1
|
Daric V, Lanoizelet M, Mayeur H, Leblond C, Darras S. Genomic Resources and Annotations for a Colonial Ascidian, the Light-Bulb Sea Squirt Clavelina lepadiformis. Genome Biol Evol 2024; 16:evae038. [PMID: 38441487 PMCID: PMC10950049 DOI: 10.1093/gbe/evae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Ascidian embryos have been studied since the birth of experimental embryology at the end of the 19th century. They represent textbook examples of mosaic development characterized by a fast development with very few cells and invariant cleavage patterns and lineages. Ascidians belong to tunicates, the vertebrate sister group, and their study is essential to shed light on the emergence of vertebrates. Importantly, deciphering developmental gene regulatory networks has been carried out mostly in two of the three ascidian orders, Phlebobranchia and Stolidobranchia. To infer ancestral developmental programs in ascidians, it is thus essential to carry out molecular embryology in the third ascidian order, the Aplousobranchia. Here, we present genomic resources for the colonial aplousobranch Clavelina lepadiformis: a transcriptome produced from various embryonic stages, and an annotated genome. The assembly consists of 184 contigs making a total of 233.6 Mb with a N50 of 8.5 Mb and a L50 of 11. The 32,318 predicted genes capture 96.3% of BUSCO orthologs. We further show that these resources are suitable to study developmental gene expression and regulation in a comparative framework within ascidians. Additionally, they will prove valuable for evolutionary and ecological studies.
Collapse
Affiliation(s)
- Vladimir Daric
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| | - Maxence Lanoizelet
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| | - Hélène Mayeur
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| | - Cécile Leblond
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| | - Sébastien Darras
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| |
Collapse
|
2
|
Steffen K, Proux-Wéra E, Soler L, Churcher A, Sundh J, Cárdenas P. Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae). G3 (Bethesda) 2023; 13:jkad192. [PMID: 37619978 PMCID: PMC10542158 DOI: 10.1093/g3journal/jkad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023]
Abstract
Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti Bowerbank 1858, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes.
Collapse
Affiliation(s)
- Karin Steffen
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden
| | - Estelle Proux-Wéra
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna SE-17121, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala University, Uppsala 752 37, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå 901 87, Sweden
| | - John Sundh
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna SE-17121, Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden
| |
Collapse
|
3
|
Dainat B, Oberhaensli S, Ory F, Dietemann V. New reference genomes of honey bee-associated bacteria Paenibacillus melissococcoides, Paenibacillus dendritiformis, and Paenibacillus thiaminolyticus. Microbiol Resour Announc 2023; 12:e0020923. [PMID: 37530538 PMCID: PMC10508097 DOI: 10.1128/mra.00209-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/18/2023] [Indexed: 08/03/2023] Open
Abstract
We sequenced the genomes of recently discovered Paenibacillus melissococcoides (CCOS 2000) and of the type strains of closely related P. thiaminolyticus (DSM 7262) and P. dendritiformis (LMG 21716). The three genomes set the basis to unambiguous diagnostic of these honey bee associated Paenibacillus bacteria.
Collapse
Affiliation(s)
- Benjamin Dainat
- Swiss Bee Research Center, Agroscope Liebefeld, Bern, Switzerland
| | - Simone Oberhaensli
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Florine Ory
- Swiss Bee Research Center, Agroscope Liebefeld, Bern, Switzerland
| | - Vincent Dietemann
- Swiss Bee Research Center, Agroscope Liebefeld, Bern, Switzerland
- Department of Ecology and Evolution, Biophore, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
4
|
Fortmann-Grote C, Hugoson E, Summers J, Theodosiou L, Rainey PB. Genome Update for Pseudomonas fluorescens Isolate SBW25. Microbiol Resour Announc 2023; 12:e0063722. [PMID: 36651771 DOI: 10.1128/mra.00637-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We report a genome update for Pseudomonas fluorescens isolate SBW25. The updated genome assembly, which was derived from the original isolate, is based on PacBio long-read sequence data. It shows three minor differences, compared with the previously published genome sequence. Original annotations were merged with recent automated annotations to preserve information.
Collapse
|
5
|
Andreotti S, Altmüller J, Quedenau C, Borodina T, Nouailles G, Teixeira Alves LG, Landthaler M, Bieniara M, Trimpert J, Wyler E. De Novo Whole Genome Assembly of the Roborovski Dwarf Hamster (Phodopus roborovskii) Genome, an Animal Model for Severe/Critical COVID-19. Genome Biol Evol 2022; 14:6626084. [PMID: 35778793 PMCID: PMC9254642 DOI: 10.1093/gbe/evac100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
The Roborovski dwarf hamster Phodopus roborovskii belongs to the Phodopus genus, one of seven within Cricetinae subfamily. Like other rodents such as mice, rats or ferrets, hamsters can be important animal models for a range of diseases. Whereas the Syrian hamster from the genus Mesocricetus is now widely used as a model for mild to moderate COVID-19, Roborovski dwarf hamster show a severe to lethal course of disease upon infection with the novel human coronavirus SARS-CoV-2.
Collapse
Affiliation(s)
- Sandro Andreotti
- Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne. Present address: Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Claudia Quedenau
- Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Tatiana Borodina
- Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Pulmonary Inflammation, Berlin, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany.,Institut für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Maximilian Bieniara
- Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| |
Collapse
|
6
|
McCann K, Grant W, Doyle SR. The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni. Wellcome Open Res 2021; 6:259. [PMID: 34796277 PMCID: PMC8564745 DOI: 10.12688/wellcomeopenres.17258.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly and annotation of an individual female
Cercopithifilaria johnstoni, a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus
Cercopithifilaria, a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite,
Onchocerca volvulus, both of which are responsible for similar eye and skin pathologies in their respective hosts.
Collapse
Affiliation(s)
- Kirsty McCann
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Warwick Grant
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Stephen R Doyle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| |
Collapse
|
7
|
Abstract
We present a genome assembly and annotation of an individual female Cercopithifilaria johnstoni, a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus Cercopithifilaria, a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite, Onchocerca volvulus, both of which are responsible for similar eye and skin pathologies in their respective hosts.
Collapse
Affiliation(s)
- Kirsty McCann
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Warwick Grant
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Stephen R. Doyle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| |
Collapse
|
8
|
Wolter LA, Mitulla M, Kalem J, Daniel R, Simon M, Wietz M. CAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain. Front Microbiol 2021; 12:628055. [PMID: 33912144 PMCID: PMC8072126 DOI: 10.3389/fmicb.2021.628055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/10/2021] [Indexed: 02/05/2023] Open
Abstract
Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62–1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62–1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain “polysaccharide niches.” Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.
Collapse
Affiliation(s)
- Laura A Wolter
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.,JST ERATO Nomura Project, Faculty of Life and Environmental Sciences, Tsukuba, Japan
| | - Maximilian Mitulla
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Jovan Kalem
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| |
Collapse
|
9
|
Nowell RW, Wilson CG, Almeida P, Schiffer PH, Fontaneto D, Becks L, Rodriguez F, Arkhipova IR, Barraclough TG. Evolutionary dynamics of transposable elements in bdelloid rotifers. eLife 2021; 10:e63194. [PMID: 33543711 PMCID: PMC7943196 DOI: 10.7554/elife.63194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms. Instead, we find that that TE content evolves relatively slowly in bdelloids and that gene families involved in RNAi-mediated TE suppression have undergone significant expansion, which might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.
Collapse
Affiliation(s)
- Reuben W Nowell
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
| | - Christopher G Wilson
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
| | - Pedro Almeida
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
- Division of Biosciences, University College LondonLondonUnited Kingdom
| | - Philipp H Schiffer
- Institute of Zoology, Section Developmental Biology, University of Cologne, KölnWormlabGermany
| | - Diego Fontaneto
- National Research Council of Italy, Water Research InstituteVerbania PallanzaItaly
| | - Lutz Becks
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary BiologyPlönGermany
- Aquatic Ecology and Evolution, University of KonstanzKonstanzGermany
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MAUnited States
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MAUnited States
| | - Timothy G Barraclough
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
| |
Collapse
|
10
|
Campoy JA, Sun H, Goel M, Jiao WB, Folz-Donahue K, Wang N, Rubio M, Liu C, Kukat C, Ruiz D, Huettel B, Schneeberger K. Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol 2020; 21:306. [PMID: 33372615 DOI: 10.1101/2020.04.24.060046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/11/2020] [Indexed: 05/26/2023] Open
Abstract
Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets. After assembling the reads of each haplotype, the contigs are scaffolded to chromosome level using a genetic map derived from the gametes. We assemble the two genomes of a diploid apricot tree based on whole-genome sequencing of 445 individual pollen grains. The two haplotype assemblies (N50: 25.5 and 25.8 Mb) feature a haplotyping precision of greater than 99% and are accurately scaffolded to chromosome-level.
Collapse
Affiliation(s)
- José A Campoy
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Hequan Sun
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Manish Goel
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Wen-Biao Jiao
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Kat Folz-Donahue
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Nan Wang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Manuel Rubio
- Departament of Plant Breeding, CEBAS-CSIC, PO Box 164, E-30100 Espinardo, Murcia, Spain
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - David Ruiz
- Departament of Plant Breeding, CEBAS-CSIC, PO Box 164, E-30100 Espinardo, Murcia, Spain
| | - Bruno Huettel
- Max Planck-Genome-center Cologne, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
- Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany.
| |
Collapse
|
11
|
Campoy JA, Sun H, Goel M, Jiao WB, Folz-Donahue K, Wang N, Rubio M, Liu C, Kukat C, Ruiz D, Huettel B, Schneeberger K. Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol 2020; 21:306. [PMID: 33372615 PMCID: PMC7771071 DOI: 10.1186/s13059-020-02235-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/11/2020] [Indexed: 12/30/2022] Open
Abstract
Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets. After assembling the reads of each haplotype, the contigs are scaffolded to chromosome level using a genetic map derived from the gametes. We assemble the two genomes of a diploid apricot tree based on whole-genome sequencing of 445 individual pollen grains. The two haplotype assemblies (N50: 25.5 and 25.8 Mb) feature a haplotyping precision of greater than 99% and are accurately scaffolded to chromosome-level.
Collapse
Affiliation(s)
- José A Campoy
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Hequan Sun
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Manish Goel
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Wen-Biao Jiao
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Kat Folz-Donahue
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Nan Wang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Manuel Rubio
- Departament of Plant Breeding, CEBAS-CSIC, PO Box 164, E-30100 Espinardo, Murcia, Spain
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - David Ruiz
- Departament of Plant Breeding, CEBAS-CSIC, PO Box 164, E-30100 Espinardo, Murcia, Spain
| | - Bruno Huettel
- Max Planck-Genome-center Cologne, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
- Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany.
| |
Collapse
|
12
|
Ejigu GF, Jung J. Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. Biology (Basel) 2020; 9:E295. [PMID: 32962098 PMCID: PMC7565776 DOI: 10.3390/biology9090295] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022]
Abstract
Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide sequences. This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders. Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines. We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation. Further, we discuss quality-control practices and the need for re-annotation, and highlight the future of annotation.
Collapse
Affiliation(s)
| | - Jaehee Jung
- Department of Information and Communication Engineering, Myongji University, Yongin-si 17058, Gyeonggi-do, Korea;
| |
Collapse
|
13
|
Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020; 18:78. [PMID: 32605573 PMCID: PMC7329446 DOI: 10.1186/s12915-020-00808-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
Collapse
Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| |
Collapse
|
14
|
Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020. [PMID: 32605573 DOI: 10.1101/589804v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
Collapse
Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| |
Collapse
|
15
|
Tiukova IA, Jiang H, Dainat J, Hoeppner MP, Lantz H, Piskur J, Sandgren M, Nielsen J, Gu Z, Passoth V. Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540. Microorganisms 2019; 7:microorganisms7110489. [PMID: 31717754 PMCID: PMC6921048 DOI: 10.3390/microorganisms7110489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 01/21/2023] Open
Abstract
Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.
Collapse
Affiliation(s)
- Ievgeniia A. Tiukova
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE-412 96 Göteborg, Sweden;
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
- Correspondence: ; Tel.: +46-31-772-3801
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
| | - Marc P. Hoeppner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Henrik Lantz
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
| | - Jure Piskur
- Department of Biology, Lund University, 223 62 Lund, Sweden;
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE-412 96 Göteborg, Sweden;
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA;
| | - Volkmar Passoth
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
| |
Collapse
|
16
|
Tiukova IA, Pettersson ME, Hoeppner MP, Olsen RA, Käller M, Nielsen J, Dainat J, Lantz H, Söderberg J, Passoth V. Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis. PLoS One 2019; 14:e0215077. [PMID: 31042716 PMCID: PMC6493715 DOI: 10.1371/journal.pone.0215077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.
Collapse
Affiliation(s)
- Ievgeniia A. Tiukova
- Chalmers University of Technology, Department of Biology and Biological Engineering, Systems and Synthetic Biology, Göteborg, Sweden
- Swedish University of Agricultural Sciences, Department of Molecular Sciences, Uppsala, Sweden
| | - Mats E. Pettersson
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
| | - Marc P. Hoeppner
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Uppsala, Sweden
- Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology, Kiel, Germany
| | - Remi-Andre Olsen
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden
| | - Max Käller
- Royal Institute of Technology, Biotechnology and Health, School of Engineering Sciences in Chemistry, SciLifeLab, Stockholm, Sweden
- Stockholm University, Department of Biochemistry and Biophysics, SciLifeLab, Stockholm, Sweden
| | - Jens Nielsen
- Chalmers University of Technology, Department of Biology and Biological Engineering, Systems and Synthetic Biology, Göteborg, Sweden
| | - Jacques Dainat
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Uppsala, Sweden
| | - Henrik Lantz
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Uppsala, Sweden
| | - Jonas Söderberg
- Uppsala University, Department of Cell and Molecular Biology, Molecular Evolution, Uppsala, Sweden
| | - Volkmar Passoth
- Swedish University of Agricultural Sciences, Department of Molecular Sciences, Uppsala, Sweden
| |
Collapse
|
17
|
Gruenstaeudl M, Hartmaring Y. EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. PLoS One 2019; 14:e0210347. [PMID: 30629718 PMCID: PMC6328100 DOI: 10.1371/journal.pone.0210347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
Background The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant and fungal DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding. Methods A Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called ‘checklists’) for a subsequent upload to the annotated sequence section of the European Nucleotide Archive (ENA). The software tool, titled ‘EMBL2checklists’, automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates files that can be uploaded via the interactive Webin submission system of ENA. Results EMBL2checklists provides a simple, platform-independent tool that automates the conversion of common DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in four recent investigations, including plant phylogenetic and fungal metagenomic studies. Discussion EMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant and fungal biologists without bioinformatics expertise to generate submission-ready checklists from common DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.
Collapse
|