliforniaUSA
- U.S. Department of Agriculture, Forest Service (USDA‐FS), Pacific Southwest, Institute of Pacific Islands ForestryHiloHawaiiUSA
| | - Zeynep A. Özsoy
- Department of Biological SciencesColorado Mesa UniversityGrand JunctionColoradoUSA
| | - Dan W. Bean
- Colorado Department of AgriculturePalisadeColoradoUSA
| | - Anne Veillet
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
| | - Meaghan I. Clark
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eliza I. Clark
- Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Patrick Moran
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS), Invasive Species and Pollinator Health Research UnitAlbanyCaliforniaUSA
| | - Ruth A. Hufbauer
- Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Paul A. Hohenlohe
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
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8
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Ballarin L, Karahan A, Salvetti A, Rossi L, Manni L, Rinkevich B, Rosner A, Voskoboynik A, Rosental B, Canesi L, Anselmi C, Pinsino A, Tohumcu BE, Jemec Kokalj A, Dolar A, Novak S, Sugni M, Corsi I, Drobne D. Stem Cells and Innate Immunity in Aquatic Invertebrates: Bridging Two Seemingly Disparate Disciplines for New Discoveries in Biology. Front Immunol 2021; 12:688106. [PMID: 34276677 PMCID: PMC8278520 DOI: 10.3389/fimmu.2021.688106] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
The scopes related to the interplay between stem cells and the immune system are broad and range from the basic understanding of organism's physiology and ecology to translational studies, further contributing to (eco)toxicology, biotechnology, and medicine as well as regulatory and ethical aspects. Stem cells originate immune cells through hematopoiesis, and the interplay between the two cell types is required in processes like regeneration. In addition, stem and immune cell anomalies directly affect the organism's functions, its ability to cope with environmental changes and, indirectly, its role in ecosystem services. However, stem cells and immune cells continue to be considered parts of two branches of biological research with few interconnections between them. This review aims to bridge these two seemingly disparate disciplines towards much more integrative and transformative approaches with examples deriving mainly from aquatic invertebrates. We discuss the current understanding of cross-disciplinary collaborative and emerging issues, raising novel hypotheses and comments. We also discuss the problems and perspectives of the two disciplines and how to integrate their conceptual frameworks to address basic equations in biology in a new, innovative way.
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Affiliation(s)
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli, Mersin, Turkey
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Lucia Manni
- Department of Biology, University of Padua, Padua, Italy
| | - Baruch Rinkevich
- Department of Biology, Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Amalia Rosner
- Department of Biology, Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States
- Department of Biology, Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Regenerative Medicine and Stem Cells, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Laura Canesi
- Department of Earth Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Chiara Anselmi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States
| | - Annalisa Pinsino
- Institute for Biomedical Research and Innovation, National Research Council, Palermo, Italy
| | - Begüm Ece Tohumcu
- Middle East Technical University, Institute of Marine Sciences, Erdemli, Mersin, Turkey
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andraž Dolar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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9
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Satou Y, Sato A, Yasuo H, Mihirogi Y, Bishop J, Fujie M, Kawamitsu M, Hisata K, Satoh N. Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages. Genome Biol Evol 2021; 13:6209075. [PMID: 33822040 PMCID: PMC8186479 DOI: 10.1093/gbe/evab068] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022] Open
Abstract
Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. Although these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. Although the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.
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Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - Atsuko Sato
- Department of Biology, Ochanomizu University, Otsuka, Bunkyo-ku, Japan.,Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, United Kingdom.,Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hitoyoshi Yasuo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Villefranche-sur-mer, France
| | - Yukie Mihirogi
- Department of Biology, Ochanomizu University, Otsuka, Bunkyo-ku, Japan
| | - John Bishop
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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10
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Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol 2021; 39:309-312. [PMID: 33288905 PMCID: PMC7954703 DOI: 10.1038/s41587-020-0711-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022]
Abstract
Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which limits their application. We present a method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day. Applied to four public human genomes, PGP1, HG002, NA12878 and HG00733, DipAsm produced haplotype-resolved assemblies with minimum contig length needed to cover 50% of the known genome (NG50) up to 25 Mb and phased ~99.5% of heterozygous sites at 98-99% accuracy, outperforming other approaches in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies for the discovery of structural variants (SVs), including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as the human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) regions. DipAsm will facilitate high-quality precision medicine and studies of individual haplotype variation and population diversity.
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Affiliation(s)
- Shilpa Garg
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | | | | | - Mike Chou
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | - Jay Ghurye
- Dovetail Genomics, Scotts Valley, CA, USA
| | | | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - David Heller
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Tobias Marschall
- Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - John Aach
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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11
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Zhao Z, Zhou Y, Wang S, Zhang X, Wang C, Li S. LDscaff: LD-based scaffolding of de novo genome assemblies. BMC Bioinformatics 2020; 21:570. [PMID: 33371875 PMCID: PMC7768660 DOI: 10.1186/s12859-020-03895-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Background Genome assembly is fundamental for de novo genome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing efforts, the information provided millions of existed whole-genome sequencing data have not been fully utilized to resolve the task of scaffolding. Genetic recombination patterns in population data indicate non-random association among alleles at different loci, can provide physical distance signals to guide scaffolding. Results In this paper, we propose LDscaff for draft genome assembly incorporating linkage disequilibrium information in population data. We evaluated the performance of our method with both simulated data and real data. We simulated scaffolds by splitting the pig reference genome and reassembled them. Gaps between scaffolds were introduced ranging from 0 to 100 KB. The genome misassembly rate is 2.43% when there is no gap. Then we implemented our method to refine the Giant Panda genome and the donkey genome, which are purely assembled by NGS data. After LDscaff treatment, the resulting Panda assembly has scaffold N50 of 3.6 MB, 2.5 times larger than the original N50 (1.3 MB). The re-assembled donkey assembly has an improved N50 length of 32.1 MB from 23.8 MB. Conclusions Our method effectively improves the assemblies with existed re-sequencing data, and is an potential alternative to the existing assemblers required for the collection of new data.
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Affiliation(s)
- Zicheng Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Yingxiao Zhou
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Shuai Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng City, 252059, Shandong, China.
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China.
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12
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Cheng YH, Liu CFJ, Yu YH, Jhou YT, Fujishima M, Tsai IJ, Leu JY. Genome plasticity in Paramecium bursaria revealed by population genomics. BMC Biol 2020; 18:180. [PMID: 33250052 PMCID: PMC7702705 DOI: 10.1186/s12915-020-00912-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/29/2020] [Indexed: 11/25/2022] Open
Abstract
Background Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. Results We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. Conclusions We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments. Supplementary information The online version contains supplementary material available at 10.1186/s12915-020-00912-2.
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Affiliation(s)
- Yu-Hsuan Cheng
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.,Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Chien-Fu Jeff Liu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Yen-Hsin Yu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Yu-Ting Jhou
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Masahiro Fujishima
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8512, Japan
| | - Isheng Jason Tsai
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jun-Yi Leu
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan. .,Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
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13
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A comparative genomics multitool for scientific discovery and conservation. Nature 2020; 587:240-245. [PMID: 33177664 PMCID: PMC7759459 DOI: 10.1038/s41586-020-2876-6] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity. A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.
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14
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Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res 2020; 30:1291-1305. [PMID: 32801147 PMCID: PMC7545148 DOI: 10.1101/gr.263566.120] [Citation(s) in RCA: 420] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced Pacific Biosciences (PacBio) HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultralong Oxford Nanopore Technologies (ONT) reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of nine complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance toward the complete assembly of human genomes.
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Affiliation(s)
- Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Robert Grothe
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
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15
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Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R, Jiggins CD. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 2020; 9:giaa088. [PMID: 32808665 PMCID: PMC7433188 DOI: 10.1093/gigascience/giaa088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. FINDINGS We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. CONCLUSIONS We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.
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Affiliation(s)
- Eugenie C Yen
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Juan A Galarza
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Tomas N Generalovic
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, Branišovská 1645/31A, 370 05 České Budějovice, Czech Republic
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street, Cambridge CB2 1TP, UK
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Johanna Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street, Cambridge CB2 1TP, UK
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16
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DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. Genome Biol Evol 2020; 12:948-964. [PMID: 32211845 PMCID: PMC7337526 DOI: 10.1093/gbe/evaa060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 12/21/2022] Open
Abstract
Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, "inflated" atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.
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Affiliation(s)
- Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
| | - William N Colgan
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Lincoln Harris
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
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17
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Norrell AE, Jones KL, Saillant EA. Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis. PLoS One 2020; 15:e0232402. [PMID: 32348345 PMCID: PMC7190162 DOI: 10.1371/journal.pone.0232402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/15/2020] [Indexed: 11/19/2022] Open
Abstract
The red snapper Lutjanus campechanus is an exploited reef fish of major economic importance in the Gulf of Mexico region. Studies of genome wide genetic variation are needed to understand the structure of wild populations and develop breeding programs for aquaculture but interpretation of these genome scans is limited by the absence of reference genome. In this work, the first draft of a reference genome was developed and characterized for the red snapper. P-454 and Illumina sequencing were conducted to produce paired-end reads that were assembled into reference contigs and scaffolds. The current assembly spans over 770 Mb, representing an estimated 69% of the red snapper genome in 67,254 scaffolds (N50 = 16,803 bp). The genome contigs were applied to map double digest Restriction-Site Associated DNA Tags and characterize Single Nucleotide Polymorphisms (SNPs) in five outbred full-sib families. The identified SNPs and 97 microsatellite loci were used to generate a high-density linkage map that includes 7,420 markers distributed across 24 linkage groups and spans 1,346.64 cM with an average inter–marker distance of 0.18 cM. Sex-specific maps revealed a 1.10:1 female to male map length ratio. A total of 4,422 genome contigs (10.5% of the assembly) were anchored to the map and used in a comparative genomic analysis of the red snapper and two model teleosts. Red snapper showed a high degree of chromosome level syntenic conservation with both medaka and spotted green puffer and a near one to one correspondence between the 24 red snapper linkage groups and corresponding medaka chromosomes was observed. This work established the first draft of a reference genome for a lutjanid fish. The obtained genomic resources will serve as a framework for the interpretation of genome scans during studies of wild populations and captive breeding programs.
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Affiliation(s)
- Adrienne E. Norrell
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, United States of America
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Eric A. Saillant
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, United States of America
- * E-mail:
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18
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Abstract
Sex chromosomes and sex determining genes can evolve fast, with the sex-linked chromosomes often differing between closely related species. Population genetics theory has been developed and tested to explain the rapid evolution of sex chromosomes and sex determination. However, we do not know why the sex chromosomes are divergent in some taxa and conserved in others. Addressing this question requires comparing closely related taxa with conserved and divergent sex chromosomes to identify biological features that could explain these differences. Cytological karyotypes suggest that muscid flies (e.g., house fly) and blow flies are such a taxonomic pair. The sex chromosomes appear to differ across muscid species, whereas they are conserved across blow flies. Despite the cytological evidence, we do not know the extent to which muscid sex chromosomes are independently derived along different evolutionary lineages. To address that question, we used genomic and transcriptomic sequence data to identify young sex chromosomes in two closely related muscid species, horn fly (Haematobia irritans) and stable fly (Stomoxys calcitrans). We provide evidence that the nascent sex chromosomes of horn fly and stable fly were derived independently from each other and from the young sex chromosomes of the closely related house fly (Musca domestica). We present three different scenarios that could have given rise to the sex chromosomes of horn fly and stable fly, and we describe how the scenarios could be distinguished. Distinguishing between these scenarios in future work could identify features of muscid genomes that promote sex chromosome divergence.
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19
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Qiu B, Fang S, Ikhwanuddin M, Wong L, Ma H. Genome survey and development of polymorphic microsatellite loci for Sillago sihama based on Illumina sequencing technology. Mol Biol Rep 2020; 47:3011-3017. [PMID: 32124169 DOI: 10.1007/s11033-020-05348-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
In this study, we first conducted a genome survey assay for Sillago sihama by Illumina sequencing platform, and then developed 15 polymorphic microsatellite loci in a wild population. A total of 129.46 Gb raw data were obtained, of which 115.07 Gb were clean data, with a sequencing depth of 179.3-folds. This genome was estimated to be 522.6 Mb in size, with the heterozygosity, repeat content and GC content being 0.63%, 21% and 44%. A total of 630,028 microsatellites were identified from the genome, of which, dinucleotide repeat was the most abundant (56.80%), followed by mononucleotide repeat (30.23%). Furthermore, 60 pairs of primers were designed and synthesized based on microsatellite sequences, of which 15 were polymorphic in a wild population. A total of 91 alleles were found, with an average of 6.07 per locus. Number of alleles, observed and expected heterozygosity per locus ranged from two to 13, from 0.250 to 0.862, and from 0.396 to 0.901, respectively. Twelve loci were highly informative (PIC > 0.5), and the others were medium informative (0.25 < PIC < 0.5). Seven loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0033). No significant linkage disequilibrium was detected between loci pairs. This study provided a large number of genomic resources and 15 polymorphic microsatellite loci that should be helpful for the further genetic studies in S. sihama.
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Affiliation(s)
- Bixun Qiu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China.,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China.,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Mhd Ikhwanuddin
- STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
| | - Lilian Wong
- STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China. .,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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20
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Kingan SB, Urban J, Lambert CC, Baybayan P, Childers AK, Coates B, Scheffler B, Hackett K, Korlach J, Geib SM. A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system. Gigascience 2019; 8:giz122. [PMID: 31609423 PMCID: PMC6791401 DOI: 10.1093/gigascience/giz122] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. RESULTS The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. CONCLUSIONS We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.
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Affiliation(s)
- Sarah B Kingan
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Julie Urban
- Department of Entomology, 501 ASI Building, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Primo Baybayan
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Anna K Childers
- USDA-ARS, Bee Research Laboratory, 10300 Baltimore Avenue, Building 306, Room 315, BARC-East, Beltsville, MD 20705, USA
| | - Brad Coates
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 2333 Genetics Laboratory, 819 Wallace Road, Ames, IA 50011, USA
| | - Brian Scheffler
- USDA-ARS, Genomics and Bioinformatics Research, 141 Experiment Station Road, Stoneville, MS 38776, USA
| | - Kevin Hackett
- USDA-ARS, Office of National Programs, George Washington Carver Center, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA
| | - Jonas Korlach
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Scott M Geib
- USDA-ARS, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, 64 Nowelo St., Hilo, HI 96720, USA
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21
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Kuon JE, Qi W, Schläpfer P, Hirsch-Hoffmann M, von Bieberstein PR, Patrignani A, Poveda L, Grob S, Keller M, Shimizu-Inatsugi R, Grossniklaus U, Vanderschuren H, Gruissem W. Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars. BMC Biol 2019; 17:75. [PMID: 31533702 PMCID: PMC6749633 DOI: 10.1186/s12915-019-0697-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022] Open
Abstract
Background Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown. Results We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars. Conclusions The genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars. Electronic supplementary material The online version of this article (10.1186/s12915-019-0697-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joel-E Kuon
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland.
| | - Weihong Qi
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Pascal Schläpfer
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Matthias Hirsch-Hoffmann
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | | | - Andrea Patrignani
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lucy Poveda
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefan Grob
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Miyako Keller
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Hervé Vanderschuren
- AgroBioChem Department, University of Liège, Passage des Déportés 2, Gembloux, Belgium
| | - Wilhelm Gruissem
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland. .,Advanced Plant Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan.
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22
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Girollet N, Rubio B, Lopez-Roques C, Valière S, Ollat N, Bert PF. De novo phased assembly of the Vitis riparia grape genome. Sci Data 2019; 6:127. [PMID: 31324816 PMCID: PMC6642119 DOI: 10.1038/s41597-019-0133-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022] Open
Abstract
Grapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.
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Affiliation(s)
- Nabil Girollet
- EGFV, Bordeaux Sciences Agro - INRA - Université de Bordeaux, ISVV, 210 chemin de Leysotte, 33882, Villenave d'Ornon, France
| | - Bernadette Rubio
- EGFV, Bordeaux Sciences Agro - INRA - Université de Bordeaux, ISVV, 210 chemin de Leysotte, 33882, Villenave d'Ornon, France
- IFV, Institut Français de la Vigne et du Vin, Domaine de l'Espîguette, 30240, Le Grau du Roi, France
| | | | - Sophie Valière
- INRA, US 1426, GeT-PlaGe, Genotoul, 31326, Castanet-Tolosan, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro - INRA - Université de Bordeaux, ISVV, 210 chemin de Leysotte, 33882, Villenave d'Ornon, France
| | - Pierre-François Bert
- EGFV, Bordeaux Sciences Agro - INRA - Université de Bordeaux, ISVV, 210 chemin de Leysotte, 33882, Villenave d'Ornon, France.
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23
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A comparative analysis of methods for de novo assembly of hymenopteran genomes using either haploid or diploid samples. Sci Rep 2019; 9:6480. [PMID: 31019201 PMCID: PMC6482151 DOI: 10.1038/s41598-019-42795-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/04/2019] [Indexed: 01/05/2023] Open
Abstract
Diverse invertebrate taxa including all 200,000 species of Hymenoptera (ants, bees, wasps and sawflies) have a haplodiploid sex determination system, where females are diploid and males are haploid. Thus, hymenopteran genome projects can make use of DNA from a single haploid male sample, which is assumed advantageous for genome assembly. For the purpose of gene annotation, transcriptome sequencing is usually conducted using RNA from a pool of individuals. We conducted a comparative analysis of genome and transcriptome assembly and annotation methods, using genetic sources of different ploidy: (1) DNA from a haploid male or a diploid female (2) RNA from the same haploid male or a pool of individuals. We predicted that the use of a haploid male as opposed to a diploid female will simplify the genome assembly and gene annotation thanks to the lack of heterozygosity. Using DNA and RNA from the same haploid individual is expected to provide better confidence in transcript-to-genome alignment, and improve the annotation of gene structure in terms of the exon/intron boundaries. The haploid genome assemblies proved to be more contiguous, with both contig and scaffold N50 size at least threefold greater than their diploid counterparts. Completeness evaluation showed mixed results. The SOAPdenovo2 diploid assembly was missing more genes than the haploid assembly. The SPAdes diploid assembly had more complete genes, but a higher level of duplicates, and a greatly overestimated genome size. When aligning the two transcriptomes against the male genome, the male transcriptome gave 2–3% more complete transcripts than the pool transcriptome for genes with comparable expression levels in both transcriptomes. However, this advantage disappears in the final results of the gene annotation pipeline that incorporates evidence from homologous proteins. The RNA pool is still required to obtain the full transcriptome with genes that are expressed in other life stages and castes. In conclusion, the use of a haploid source material for a de novo genome project provides a substantial advantage to the quality of the genome draft and the use of RNA from the same haploid individual for transcriptome to genome alignment provides a minor advantage for genes that are expressed in the adult male.
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24
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Ratcliffe LE, Asiedu EK, Pickett CJ, Warburton MA, Izzi SA, Meedel TH. The Ciona myogenic regulatory factor functions as a typical MRF but possesses a novel N-terminus that is essential for activity. Dev Biol 2019; 448:210-225. [PMID: 30365920 PMCID: PMC6478573 DOI: 10.1016/j.ydbio.2018.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/28/2018] [Accepted: 10/16/2018] [Indexed: 11/26/2022]
Abstract
Electroporation-based assays were used to test whether the myogenic regulatory factor (MRF) of Ciona intestinalis (CiMRF) interferes with endogenous developmental programs, and to evaluate the importance of its unusual N-terminus for muscle development. We found that CiMRF suppresses both notochord and endoderm development when it is expressed in these tissues by a mechanism that may involve activation of muscle-specific microRNAs. Because these results add to a large body of evidence demonstrating the exceptionally high degree of functional conservation among MRFs, we were surprised to discover that non-ascidian MRFs were not myogenic in Ciona unless they formed part of a chimeric protein containing the CiMRF N-terminus. Equally surprising, we found that despite their widely differing primary sequences, the N-termini of MRFs of other ascidian species could form chimeric MRFs that were also myogenic in Ciona. This domain did not rescue the activity of a Brachyury protein whose transcriptional activation domain had been deleted, and so does not appear to constitute such a domain. Our results indicate that ascidians have previously unrecognized and potentially novel requirements for MRF-directed myogenesis. Moreover, they provide the first example of a domain that is essential to the core function of an important family of gene regulatory proteins, one that, to date, has been found in only a single branch of the family.
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Affiliation(s)
- Lindsay E Ratcliffe
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Emmanuel K Asiedu
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - C J Pickett
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Megan A Warburton
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Stephanie A Izzi
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Thomas H Meedel
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
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25
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Initiation of the zygotic genetic program in the ascidian embryo. Semin Cell Dev Biol 2018; 84:111-117. [DOI: 10.1016/j.semcdb.2018.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
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26
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Roach MJ, Schmidt SA, Borneman AR. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics 2018; 19:460. [PMID: 30497373 PMCID: PMC6267036 DOI: 10.1186/s12859-018-2485-7] [Citation(s) in RCA: 663] [Impact Index Per Article: 94.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/12/2018] [Indexed: 12/04/2022] Open
Abstract
Background Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembly of highly heterozygous genomes is still problematic when regional heterogeneity is so high that haplotype homology is not recognised during assembly. This results in regional duplication rather than consolidation into allelic variants and can cause issues with downstream analysis, for example variant discovery, or haplotype reconstruction using the diploid assembly with unpaired allelic contigs. Results A new pipeline—Purge Haplotigs—was developed specifically for third-gen sequencing-based assemblies to automate the reassignment of allelic contigs, and to assist in the manual curation of genome assemblies. The pipeline uses a draft haplotype-fused assembly or a diploid assembly, read alignments, and repeat annotations to identify allelic variants in the primary assembly. The pipeline was tested on a simulated dataset and on four recent diploid (phased) de novo assemblies from third-generation long-read sequencing, and compared with a similar tool. After processing with Purge Haplotigs, haploid assemblies were less duplicated with minimal impact on genome completeness, and diploid assemblies had more pairings of allelic contigs. Conclusions Purge Haplotigs improves the haploid and diploid representations of third-gen sequencing based genome assemblies by identifying and reassigning allelic contigs. The implementation is fast and scales well with large genomes, and it is less likely to over-purge repetitive or paralogous elements compared to alignment-only based methods. The software is available at https://bitbucket.org/mroachawri/purge_haplotigs under a permissive MIT licence. Electronic supplementary material The online version of this article (10.1186/s12859-018-2485-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael J Roach
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, SA, 5064, Australia.
| | - Simon A Schmidt
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, SA, 5064, Australia
| | - Anthony R Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, SA, 5064, Australia
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27
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Roach MJ, Johnson DL, Bohlmann J, van Vuuren HJJ, Jones SJM, Pretorius IS, Schmidt SA, Borneman AR. Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PLoS Genet 2018; 14:e1007807. [PMID: 30458008 PMCID: PMC6279053 DOI: 10.1371/journal.pgen.1007807] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/04/2018] [Accepted: 11/02/2018] [Indexed: 01/08/2023] Open
Abstract
Chardonnay is the basis of some of the world's most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propagation. However, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a high-quality, diploid-phased Chardonnay genome assembly was produced from single-molecule real time sequencing, and combined with re-sequencing data from 15 different Chardonnay clones. There were 1620 markers identified that distinguish the 15 clones. These markers were reliably used for clonal identification of independently sourced genomic material, as well as in identifying a potential genetic basis for some clonal phenotypic differences. The predicted parentage of the Chardonnay haplomes was elucidated by mapping sequence data from the predicted parents of Chardonnay (Gouais blanc and Pinot noir) against the Chardonnay reference genome. This enabled the detection of instances of heterosis, with differentially-expanded gene families being inherited from the parents of Chardonnay. Most surprisingly however, the patterns of nucleotide variation present in the Chardonnay genome indicate that Pinot noir and Gouais blanc share an extremely high degree of kinship that has resulted in the Chardonnay genome displaying characteristics that are indicative of inbreeding.
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Affiliation(s)
- Michael J. Roach
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Daniel L. Johnson
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Joerg Bohlmann
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hennie J. J. van Vuuren
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J. M. Jones
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Isak S. Pretorius
- Chancellery, Macquarie University, Sydney, New South Wales, Australia
| | - Simon A. Schmidt
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Anthony R. Borneman
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
- Department of Genetics and Evolution, University of Adelaide, South Australia, Australia
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28
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Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM. De novo assembly of haplotype-resolved genomes with trio binning. Nat Biotechnol 2018; 36:nbt.4277. [PMID: 30346939 PMCID: PMC6476705 DOI: 10.1038/nbt.4277] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 09/10/2018] [Indexed: 12/20/2022]
Abstract
Complex allelic variation hampers the assembly of haplotype-resolved sequences from diploid genomes. We developed trio binning, an approach that simplifies haplotype assembly by resolving allelic variation before assembly. In contrast with prior approaches, the effectiveness of our method improved with increasing heterozygosity. Trio binning uses short reads from two parental genomes to first partition long reads from an offspring into haplotype-specific sets. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction. We used trio binning to recover both haplotypes of a diploid human genome and identified complex structural variants missed by alternative approaches. We sequenced an F1 cross between the cattle subspecies Bos taurus taurus and Bos taurus indicus and completely assembled both parental haplotypes with NG50 haplotig sizes of >20 Mb and 99.998% accuracy, surpassing the quality of current cattle reference genomes. We suggest that trio binning improves diploid genome assembly and will facilitate new studies of haplotype variation and inheritance.
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Affiliation(s)
- Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Brian P. Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Alexander T. Dilthey
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
- Institute of Medical Microbiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, North Rhine-Westphalia, Germany
| | - Derek M. Bickhart
- Cell Wall Biology and Utilization Laboratory, ARS USDA, Madison, Wisconsin, USA
| | | | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy SA, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide SA, Australia
| | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy SA, Australia
| | | | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
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29
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Huang X, Li S, Gao Y, Zhan A. Genome-Wide Identification, Characterization and Expression Analyses of Heat Shock Protein-Related Genes in a Highly Invasive Ascidian Ciona savignyi. Front Physiol 2018; 9:1043. [PMID: 30108524 PMCID: PMC6079275 DOI: 10.3389/fphys.2018.01043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/13/2018] [Indexed: 12/02/2022] Open
Abstract
Biological response to rapid changing environments is an outstanding research question in ecology and evolution. Biological invasions provide excellent "natural" experiments to study such a complex response process, as invaders often encounter rapidly changing environments during biological invasions. The regulation of heat shock proteins (Hsp) is a common pathway responsible for various environmental stresses; however, the comprehensive study on Hsp system across the whole genome and potential roles in determining invasion success are still largely unexplored. Here, we used a marine invasive model ascidian, Ciona savignyi, to investigate transcriptional response of Hsp-related genes to harsh environments. We identified 32 genes, including three Hsp20, six Hsp40, ten Hsp60, eight Hsp70, three Hsp90, one Hsp100, and one heat shock transcription factor (Hsf), across the whole genome of C. savignyi. We further characterized gene structure and protein motifs, and identified potential heat shock elements (HSEs) in promoters of Hsp genes. The expression analysis showed that most Hsp genes, but not all, were involved in transcriptional response to temperature and salinity challenges in a duration- and stress-specific pattern, and the maximum amplitude of induction occurred in Hsp70-4 after 1-h of high temperature treatment. However, the Hsf gene was scarcely induced and limited interactions were predicted between Hsp and Hsf genes. Our study provide the first systematic genome-wide analysis of Hsp and Hsf family in the marine invasive model ascidian, and our results are expected to dissect Hsp-based molecular mechanisms responsible for extreme environmental adaptation using Ciona as a model system.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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30
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Abstract
Ascidians are tunicates, which constitute the sister group of vertebrates. The ascidian genome contains two Zic genes, called Zic-r.a (also called Macho-1) and Zic-r.b (ZicL). The latter is a multi-copy gene, and the precise copy number has not yet been determined. Zic-r.a is maternally expressed, and soon after fertilization Zic-r.a mRNA is localized in the posterior pole of the zygote. Zic-r.a protein is translated there and is involved in specification of posterior fate; in particular it is important for specification of muscle fate. Zic-r.a is also expressed zygotically in neural cells of the tailbud stage. On the other hand, Zic-r.b is first expressed in marginal cells of the vegetal hemisphere of 32-cell embryos and then in neural cells that contribute to the central nervous system during gastrulation. Zic-r.b is required first for specification of mesodermal tissues and then for specification of the central nervous system. Their upstream and downstream genetic pathways have been studied extensively by functional assays, which include gene knockdown and chromatin immunoprecipitation assays. Thus, ascidian Zic genes play central roles in specification of mesodermal and neural fates.
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Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan.
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
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31
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Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T. A graph-based approach to diploid genome assembly. Bioinformatics 2018; 34:i105-i114. [PMID: 29949989 PMCID: PMC6022571 DOI: 10.1093/bioinformatics/bty279] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Motivation Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and disease. Current assembly approaches often collapse the two sequences into one haploid consensus sequence and, therefore, fail to capture the diploid nature of the organism under study. Thus, building an assembler capable of producing accurate and complete diploid assemblies, while being resource-efficient with respect to sequencing costs, is a key challenge to be addressed by the bioinformatics community. Results We present a novel graph-based approach to diploid assembly, which combines accurate Illumina data and long-read Pacific Biosciences (PacBio) data. We demonstrate the effectiveness of our method on a pseudo-diploid yeast genome and show that we require as little as 50× coverage Illumina data and 10× PacBio data to generate accurate and complete assemblies. Additionally, we show that our approach has the ability to detect and phase structural variants. Availability and implementation https://github.com/whatshap/whatshap. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shilpa Garg
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany
- Department of Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Mikko Rautiainen
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany
- Department of Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Adam M Novak
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Erik Garrison
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany
- Department of Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany
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32
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Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ. De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. Sci Rep 2018; 8:5518. [PMID: 29615780 PMCID: PMC5882950 DOI: 10.1038/s41598-018-23749-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/20/2018] [Indexed: 01/17/2023] Open
Abstract
Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome. Analysing genome size, gene number, repetitive elements, orthologs clustering and gene ontology terms show that B. leachii has a genomic architecture similar to that of most solitary tunicates, while other recently sequenced colonial ascidians have undergone genome expansion. In addition, ortholog clustering has identified groups of candidate genes for the study of colonialism and whole-body regeneration. By analysing the structure and composition of conserved gene linkages, we observed examples of cluster breaks and gene dispersions, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. We also found lineage-specific gene gain and loss within conserved cell-signalling pathways. Such examples of genetic changes within conserved cell-signalling pathways commonly associated with regeneration and development that may underlie some of the diverse regenerative abilities observed in tunicates. Overall, these results provide a novel resource for the study of tunicates and of colonial ascidians.
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Affiliation(s)
- Simon Blanchoud
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Kim Rutherford
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Lisa Zondag
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Megan J Wilson
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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33
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Shimai K, Kusakabe TG. The Use of cis-Regulatory DNAs as Molecular Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [DOI: 10.1007/978-981-10-7545-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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34
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Clonorchis sinensis and Clonorchiasis: The Relevance of Exploring Genetic Variation. ADVANCES IN PARASITOLOGY 2018; 100:155-208. [PMID: 29753338 DOI: 10.1016/bs.apar.2018.03.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Parasitic trematodes (flukes) cause substantial mortality and morbidity in humans. The Chinese liver fluke, Clonorchis sinensis, is one of the most destructive parasitic worms in humans in China, Vietnam, Korea and the Russian Far East. Although C. sinensis infection can be controlled relatively well using anthelmintics, the worm is carcinogenic, inducing cholangiocarcinoma and causing major suffering in ~15 million people in Asia. This chapter provides an account of C. sinensis and clonorchiasis research-covering aspects of biology, epidemiology, pathogenesis and immunity, diagnosis, treatment and control, genetics and genomics. It also describes progress in the area of molecular biology (genetics, genomics, transcriptomics and proteomics) and highlights challenges associated with comparative genomics and population genetics. It then reviews recent advances in the sequencing and characterisation of the mitochondrial and nuclear genomes for a Korean isolate of C. sinensis and summarises salient comparative genomic work and the implications thereof. The chapter concludes by considering how advances in genomic and informatics will enable research on the genetics of C. sinensis and related parasites, as well as the discovery of new fluke-specific intervention targets.
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35
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Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms. Trends Genet 2017; 34:121-132. [PMID: 29198378 DOI: 10.1016/j.tig.2017.11.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023]
Abstract
The application of genomic approaches to 'obscure model organisms' (OMOs), meaning species with no prior genomic resources, enables increasingly sophisticated studies of the genomic basis of evolution, acclimatization, and adaptation in real ecological contexts. I consider here ecological questions that can be addressed using OMOs, and indicate optimal sequencing and data-handling solutions for each case. With this I hope to promote the diversity of OMO-based projects that would capitalize on the peculiarities of the natural history of OMOs and could feasibly be completed within the scope of a single PhD thesis.
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36
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Huang X, Li S, Ni P, Gao Y, Jiang B, Zhou Z, Zhan A. Rapid response to changing environments during biological invasions: DNA methylation perspectives. Mol Ecol 2017; 26:6621-6633. [PMID: 29057612 DOI: 10.1111/mec.14382] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 10/01/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Abstract
Dissecting complex interactions between species and their environments has long been a research hot spot in the fields of ecology and evolutionary biology. The well-recognized Darwinian evolution has well-explained long-term adaptation scenarios; however, "rapid" processes of biological responses to environmental changes remain largely unexplored, particularly molecular mechanisms such as DNA methylation that have recently been proposed to play crucial roles in rapid environmental adaptation. Invasive species, which have capacities to successfully survive rapidly changing environments during biological invasions, provide great opportunities to study molecular mechanisms of rapid environmental adaptation. Here, we used the methylation-sensitive amplified polymorphism (MSAP) technique in an invasive model ascidian, Ciona savignyi, to investigate how species interact with rapidly changing environments at the whole-genome level. We detected quite rapid DNA methylation response: significant changes of DNA methylation frequency and epigenetic differentiation between treatment and control groups occurred only after 1 hr of high-temperature exposure or after 3 hr of low-salinity challenge. In addition, we detected time-dependent hemimethylation changes and increased intragroup epigenetic divergence induced by environmental stresses. Interestingly, we found evidence of DNA methylation resilience, as most stress-induced DNA methylation variation maintained shortly (~48 hr) and quickly returned back to the control levels. Our findings clearly showed that invasive species could rapidly respond to acute environmental changes through DNA methylation modifications, and rapid environmental changes left significant epigenetic signatures at the whole-genome level. All these results provide fundamental background to deeply investigate the contribution of DNA methylation mechanisms to rapid contemporary environmental adaptation.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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37
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Tigano A, Sackton TB, Friesen VL. Assembly and RNA-free annotation of highly heterozygous genomes: The case of the thick-billed murre (Uria lomvia). Mol Ecol Resour 2017; 18:79-90. [PMID: 28815912 DOI: 10.1111/1755-0998.12712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 08/02/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Abstract
Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick-billed murre (Uria lomvia), an arctic colonial seabird. In this study, we tested the performance of three genome assemblers, ray/sscape, soapdenovo2 and platanus, in assembling the highly heterozygous genome of the thick-billed murre. Our results show that platanus, an assembler specifically designed for heterozygous genomes, outperforms the other two approaches and produces a highly contiguous (N50 = 15.8 Mb) and complete genome assembly (93% presence of genes from the Benchmarking Universal Single Copy Ortholog [BUSCO] gene set). Additionally, we annotated the thick-billed murre genome using a homology-based approach that takes advantage of the genomic resources available for birds and other taxa. Our study will be useful for those researchers who are approaching assembly and annotation of highly heterozygous genomes, or genomes of species of conservation concern, and/or who have limited financial resources.
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Affiliation(s)
- Anna Tigano
- Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Vicki L Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
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38
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Huang S, Kang M, Xu A. HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. Bioinformatics 2017; 33:2577-2579. [PMID: 28407147 PMCID: PMC5870766 DOI: 10.1093/bioinformatics/btx220] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/31/2017] [Accepted: 04/11/2017] [Indexed: 11/12/2022] Open
Abstract
SUMMARY De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers. HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies. Using HM2, we demonstrate that two haploid sub-assemblies reconstructed from a real, highly-polymorphic diploid assembly show greatly improved continuity. AVAILABILITY AND IMPLEMENTATION Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/. CONTACT hshengf2@mail.sysu.edu.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shengfeng Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Mingjing Kang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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39
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Wang K, Dantec C, Lemaire P, Onuma TA, Nishida H. Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi. BMC Genomics 2017; 18:314. [PMID: 28427349 PMCID: PMC5399378 DOI: 10.1186/s12864-017-3707-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi have not been previously studied. RESULTS We report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods. Experimental validation suggests that more than half of these candidate miRNAs are expressed during embryogenesis. The majority of predicted H. roretzi miRNAs appear specific to ascidians or tunicates, and only 32 candidates, belonging to 25 families, are widely conserved across metazoans. CONCLUSION Our study presents a comprehensive identification of candidate H. roretzi miRNAs. This resource will facilitate the study of the mechanisms for miRNA-controlled gene regulatory networks during ascidian development. Further, our analysis suggests that the majority of Halocynthia miRNAs are specific to ascidian or tunicates, with only a small number of widely conserved miRNAs. This result is consistent with the general notion that animal miRNAs are less conserved between taxa than plant ones.
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Affiliation(s)
- Kai Wang
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan. .,Present address: Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, People's Republic of China.
| | - Christelle Dantec
- Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090, Montpellier, France
| | - Patrick Lemaire
- Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090, Montpellier, France
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
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40
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Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 2017; 356:92-95. [PMID: 28336562 PMCID: PMC5635820 DOI: 10.1126/science.aal3327] [Citation(s) in RCA: 1640] [Impact Index Per Article: 205.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/13/2017] [Indexed: 01/04/2023]
Abstract
The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aeaegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species.
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Affiliation(s)
- Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA
| | - Sanjit S Batra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Sarah K Nyquist
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Marie Hoeger
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Ido Machol
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Eric S Lander
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Biology, MIT, Cambridge, MA 02139, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Aviva Presser Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
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41
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Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res 2017; 27:824-834. [PMID: 28298430 PMCID: PMC5411777 DOI: 10.1101/gr.213959.116] [Citation(s) in RCA: 2480] [Impact Index Per Article: 310.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/13/2017] [Indexed: 01/25/2023]
Abstract
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.
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Affiliation(s)
- Sergey Nurk
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Dmitry Meleshko
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004.,Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia 198515
| | - Pavel A Pevzner
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004.,Department of Computer Science and Engineering, University of California, San Diego, California 92093-0404, USA
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42
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Epigenetic divergence of key genes associated with water temperature and salinity in a highly invasive model ascidian. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1409-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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Tørresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, Walenz BP, Knight J, Ekholm JM, Peluso P, Edvardsen RB, Tooming-Klunderud A, Skage M, Lien S, Jakobsen KS, Nederbragt AJ. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 2017; 18:95. [PMID: 28100185 PMCID: PMC5241972 DOI: 10.1186/s12864-016-3448-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/20/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies. RESULTS By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual. CONCLUSIONS The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.
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Affiliation(s)
- Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
- Department of Natural Sciences, University of Agder, Kristiansand, NO-4604 Norway
| | - William B. Reinar
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Harald Grove
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, NO-1432 Norway
| | - Jason R. Miller
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, 20850 MD USA
| | - Brian P. Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 MD USA
| | - James Knight
- Yale School of Medicine, Yale University, New Haven, 06520 CT USA
| | | | | | | | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Morten Skage
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, NO-1432 Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Alexander J. Nederbragt
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Oslo, NO-0316 Norway
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Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O’Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 2016; 13:1050-1054. [PMID: 27749838 PMCID: PMC5503144 DOI: 10.1038/nmeth.4035] [Citation(s) in RCA: 1286] [Impact Index Per Article: 142.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/25/2016] [Indexed: 02/06/2023]
Abstract
While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata, samples that have challenged short-read assembly approaches. The FALCON-based assemblies are substantially more contiguous and complete than alternate short- or long-read approaches. The phased diploid assembly enabled the study of haplotype structure and heterozygosities between homologous chromosomes, including the identification of widespread heterozygous structural variation within coding sequences.
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Affiliation(s)
| | - Paul Peluso
- Pacific Biosciences, Menlo Park, CA 94025, USA
| | - Fritz J. Sedlazeck
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Maria Nattestad
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Ronan O’Malley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Grant R. Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Universita’ degli Studi di Verona, Verona, Italy
| | - Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, CA, USA
| | | | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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45
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Andere AA, Platt RN, Ray DA, Picard CJ. Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research. BMC Genomics 2016; 17:842. [PMID: 27793085 PMCID: PMC5084420 DOI: 10.1186/s12864-016-3187-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/22/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Blow flies (Diptera: Calliphoridae) are important medical, veterinary and forensic insects encompassing 8 % of the species diversity observed in the calyptrate insects. Few genomic resources exist to understand the diversity and evolution of this group. RESULTS We present the hybrid (short and long reads) draft assemblies of the male and female genomes of the common North American blow fly, Phormia regina (Diptera: Calliphoridae). The 550 and 534 Mb draft assemblies contained 8312 and 9490 predicted genes in the female and male genomes, respectively; including > 93 % conserved eukaryotic genes. Putative X and Y chromosomes (21 and 14 Mb, respectively) were assembled and annotated. The P. regina genomes appear to contain few mobile genetic elements, an almost complete absence of SINEs, and most of the repetitive landscape consists of simple repetitive sequences. Candidate gene approaches were undertaken to annotate insecticide resistance, sex-determining, chemoreceptors, and antimicrobial peptides. CONCLUSIONS This work yielded a robust, reliable reference calliphorid genome from a species located in the middle of a calliphorid phylogeny. By adding an additional blow fly genome, the ability to tease apart what might be true of general calliphorids vs. what is specific of two distinct lineages now exists. This resource will provide a strong foundation for future studies into the evolution, population structure, behavior, and physiology of all blow flies.
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Affiliation(s)
- Anne A. Andere
- Department of Biology, Indiana University Purdue University Indianapolis, 723 W. Michigan Street, Indianapolis, IN 46202 USA
| | - Roy N. Platt
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX 79403-3131 USA
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX 79403-3131 USA
| | - Christine J. Picard
- Department of Biology, Indiana University Purdue University Indianapolis, 723 W. Michigan Street, Indianapolis, IN 46202 USA
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46
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Abstract
Cardiac cell specification and the genetic determinants that govern this process are highly conserved among Chordates. Recent studies have established the importance of evolutionarily-conserved mechanisms in the study of congenital heart defects and disease, as well as cardiac regeneration. As a basal Chordate, the Ciona model system presents a simple scaffold that recapitulates the basic blueprint of cardiac development in Chordates. Here we will focus on the development and cellular structure of the heart of the ascidian Ciona as compared to other Chordates, principally vertebrates. Comparison of the Ciona model system to heart development in other Chordates presents great potential for dissecting the genetic mechanisms that underlie congenital heart defects and disease at the cellular level and might provide additional insight into potential pathways for therapeutic cardiac regeneration.
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47
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Lemaire P, Piette J. Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley. Open Biol 2016; 5:150053. [PMID: 26085517 PMCID: PMC4632506 DOI: 10.1098/rsob.150053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review is a tribute to the remarkable contributions of Thomas Huxley to the biology of tunicates, the likely sister group of vertebrates. In 1851, the great biologist and philosopher published two landmark papers on pelagic tunicates in the Philosophical Transactions of the Royal Society. They were dedicated to the description of the adult anatomy and life cycle of thaliaceans and appendicularians, the pelagic relatives of ascidians. In the first part of this review, we discuss the novel anatomical observations and evolutionary hypotheses made by Huxley, which would have a lasting influence on tunicate biology. We also briefly comment on the more philosophical reflections of Huxley on individuality. In the second part, we stress the originality and relevance of past and future studies of tunicates in the resolution of major biological issues. In particular, we focus on the complex relationship between genotype and phenotype and the phenomenon of developmental system drift. We propose that more than 150 years after Huxley's papers, tunicate embryos are still worth studying in their own right, independently of their evolutionary proximity to vertebrates, as they provide original and crucial insights into the process of animal evolution. Tunicates are still at the forefront of biological research.
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Affiliation(s)
- Patrick Lemaire
- Centre de Recherches de Biochimie Macromoléculaire. UMR 5237, Centre National de la Recherche Scientifique, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Jacques Piette
- Centre de Recherches de Biochimie Macromoléculaire. UMR 5237, Centre National de la Recherche Scientifique, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier cedex 5, France
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48
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Krehenwinkel H, Rödder D, Tautz D. Eco-genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture. GLOBAL CHANGE BIOLOGY 2015; 21:4320-32. [PMID: 26183328 DOI: 10.1111/gcb.13042] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/05/2015] [Accepted: 07/01/2015] [Indexed: 05/28/2023]
Abstract
Poleward range expansions are commonly attributed to global change, but could alternatively be driven by rapid evolutionary adaptation. A well-documented example of a range expansion during the past decades is provided by the European wasp spider Argiope bruennichi. Using ecological niche modeling, thermal tolerance experiments and a genome-wide analysis of gene expression divergence, we show that invasive populations have adapted to novel climatic conditions in the course of their expansion. Their climatic niche shift is mirrored in an increased cold tolerance and a population-specific and functionally differentiated gene expression response. We generated an Argiope reference genome sequence and used population genome resequencing to assess genomic changes associated with the new climatic adaptations. We find clear genetic differentiation and a significant admixture with alleles from East Asian populations in the invasive Northern European populations. Population genetic modeling suggests that at least some of these introgressing alleles have contributed to the new adaptations during the expansion. Our results thus confirm the notion that range expansions are not a simple consequence of climate change, but are accompanied by fast genetic changes and adaptations that may be fuelled through admixture between long separated lineages.
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Affiliation(s)
- Henrik Krehenwinkel
- Max-Planck Institute for Evolutionary Biology, Plön, 24306, Germany
- University of California Berkeley, Department of Environmental Science, Policy, and Management, Berkeley, CA, 94720-3114, USA
| | - Dennis Rödder
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, 53113, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, Plön, 24306, Germany
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49
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Huang X, Gao Y, Jiang B, Zhou Z, Zhan A. Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi. Gene 2015; 576:79-87. [PMID: 26428313 DOI: 10.1016/j.gene.2015.09.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/16/2015] [Accepted: 09/25/2015] [Indexed: 12/20/2022]
Abstract
As invasive species have successfully colonized a wide range of dramatically different local environments, they offer a good opportunity to study interactions between species and rapidly changing environments. Gene expression represents one of the primary and crucial mechanisms for rapid adaptation to local environments. Here, we aim to select reference genes for quantitative gene expression analysis based on quantitative Real-Time PCR (qRT-PCR) for a model invasive ascidian, Ciona savignyi. We analyzed the stability of ten candidate reference genes in three tissues (siphon, pharynx and intestine) under two key environmental stresses (temperature and salinity) in the marine realm based on three programs (geNorm, NormFinder and delta Ct method). Our results demonstrated only minor difference for stability rankings among the three methods. The use of different single reference gene might influence the data interpretation, while multiple reference genes could minimize possible errors. Therefore, reference gene combinations were recommended for different tissues - the optimal reference gene combination for siphon was RPS15 and RPL17 under temperature stress, and RPL17, UBQ and TubA under salinity treatment; for pharynx, TubB, TubA and RPL17 were the most stable genes under temperature stress, while TubB, TubA and UBQ were the best under salinity stress; for intestine, UBQ, RPS15 and RPL17 were the most reliable reference genes under both treatments. Our results suggest that the necessity of selection and test of reference genes for different tissues under varying environmental stresses. The results obtained here are expected to reveal mechanisms of gene expression-mediated invasion success using C. savignyi as a model species.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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50
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Cameron RA, Kudtarkar P, Gordon SM, Worley KC, Gibbs RA. Do echinoderm genomes measure up? Mar Genomics 2015; 22:1-9. [PMID: 25701080 PMCID: PMC4489978 DOI: 10.1016/j.margen.2015.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 11/19/2022]
Abstract
Echinoderm genome sequences are a corpus of useful information about a clade of animals that serve as research models in fields ranging from marine ecology to cell and developmental biology. Genomic information from echinoids has contributed to insights into the gene interactions that drive the developmental process at the molecular level. Such insights often rely heavily on genomic information and the kinds of questions that can be asked thus depend on the quality of the sequence information. Here we describe the history of echinoderm genomic sequence assembly and present details about the quality of the data obtained. All of the sequence information discussed here is posted on the echinoderm information web system, Echinobase.org.
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Affiliation(s)
- R Andrew Cameron
- Division of Biology 139-74, California Institute of Technology, Pasadena, CA, USA.
| | - Parul Kudtarkar
- Division of Biology 139-74, California Institute of Technology, Pasadena, CA, USA
| | - Susan M Gordon
- Division of Biology 139-74, California Institute of Technology, Pasadena, CA, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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