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Romanenko SA, Kliver SF, Serdyukova NA, Perelman PL, Trifonov VA, Seluanov A, Gorbunova V, Azpurua J, Pereira JC, Ferguson-Smith MA, Graphodatsky AS. Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human. Sci Rep 2023; 13:21055. [PMID: 38030702 PMCID: PMC10687270 DOI: 10.1038/s41598-023-46595-x] [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: 06/08/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.
| | - Sergei F Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, Copenhagen, Denmark
| | - Natalia A Serdyukova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jorge Azpurua
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Jorge C Pereira
- Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
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2
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Poisson W, Bastien A, Gilbert I, Carrier A, Prunier J, Robert C. Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding. Genet Sel Evol 2023; 55:47. [PMID: 37430194 DOI: 10.1186/s12711-023-00819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND The frequency of chromosomal rearrangements in Canadian breeding boars has been estimated at 0.91 to 1.64%. These abnormalities are widely recognized as a potential cause of subfertility in livestock production. Since artificial insemination is practiced in almost all intensive pig production systems, the use of elite boars carrying cytogenetic defects that have an impact on fertility can lead to major economic losses. To avoid keeping subfertile boars in artificial insemination centres and spreading chromosomal defects within populations, cytogenetic screening of boars is crucial. Different techniques are used for this purpose, but several issues are frequently encountered, i.e. environmental factors can influence the quality of results, the lack of genomic information outputted by these techniques, and the need for prior cytogenetic skills. The aim of this study was to develop a new pig karyotyping method based on fluorescent banding patterns. RESULTS The use of 207,847 specific oligonucleotides generated 96 fluorescent bands that are distributed across the 18 autosomes and the sex chromosomes. Tested alongside conventional G-banding, this oligo-banding method allowed us to identify four chromosomal translocations and a rare unbalanced chromosomal rearrangement that was not detected by conventional banding. In addition, this method allowed us to investigate chromosomal imbalance in spermatozoa. CONCLUSIONS The use of oligo-banding was found to be appropriate for detecting chromosomal aberrations in a Canadian pig nucleus and its convenient design and use make it an interesting tool for livestock karyotyping and cytogenetic studies.
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Affiliation(s)
- William Poisson
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Alexandre Bastien
- Plateforme d'imagerie et microscopie, Institut de biologie intégrative et des systèmes, Université Laval, Québec, QC, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Julien Prunier
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada.
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3
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Poisson W, Prunier J, Carrier A, Gilbert I, Mastromonaco G, Albert V, Taillon J, Bourret V, Droit A, Côté SD, Robert C. Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights. BMC Genomics 2023; 24:142. [PMID: 36959567 PMCID: PMC10037892 DOI: 10.1186/s12864-023-09189-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining. RESULTS We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids. CONCLUSIONS Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus.
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Affiliation(s)
- William Poisson
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | - Julien Prunier
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | | | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Arnaud Droit
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Steeve D Côté
- Caribou Ungava, Département de biologie and Centre d'études nordiques, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada.
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada.
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Albert PS, Birchler JA. Nitrous Oxide-Induced Metaphase Arrest: A Technique for Somatic Chromosome Analysis. Methods Mol Biol 2023; 2672:129-139. [PMID: 37335472 DOI: 10.1007/978-1-0716-3226-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Procedures to arrest metaphase chromosomes are used for determining chromosome numbers, chromosomal aberrations, and natural chromosome variation, as well as chromosome sorting. Here is described a technique of nitrous oxide gas treatment of freshly harvested root tips that is highly effective at producing an excellent mitotic index together with well-spread chromosomes. The details of the treatment and equipment used are provided. The metaphase spreads can be used directly for determining chromosome numbers or for in situ hybridization to reveal chromosomal features.
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Affiliation(s)
- Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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5
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Parakkunnel R, Bhojaraja Naik K, Susmita C, Girimalla V, Bhaskar KU, Sripathy KV, Shantharaja CS, Aravindan S, Kumar S, Lakhanpaul S, Bhat KV. Evolution and co-evolution: insights into the divergence of plant heat shock factor genes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1029-1047. [PMID: 35722513 PMCID: PMC9203654 DOI: 10.1007/s12298-022-01183-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/04/2022] [Indexed: 05/03/2023]
Abstract
The Heat Shock Factor (Hsf) genes are widely distributed across the plant kingdom regulating the plant response to various abiotic stresses. In addition to natural selection, breeding and accelerated selection changed the structure and function of Hsf genes. 1076 Hsf genes from 30 genera from primitive algae to the most advanced plant species and major crop plants were used for phylogenetic analysis. The interspecific divergence was studied with 11 members of genus Oryza while intraspecific divergence was studied with sesame pan-genome adapted to diverse ecological niches. B2 genes in eudicots and monocots originated separately while A1 gave rise to the recently evolved Class-C genes and land colonization happened with evolution of A1 genes. An increase in the number of lineages in the Oryza clade with the evolution of AA genome indicated independent domestication and positive selection was observed in > 53% of loci whereas the highly conserved homologues were under purifying selection. The paralogous genes under positive selection exhibited more domain changes for diversified function and increased fitness. A significant co-evolving cluster involving amino acids Phenylalanine, Lysine and Valine played crucial role in maintaining hydrophobic core along with highly conserved Tryptophan residues. A mutation of Glutamic acid to Glutamine was observed in A8 genes of Lamiales affecting protein solvency. Breeding resulted in accumulation of mutations reducing the hydrophobicity of proteins and a further reduction in protein aggregation. This study identify genome duplications, non-neutral selection and co-evolving residues as causing drastic changes in the conserved domain of Hsf proteins. Supplementary information The online version contains supplementary material available at 10.1007/s12298-022-01183-7.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - K Bhojaraja Naik
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - C Susmita
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh 275103 India
| | - Vanishree Girimalla
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - K Udaya Bhaskar
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - KV Sripathy
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - CS Shantharaja
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - S Aravindan
- 4Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, 110012 India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh 275103 India
| | | | - KV Bhat
- 4Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, 110012 India
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6
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Neale DB, Zimin AV, Zaman S, Scott AD, Shrestha B, Workman RE, Puiu D, Allen BJ, Moore ZJ, Sekhwal MK, De La Torre AR, McGuire PE, Burns E, Timp W, Wegrzyn JL, Salzberg SL. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3 (BETHESDA, MD.) 2022; 12:6460957. [PMID: 35100403 PMCID: PMC8728005 DOI: 10.1093/g3journal/jkab380] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Alison D Scott
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Bikash Shrestha
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Rachael E Workman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Zane J Moore
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Manoj K Sekhwal
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Emily Burns
- Save the Redwoods League, San Francisco, CA 94104, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
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7
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Tello-Ruiz MK, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol 2022; 2443:101-131. [PMID: 35037202 DOI: 10.1007/978-1-0716-2067-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end-users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.
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Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, USA.
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8
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Ha J, Satyawan D, Jeong H, Lee E, Cho KH, Kim MY, Lee SH. A near-complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program. THE PLANT GENOME 2021; 14:e20121. [PMID: 34275211 DOI: 10.1002/tpg2.20121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Mungbean (Vigna radiata L.), a fast-growing legume species, is an important source of carbohydrates and proteins in developing countries of Asia. Here, we constructed a near-complete genome sequence of mungbean with a scaffold N50 value of 5.2 Mb and only a 0.4% gap, with a total scaffold size of 475 Mb. We identified several misassembled pseudomolecules (Chr03, Chr04, Chr05, and Chr08) in the previous draft assembly; Chr03, Chr04, and Chr08 were assembled into one chromosome, and Chr05 was broken into two chromosomes in the improved reference genome assembly, thus providing more accurate linkage information to breeders. Additionally, using an ultra-high-resolution linkage map constructed based on resequencing data, we identified several quantitative trait loci (QTLs) and the underlying candidate genes affecting synchronous pod maturity (SPM). Mungbean homologs of two soybean ([Glycine max (L.) Merr.] flowering genes, E3 (phytochrome A) and J (early flowering 3), were identified as candidate genes for the QTLs, and the candidate genes for plant height, node number, and SPM showed critical nucleotide substitutions between the reference cultivar and other genotypes (landraces and wild accessions). Based on the analysis of genetic diversity among 276 accessions collected from 23 countries, we identified 36 selective sweep regions and observed that the overall genetic diversity of cultivars decreased to 30% of that in wild accessions postdomestication. The near-complete genome sequence of mungbean represents an important resource for genome-assisted improvement in the mungbean breeding program.
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Affiliation(s)
- Jungmin Ha
- Dep. of Plant Science, Gangneung-Wonju National Univ., Gangneung, Republic of Korea
| | - Dani Satyawan
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD-IAARD), Jl. Tentara Pelajar No. 3A, Bogor, 16111, Indonesia
| | - Haneul Jeong
- Dep. of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National Univ., Seoul, 08826, Republic of Korea
| | - Eunsoo Lee
- Dep. of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National Univ., Seoul, 08826, Republic of Korea
| | - Kang-Heum Cho
- Dep. of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National Univ., Seoul, 08826, Republic of Korea
| | - Moon Young Kim
- Dep. of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National Univ., Seoul, 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National Univ., Seoul, 08826, Republic of Korea
| | - Suk-Ha Lee
- Dep. of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National Univ., Seoul, 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National Univ., Seoul, 08826, Republic of Korea
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9
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Plackett ARG, Emms DM, Kelly S, Hetherington AM, Langdale JA. Conditional stomatal closure in a fern shares molecular features with flowering plant active stomatal responses. Curr Biol 2021; 31:4560-4570.e5. [PMID: 34450089 DOI: 10.1016/j.cub.2021.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/23/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Stomata evolved as plants transitioned from water to land, enabling carbon dioxide uptake and water loss to be controlled. In flowering plants, the most recently divergent land plant lineage, stomatal pores actively close in response to drought. In this response, the phytohormone abscisic acid (ABA) triggers signaling cascades that lead to ion and water loss in the guard cells of the stomatal complex, causing a reduction in turgor and pore closure. Whether this stimulus-response coupling pathway acts in other major land plant lineages is unclear, with some investigations reporting that stomatal closure involves ABA but others concluding that closure is passive. Here, we show that in the model fern Ceratopteris richardii active stomatal closure is conditional on sensitization by pre-exposure to either low humidity or exogenous ABA and is promoted by ABA. RNA-seq analysis and de novo transcriptome assembly reconstructed the protein-coding complement of the C. richardii genome, with coverage comparable to other plant models, enabling transcriptional signatures of stomatal sensitization and closure to be inferred. In both cases, changes in abundance of homologs of ABA, Ca2+, and ROS-related signaling components were observed, suggesting that the closure-response pathway is conserved in ferns and flowering plants. These signatures further suggested that sensitization is achieved by lowering the threshold required for a subsequent closure-inducing signal to trigger a response. We conclude that the canonical signaling network for active stomatal closure functioned in at least a rudimentary form in the stomata of the last common ancestor of ferns and flowering plants.
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Affiliation(s)
- Andrew R G Plackett
- University of Oxford, Department of Plant Sciences, South Parks Road, Oxford OX1 3RB, UK.
| | - David M Emms
- University of Oxford, Department of Plant Sciences, South Parks Road, Oxford OX1 3RB, UK
| | - Steven Kelly
- University of Oxford, Department of Plant Sciences, South Parks Road, Oxford OX1 3RB, UK
| | - Alistair M Hetherington
- University of Bristol, School of Biological Sciences, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jane A Langdale
- University of Oxford, Department of Plant Sciences, South Parks Road, Oxford OX1 3RB, UK
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10
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Mukherjee K, Rossi M, Salmela L, Boucher C. Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. Algorithms Mol Biol 2021; 16:6. [PMID: 34034751 PMCID: PMC8147420 DOI: 10.1186/s13015-021-00182-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/13/2021] [Indexed: 11/10/2022] Open
Abstract
Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770-15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics' Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as RMAPPER, and compare its performance against the assembler of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770-15775, 2006) and Solve by Bionano Genomics on data from three genomes: E. coli, human, and climbing perch fish (Anabas Testudineus). Our method was able to successfully run on all three genomes. The method of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770-15775, 2006) only successfully ran on E. coli. Moreover, on the human genome RMAPPER was at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies. Our software, RMAPPER is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/Rmapper .
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Vlachonasios K, Poulios S, Mougiou N. The Histone Acetyltransferase GCN5 and the Associated Coactivators ADA2: From Evolution of the SAGA Complex to the Biological Roles in Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:308. [PMID: 33562796 PMCID: PMC7915528 DOI: 10.3390/plants10020308] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 01/08/2023]
Abstract
Transcription of protein-encoding genes starts with forming a pre-initiation complex comprised of RNA polymerase II and several general transcription factors. To activate gene expression, transcription factors must overcome repressive chromatin structure, which is accomplished with multiprotein complexes. One such complex, SAGA, modifies the nucleosomal histones through acetylation and other histone modifications. A prototypical histone acetyltransferase (HAT) known as general control non-repressed protein 5 (GCN5), was defined biochemically as the first transcription-linked HAT with specificity for histone H3 lysine 14. In this review, we analyze the components of the putative plant SAGA complex during plant evolution, and current knowledge on the biological role of the key components of the HAT module, GCN5 and ADA2b in plants, will be summarized.
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Affiliation(s)
- Konstantinos Vlachonasios
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.P.); (N.M.)
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12
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Hoang PTN, Fiebig A, Novák P, Macas J, Cao HX, Stepanenko A, Chen G, Borisjuk N, Scholz U, Schubert I. Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. Sci Rep 2020; 10:19230. [PMID: 33154426 PMCID: PMC7645714 DOI: 10.1038/s41598-020-75728-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022] Open
Abstract
Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the monocot order Alismatales. They display the most rapid growth among flowering plants, vary ~ 14-fold in genome size and comprise five genera. Spirodela is the phylogenetically oldest genus with only two mainly asexually propagating species: S. polyrhiza (2n = 40; 160 Mbp/1C) and S. intermedia (2n = 36; 160 Mbp/1C). This study combined comparative cytogenetics and de novo genome assembly based on PacBio, Illumina and Oxford Nanopore (ON) reads to obtain the first genome reference for S. intermedia and to compare its genomic features with those of the sister species S. polyrhiza. Both species' genomes revealed little more than 20,000 putative protein-coding genes, very low rDNA copy numbers and a low amount of repetitive sequences, mainly Ty3/gypsy retroelements. The detection of a few new small chromosome rearrangements between both Spirodela species refined the karyotype and the chromosomal sequence assignment for S. intermedia.
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Affiliation(s)
- Phuong T N Hoang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
- Biology Faculty, Dalat University, District 8, Dalat City, Lamdong Province, Vietnam
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | - Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany.
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13
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Mayrose I, Lysak MA. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biol Evol 2020; 13:5923296. [PMID: 33566095 PMCID: PMC7875004 DOI: 10.1093/gbe/evaa220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
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Affiliation(s)
- Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Muggli MD, Puglisi SJ, Boucher C. Kohdista: an efficient method to index and query possible Rmap alignments. Algorithms Mol Biol 2019; 14:25. [PMID: 31867049 PMCID: PMC6907254 DOI: 10.1186/s13015-019-0160-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/19/2019] [Indexed: 11/23/2022] Open
Abstract
Background Genome-wide optical maps are ordered high-resolution restriction maps that give the position of occurrence of restriction cut sites corresponding to one or more restriction enzymes. These genome-wide optical maps are assembled using an overlap-layout-consensus approach using raw optical map data, which are referred to as Rmaps. Due to the high error-rate of Rmap data, finding the overlap between Rmaps remains challenging. Results We present Kohdista, which is an index-based algorithm for finding pairwise alignments between single molecule maps (Rmaps). The novelty of our approach is the formulation of the alignment problem as automaton path matching, and the application of modern index-based data structures. In particular, we combine the use of the Generalized Compressed Suffix Array (GCSA) index with the wavelet tree in order to build Kohdista. We validate Kohdista on simulated E. coli data, showing the approach successfully finds alignments between Rmaps simulated from overlapping genomic regions. Conclusion we demonstrate Kohdista is the only method that is capable of finding a significant number of high quality pairwise Rmap alignments for large eukaryote organisms in reasonable time.
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15
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Marchant DB, Sessa EB, Wolf PG, Heo K, Barbazuk WB, Soltis PS, Soltis DE. The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly. Sci Rep 2019; 9:18181. [PMID: 31796775 PMCID: PMC6890710 DOI: 10.1038/s41598-019-53968-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 11/04/2019] [Indexed: 01/04/2023] Open
Abstract
Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
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Affiliation(s)
- D Blaine Marchant
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Paul G Wolf
- Department of Biology, Utah State University, Logan, UT, 84322, USA
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Kweon Heo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
- The Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
- The Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
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16
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Sousa TDJ, Parise D, Profeta R, Parise MTD, Gomide ACP, Kato RB, Pereira FL, Figueiredo HCP, Ramos R, Brenig B, Costa da Silva ALD, Ghosh P, Barh D, Góes-Neto A, Azevedo V. Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes. Sci Rep 2019; 9:16387. [PMID: 31705053 PMCID: PMC6841979 DOI: 10.1038/s41598-019-52695-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 10/18/2019] [Indexed: 12/29/2022] Open
Abstract
The number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously. Also, the greatest challenge to the assembly progress is the presence of repetitive DNA regions. This article highlights the use of optical mapping, to detect and correct assembly errors in Corynebacterium pseudotuberculosis. We also demonstrate that choosing a reference genome should be done with caution to avoid assembly errors and loss of genetic information.
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Affiliation(s)
- Thiago de Jesus Sousa
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Doglas Parise
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Profeta
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Anne Cybelle Pinto Gomide
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Bentos Kato
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Luiz Pereira
- National Reference Laboratory for Aquatic Animal Diseases (AQUACEN) of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique Cesar Pereira Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases (AQUACEN) of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rommel Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University Göttingen, Göttingen, Germany
| | | | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, United States
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology, Nonakuri West Bengal, India
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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17
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Vaattovaara A, Brandt B, Rajaraman S, Safronov O, Veidenberg A, Luklová M, Kangasjärvi J, Löytynoja A, Hothorn M, Salojärvi J, Wrzaczek M. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Commun Biol 2019; 2:56. [PMID: 30775457 PMCID: PMC6368629 DOI: 10.1038/s42003-019-0306-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/14/2019] [Indexed: 01/01/2023] Open
Abstract
Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 emerged in secreted proteins. Domain duplications and rearrangements led to the appearance of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). The DUF26 is land plant-specific but structural analyses of PDLP ectodomains revealed strong similarity to fungal lectins and thus may constitute a group of plant carbohydrate-binding proteins. CRKs expanded through tandem duplications and preferential retention of duplicates following whole genome duplications, whereas PDLPs evolved according to the dosage balance hypothesis. We propose that new gene families mainly expand through small-scale duplications, while fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.
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Affiliation(s)
- Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Benjamin Brandt
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Omid Safronov
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Andres Veidenberg
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5 (POB56), FI-00014 Helsinki, Finland
| | - Markéta Luklová
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
- Present Address: Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC—Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5 (POB56), FI-00014 Helsinki, Finland
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
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18
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Shining a Spotlight on DNA: Single-Molecule Methods to Visualise DNA. Molecules 2019; 24:molecules24030491. [PMID: 30704053 PMCID: PMC6384704 DOI: 10.3390/molecules24030491] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/17/2019] [Accepted: 01/29/2019] [Indexed: 11/29/2022] Open
Abstract
The ability to watch single molecules of DNA has revolutionised how we study biological transactions concerning nucleic acids. Many strategies have been developed to manipulate DNA molecules to investigate mechanical properties, dynamics and protein–DNA interactions. Imaging methods using small molecules and protein-based probes to visualise DNA have propelled our understanding of complex biochemical reactions involving DNA. This review focuses on summarising some of the methodological developments made to visualise individual DNA molecules and discusses how these probes have been used in single-molecule biophysical assays.
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19
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Mukherjee K, Washimkar D, Muggli MD, Salmela L, Boucher C. Error correcting optical mapping data. Gigascience 2018; 7:5005021. [PMID: 29846578 PMCID: PMC6007263 DOI: 10.1093/gigascience/giy061] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/16/2018] [Indexed: 12/31/2022] Open
Abstract
Optical mapping is a unique system that is capable of producing high-resolution, high-throughput genomic map data that gives information about the structure of a genome . Recently it has been used for scaffolding contigs and for assembly validation for large-scale sequencing projects, including the maize, goat, and Amborella genomes. However, a major impediment in the use of this data is the variety and quantity of errors in the raw optical mapping data, which are called Rmaps. The challenges associated with using Rmap data are analogous to dealing with insertions and deletions in the alignment of long reads. Moreover, they are arguably harder to tackle since the data are numerical and susceptible to inaccuracy. We develop cOMet to error correct Rmap data, which to the best of our knowledge is the only optical mapping error correction method. Our experimental results demonstrate that cOMet has high prevision and corrects 82.49% of insertion errors and 77.38% of deletion errors in Rmap data generated from the Escherichia coli K-12 reference genome. Out of the deletion errors corrected, 98.26% are true errors. Similarly, out of the insertion errors corrected, 82.19% are true errors. It also successfully scales to large genomes, improving the quality of 78% and 99% of the Rmaps in the plum and goat genomes, respectively. Last, we show the utility of error correction by demonstrating how it improves the assembly of Rmap data. Error corrected Rmap data results in an assembly that is more contiguous and covers a larger fraction of the genome.
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Affiliation(s)
- Kingshuk Mukherjee
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville
| | - Darshan Washimkar
- Department of Computer Science, Colorado State University, Fort Collins
| | - Martin D Muggli
- Department of Computer Science, Colorado State University, Fort Collins
| | - Leena Salmela
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville
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20
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Hoang PNT, Michael TP, Gilbert S, Chu P, Motley ST, Appenroth KJ, Schubert I, Lam E. Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:670-684. [PMID: 30054939 DOI: 10.1111/tpj.14049] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/29/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable crops. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through vegetative propagation. Whole-genome sequencing using different approaches and clones yielded two reference maps. One for clone 9509, supported in its assembly by optical mapping of single DNA molecules, and one for clone 7498, supported by cytogenetic assignment of 96 fingerprinted bacterial artificial chromosomes (BACs) to its 20 chromosomes. However, these maps differ in the composition of several individual chromosome models. We validated both maps further to resolve these differences and addressed whether they could be due to chromosome rearrangements in different clones. For this purpose, we applied sequential multicolor fluorescence in situ hybridization (mcFISH) to seven S. polyrhiza clones, using 106 BACs that were mapped onto the 39 pseudomolecules for clone 7498. Furthermore we integrated high-depth Oxford Nanopore (ON) sequence data for clone 9509 to validate and revise the previously assembled chromosome models. We found no major structural rearrangements between these seven clones, identified seven chimeric pseudomolecules and Illumina assembly errors in the previous maps, respectively. A new S. polyrhiza genome map with high contiguity was produced with the ON sequence data and genome-wide synteny analysis supported the occurrence of two Whole Genome Duplication events during its evolution. This work generated a high confidence genome map for S. polyrhiza at the chromosome scale, and illustrates the complementarity of independent approaches to produce whole-genome assemblies in the absence of a genetic map.
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Affiliation(s)
- Phuong N T Hoang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, D-06466, Germany
- Dalat University, Lamdong Province, Vietnam
| | | | - Sarah Gilbert
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Philomena Chu
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | | | - Klaus J Appenroth
- Department of Plant Physiology, Matthias-Schleiden-Institute, Friedrich-Schiller- University of Jena, Jena, D-07743, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, D-06466, Germany
| | - Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
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21
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Prabhakaran Mariyamma N, Clarke KJ, Yu H, Wilton EE, Van Dyk J, Hou H, Schultz EA. Members of the Arabidopsis FORKED1-LIKE gene family act to localize PIN1 in developing veins. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4773-4790. [PMID: 29982821 PMCID: PMC6137986 DOI: 10.1093/jxb/ery248] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
The reticulate leaf vein pattern typical of angiosperms is proposed to have been a driving force for their evolutionary success. Vein pattern is established through auxin canalization via the auxin efflux protein PINFORMED1 (PIN1). During formation of vein loops, PIN1 cellular localization is increasingly restricted to either the basal side of cells in the lower domain or to the apical side in the upper domain. We previously identified the gene FORKED1 (FKD1) to be required for PIN1 asymmetric localization and for the formation of closed vein loops. FKD1 encodes a plant-specific protein with a domain of unknown function (DUF828) and a Pleckstrin-like homology domain. The Arabidopsis genome encodes eight similar proteins, which we term the FORKED1-LIKE (FL) gene family. Five FL family members localize primarily to the trans-Golgi network or the Golgi, and several co-localize with FKD1-green flourescent protein (GFP) and RABA1c, suggesting action in the secretory pathway. While single FL gene family mutations do not result in vein pattern defects, triple mutants with mutations in FKD1, FL2, and FL3 result in a more symmetric PIN1 localization and a highly disconnected vein pattern. Our data suggest that FL genes act redundantly with FKD1 in the secretory pathway to establish appropriate PIN1 localization in provascular tissue.
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Affiliation(s)
| | - Kurtis J Clarke
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Houlin Yu
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Emily E Wilton
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Jordan Van Dyk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Hongwei Hou
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
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Waminal NE, Pellerin RJ, Kim NS, Jayakodi M, Park JY, Yang TJ, Kim HH. Rapid and Efficient FISH using Pre-Labeled Oligomer Probes. Sci Rep 2018; 8:8224. [PMID: 29844509 PMCID: PMC5974128 DOI: 10.1038/s41598-018-26667-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/17/2018] [Indexed: 12/29/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is used to visualize the distribution of DNA elements within a genome. Conventional methods for FISH take 1-2 days. Here, we developed a simplified, rapid FISH technique using pre-labeled oligonucleotide probes (PLOPs) and tested the procedure using 18 PLOPs from 45S and 5S rDNA, Arabidopsis-type telomere, and newly-identified Panax ginseng-specific tandem repeats. The 16 developed rDNA PLOPs can be universally applied to plants and animals. The telomere PLOPs can be utilized in most plants with Arabidopsis-type telomeres. The ginseng-specific PLOP can be used to distinguish P. ginseng from related Panax species. Differential labeling of PLOPs allowed us to simultaneously visualize different target loci while reducing the FISH hybridization time from ~16 h to 5 min. PLOP-FISH is efficient, reliable, and rapid, making it ideal for routine analysis, especially of newly sequenced genomes using either universal or specific targets, such as novel tandem repeats identified from whole-genome sequencing data.
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Affiliation(s)
- Nomar Espinosa Waminal
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea.,Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Remnyl Joyce Pellerin
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea
| | - Nam-Soo Kim
- Department of Molecular Biosciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Hyun Hee Kim
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea.
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23
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Functional diversification of Arabidopsis SEC1-related SM proteins in cytokinetic and secretory membrane fusion. Proc Natl Acad Sci U S A 2018; 115:6309-6314. [PMID: 29844177 DOI: 10.1073/pnas.1722611115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sec1/Munc18 (SM) proteins contribute to membrane fusion by interacting with Qa-SNAREs or nascent trans-SNARE complexes. Gymnosperms and the basal angiosperm Amborella have only a single SEC1 gene related to the KEULE gene in Arabidopsis However, the genomes of most angiosperms including Arabidopsis encode three SEC1-related SM proteins of which only KEULE has been functionally characterized as interacting with the cytokinesis-specific Qa-SNARE KNOLLE during cell-plate formation. Here we analyze the closest paralog of KEULE named SEC1B. In contrast to the cytokinesis defects of keule mutants, sec1b mutants are homozygous viable. However, the keule sec1b double mutant was nearly gametophytically lethal, displaying collapsed pollen grains, which suggests substantial overlap between SEC1B and KEULE functions in secretion-dependent growth. SEC1B had a strong preference for interaction with the evolutionarily ancient Qa-SNARE SYP132 involved in secretion and cytokinesis, whereas KEULE interacted with both KNOLLE and SYP132. This differential interaction with Qa-SNAREs is likely conferred by domains 1 and 2a of the two SM proteins. Comparative analysis of all four possible combinations of the relevant SEC1 Qa-SNARE double mutants revealed that in cytokinesis, the interaction of SEC1B with KNOLLE plays no role, whereas the interaction of KEULE with KNOLLE is prevalent and functionally as important as the interactions of both SEC1B and KEU with SYP132 together. Our results suggest that functional diversification of the two SEC1-related SM proteins during angiosperm evolution resulted in enhanced interaction of SEC1B with Qa-SNARE SYP132, and thus a predominant role of SEC1B in secretion.
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Lyu H, He Z, Wu CI, Shi S. Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes. THE NEW PHYTOLOGIST 2018; 217:428-438. [PMID: 28960318 DOI: 10.1111/nph.14784] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/10/2017] [Indexed: 05/18/2023]
Abstract
Several clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing. To study this molecular convergence, we sequenced multiple mangrove genomes. In this study, we focused on the evolution of transposable elements (TEs) in relation to the genome size evolution. TEs, generally considered genomic parasites, are the most common components of woody plant genomes. Analyzing the long terminal repeat-retrotransposon (LTR-RT) type of TE, we estimated their death rates by counting solo-LTRs and truncated elements. We found that all lineages of mangroves massively and convergently reduce TE loads in comparison to their nonmangrove relatives; as a consequence, genome size reduction happens independently in all six mangrove lineages; TE load reduction in mangroves can be attributed to the paucity of young elements; the rarity of young LTR-RTs is a consequence of fewer births rather than access death. In conclusion, mangrove genomes employ a convergent strategy of TE load reduction by suppressing element origination in their independent adaptation to a new environment.
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Affiliation(s)
- Haomin Lyu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
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25
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Wang X, Fu S, Zhang X, Han X, Liu S, Kang L, Zhang Y, Liu Y. Visible laser-assisted reduction of plasmonic Ag nanoparticles with narrow-band optical absorption for colored holographic reconstruction. OPTICS EXPRESS 2017; 25:31253-31262. [PMID: 29245802 DOI: 10.1364/oe.25.031253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
Noble metal plasmonic resonance has been utilized in optical data storage widely for its excellent photo-transformation efficiency. TiO2 nanoporous films deposited with Ag nanoparticles present outstanding polarization-response and color-modulation ability. However, the low exposure-sensitivity at single wavelength inhibits their application in optical information processing, which is urgent to be improved by innovative methods. Here, we report that Ag nanoparticles were deposited efficiently via continuous laser irradiation in the TiO2 nanoporous film treated by tannic acid, presenting high-efficient monochromic absorption property. As a result, two sets of holograms were recorded sequentially at the same point of the film with orthogonal circular polarization configurations. The colored reconstruction of the mixed holograms was achieved by utilizing laser polarization state as chrominance segmentation channel. Our method provides a distinctive route for enhancing the photo-energy conversion efficiency of plasmonic nanoparticles, and paves a way to develop advanced display device.
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26
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Kang L, George P, Price DK, Sharakhov I, Michalak P. Mapping Genomic Scaffolds to Chromosomes Using Laser Capture Microdissection in Application to Hawaiian Picture-Winged Drosophila. Cytogenet Genome Res 2017; 152:204-212. [PMID: 29130948 DOI: 10.1159/000481790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2017] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing technologies have led to a decreased cost and an increased throughput in genome sequencing. Yet, many genome assemblies based on short sequencing reads have been assembled only to the scaffold level due to the lack of sufficient chromosome mapping information. Traditional ways of mapping scaffolds to chromosomes require a large amount of laboratory work and time to generate genetic and/or physical maps. To address this problem, we conducted a rapid technique which uses laser capture microdissection and enables mapping scaffolds of de novo genome assemblies directly to chromosomes in Hawaiian picture-winged Drosophila. We isolated and sequenced intact chromosome arms from larvae of D. differens. By mapping the reads of each chromosome to the recently assembled scaffolds from 3 Hawaiian picture-winged Drosophila species, at least 67% of the scaffolds were successfully assigned to chromosome arms. Even though the scaffolds are not ordered within a chromosome, the fast-generated chromosome information allows for chromosome-related analyses after genome assembling. We utilize this new information to test the faster-X evolution effect for the first time in these Hawaiian picture-winged Drosophila species.
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Affiliation(s)
- Lin Kang
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
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27
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Zhao P, Wang L, Zhao X, Chen G, Ma XF. A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. PLoS One 2017; 12:e0183778. [PMID: 28859098 PMCID: PMC5578489 DOI: 10.1371/journal.pone.0183778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 08/10/2017] [Indexed: 11/25/2022] Open
Abstract
Braya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B. humilis is mainly found on the Qinghai-Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78.41% were annotated by BLASTing versus public protein databases. The B. humilis transcriptome is characterized by a high level of sequence conservation compared with its close relative, Arabidopsis thaliana. We also used reciprocal blast to identify shared orthologous genes between B. humilis and four other sequenced Brassicaceae species (i.e. A. thaliana, A. lyrata, Capsella rubella, and Thellungiella parvula). To enable precise characterization of orthologous genes, the early-diverging basal angiosperm Amborella trichopoda was also included. A total of 6,689 orthologous genes were identified before stricter criteria for the determination of e-values, amino acid hit lengths, and identity values was applied to further reduce this list. This led to a final list of 381 core orthologous genes for B. humilis; 39 out of these genes are involved in salt and osmotic stress responses and estimations of nonsynonymous/synonymous substitution ratios for this species and A. thaliana orthologs show that these genes are under purifying selection in B. humilis. Expression of six genes was detected in B. humilis seedlings under salt and osmotic stress treatments. Comparable expression patterns to their counterparts in Arabidopsis suggest that these orthologous genes are both sequence and functional conservation. The results of this study demonstrate that the environmental adaptations of B. humilis are mainly the results of preexisting genetic components. Future work will be required to characterize the expression patterns of these orthologous genes in natural populations and will provide further insights into the adaptive mechanisms underlying the wide range of B. humilis adaptations.
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Affiliation(s)
- Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
- Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
| | - Lirong Wang
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, P. R. China
| | - Xin Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
- Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
- Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
- Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P. R. China
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28
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Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia. Chromosoma 2017; 126:729-739. [PMID: 28756515 DOI: 10.1007/s00412-017-0636-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/06/2017] [Accepted: 07/12/2017] [Indexed: 10/19/2022]
Abstract
The monophyletic duckweeds comprising five genera within the monocot order Alismatales are neotenic, free-floating, aquatic organisms with fast vegetative propagation. Some species are considered for efficient biomass production, for life stock feeding, and for (simultaneous) wastewater phytoremediation. The ancestral genus Spirodela consists of only two species, Spirodela polyrhiza and Spirodela intermedia, both with a similar small genome (~160 Mbp/1C). Reference genome drafts and a physical map of 96 BACs on the 20 chromosome pairs of S. polyrhiza strain 7498 are available and provide useful tools for further evolutionary studies within and between duckweed genera. Here we applied sequential comparative multicolor fluorescence in situ hybridization (mcFISH) to address homeologous chromosomes in S. intermedia (2n = 36), to detect chromosome rearrangements between both species and to elucidate the mechanisms which may have led to the chromosome number alteration after their evolutionary separation. Ten chromosome pairs proved to be conserved between S. polyrhiza and S. intermedia, the remaining ones experienced, depending on the assumed direction of evolution, translocations, inversion, and fissions, respectively. These results represent a first step to unravel karyotype evolution among duckweeds and are anchor points for future genome assembly of S. intermedia.
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Kucukoglu M, Nilsson J, Zheng B, Chaabouni S, Nilsson O. WUSCHEL-RELATED HOMEOBOX4 (WOX4)-like genes regulate cambial cell division activity and secondary growth in Populus trees. THE NEW PHYTOLOGIST 2017; 215:642-657. [PMID: 28609015 DOI: 10.1111/nph.14631] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/23/2017] [Indexed: 05/12/2023]
Abstract
Plant secondary growth derives from the meristematic activity of the vascular cambium. In Arabidopsis thaliana, cell divisions in the cambium are regulated by the transcription factor WOX4, a key target of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-RELATED 41 (CLE41) signaling pathway. However, function of the WOX4-like genes in plants that are dependent on a much more prolific secondary growth, such as trees, remains unclear. Here, we investigate the role of WOX4 and CLE41 homologs for stem secondary growth in Populus trees. In Populus, PttWOX4 genes are specifically expressed in the cambial region during vegetative growth, but not after growth cessation and during dormancy, possibly involving a regulation by auxin. In PttWOX4a/b RNAi trees, primary growth was not affected whereas the width of the vascular cambium was severely reduced and secondary growth was greatly diminished. Our data show that in Populus trees, PttWOX4 genes control cell division activity in the vascular cambium, and hence growth in stem girth. This activity involves the positive regulation of PttWOX4a/b through PttCLE41-related genes. Finally, expression profiling suggests that the CLE41 signaling pathway is an evolutionarily conserved program for the regulation of vascular cambium activity between angiosperm and gymnosperm tree species.
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Affiliation(s)
- Melis Kucukoglu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Jeanette Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Salma Chaabouni
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Ove Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
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Abstract
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These “fingerprints” of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility.
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31
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Yuan Y, Bayer PE, Batley J, Edwards D. Improvements in Genomic Technologies: Application to Crop Genomics. Trends Biotechnol 2017; 35:547-558. [DOI: 10.1016/j.tibtech.2017.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 12/13/2022]
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32
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Jiao WB, Schneeberger K. The impact of third generation genomic technologies on plant genome assembly. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:64-70. [PMID: 28231512 DOI: 10.1016/j.pbi.2017.02.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 05/20/2023]
Abstract
Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in. However, such assemblies are typically not based on the entire breadth of genomic technologies including genetic and physical maps and their contiguities tend to be low compared to the full-length gold standard reference sequences. Recently emerging third generation genomic technologies like long-read sequencing or optical mapping promise to bridge this quality gap and enable simple and cost-effective solutions for chromosomal-level assemblies.
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Affiliation(s)
- Wen-Biao Jiao
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Genome Plasticity and Computational Genomics, Cologne, Germany
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Genome Plasticity and Computational Genomics, Cologne, Germany.
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33
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Anger N, Fogliani B, Scutt CP, Gâteblé G. Dioecy in Amborella trichopoda: evidence for genetically based sex determination and its consequences for inferences of the breeding system in early angiosperms. ANNALS OF BOTANY 2017; 119:591-597. [PMID: 28110266 PMCID: PMC5604545 DOI: 10.1093/aob/mcw278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/09/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS This work aimed to gain insight into the breeding system at the base of living angiosperms through both character state reconstructions and the study of sex ratios and phenotypes in the likely sister to all other living angiosperms, Amborella trichopoda . METHODS Sex phenotypes were mapped onto a phylogeny of basally diverging angiosperms using maximum parsimony. In parallel, sex ratios and phenotypes were studied over two consecutive flowering seasons in an ex situ population of A. trichopoda , while the sex ratio of an in situ population was also assessed. KEY RESULTS Parsimony analyses failed to resolve the breeding system present at the base of living angiosperms, but indicated the importance of A. trichopoda for the future elucidation of this question. The ex situ A. trichopoda population studied showed a primary sex ratio close to 1:1, though sex ratio bias was found in the in situ population studied. Instances of sexual instability were quantified in both populations. CONCLUSIONS Sex ratio data support the presence of genetic sex determination in A. trichopoda , whose further elucidation may guide inferences on the breeding system at the base of living angiosperms. Sexual instability in A. trichopoda suggests the operation of epigenetic mechanisms, and the evolution of dioecy via a gynodioecious intermediate.
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Affiliation(s)
- Nicolas Anger
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
| | - Bruno Fogliani
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
- Université de la Nouvelle-Calédonie (UNC), Laboratoire Insulaire du Vivant et de l'Environnement (LIVE), 98851 Nouméa, New Caledonia
| | - Charles P. Scutt
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667: CNRS-INRA-Université de Lyon), Ecole Normale Supérieure de Lyon (ENS-Lyon), 46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Gildas Gâteblé
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
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34
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Bolser DM, Staines DM, Perry E, Kersey PJ. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data. Methods Mol Biol 2017; 1533:1-31. [PMID: 27987162 DOI: 10.1007/978-1-4939-6658-5_1] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for 39 sequenced plant species. Available data includes genome sequence, gene models, functional annotation, and polymorphic loci; for the latter, additional information including population structure, individual genotypes, linkage, and phenotype data is available for some species. Comparative data is also available, including genomic alignments and "gene trees," which show the inferred evolutionary history of each gene family represented in the resource. Access to the data is provided through a genome browser, which incorporates many specialist interfaces for different data types, through a variety of programmatic interfaces, and via a specialist data mining tool supporting rapid filtering and retrieval of bulk data. Genomic data from many non-plant species, including those of plant pathogens, pests, and pollinators, is also available via the same interfaces through other divisions of Ensembl.Ensembl Plants is updated 4-6 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.eu ).
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Affiliation(s)
- Dan M Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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35
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Delaux PM. Comparative phylogenomics of symbiotic associations. THE NEW PHYTOLOGIST 2017; 213:89-94. [PMID: 27582420 DOI: 10.1111/nph.14161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/19/2016] [Indexed: 05/25/2023]
Abstract
89 I. 89 II. 90 III. 90 IV. 91 V. 92 VI. 93 References 93 SUMMARY: Understanding the genetic bases of complex traits has been a main challenge in biology for decades. Comparative phylogenomics offers an opportunity to identify candidate genes associated with these complex traits. This approach initially developed in prokaryotes consists in looking at shared coevolution between genes and traits. It thus requires a precise reconstruction of the trait evolution, a large genomic sampling in the clades of interest and an accurate definition of orthogroups. Recently, with the growing body of sequenced plant genomes, comparative genomics has been successfully applied to plants to study the widespread arbuscular mycorrhizal symbiosis. Here I will use these findings to illustrate the main principles of comparative phylogenomic approaches and propose directions to improve our understanding of symbiotic associations.
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Affiliation(s)
- Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France
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van Dijk ADJ. Species-Specific Genome Sequence Databases: A Practical Review. Methods Mol Biol 2016; 1533:173-181. [PMID: 27987170 DOI: 10.1007/978-1-4939-6658-5_9] [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] [Indexed: 03/15/2023]
Abstract
This chapter presents a use case illustrating the search for homologues of a known protein in species-specific genome sequence databases. The results from different species-specific resources are compared to each other and to results obtained from a more general genome sequence database (Phytozome). Various options and settings relevant when searching these databases are discussed. For example, it is shown how the choice of reference sequence set in a given database influences the results one obtains. The provided examples illustrate some problems and pitfalls related to interpreting results obtained from species-specific genome sequence databases.
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Affiliation(s)
- A D J van Dijk
- Applied Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Laboratory of Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Biometris, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Chaney L, Sharp AR, Evans CR, Udall JA. Genome Mapping in Plant Comparative Genomics. TRENDS IN PLANT SCIENCE 2016; 21:770-780. [PMID: 27289181 DOI: 10.1016/j.tplants.2016.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 05/10/2023]
Abstract
Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.
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Affiliation(s)
- Lindsay Chaney
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Aaron R Sharp
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Carrie R Evans
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Joshua A Udall
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA.
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Zhang L, Yang X, Tian L, Chen L, Yu W. Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation. THE NEW PHYTOLOGIST 2016; 211:1424-39. [PMID: 27176118 DOI: 10.1111/nph.13999] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/31/2016] [Indexed: 05/17/2023]
Abstract
The cultivated peanut Arachis hypogaea (AABB) is thought to have originated from the hybridization of Arachis duranensis (AA) and Arachis ipaënsis (BB) followed by spontaneous chromosome doubling. In this study, we cloned and analyzed chromosome markers from cultivated peanut and its wild relatives. A fluorescence in situ hybridization (FISH)-based karyotyping cocktail was developed with which to study the karyotypes and chromosome evolution of peanut and its wild relatives. Karyotypes were constructed in cultivated peanut and its two putative progenitors using our FISH-based karyotyping system. Comparative karyotyping analysis revealed that chromosome organization was highly conserved in cultivated peanut and its two putative progenitors, especially in the B genome chromosomes. However, variations existed between A. duranensis and the A genome chromosomes in cultivated peanut, especially for the distribution of the interstitial telomere repeats (ITRs). A search of additional A. duranensis varieties from different geographic regions revealed both numeric and positional variations of ITRs, which were similar to the variations in tetraploid peanut varieties. The results provide evidence for the origin of cultivated peanut from the two diploid ancestors, and also suggest that multiple hybridization events of A. ipaënsis with different varieties of A. duranensis may have occurred during the origination of peanut.
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Affiliation(s)
- Laining Zhang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Xiaoyu Yang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - Lei Chen
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Weichang Yu
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
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The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. Sci Rep 2016; 6:30444. [PMID: 27457880 PMCID: PMC4960570 DOI: 10.1038/srep30444] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Abstract
Basic leucine zippers (bZIPs) form a large plant transcription factor family. C and S1 bZIP groups can heterodimerize, fulfilling crucial roles in seed development and stress response. S1 sequences also harbor a unique regulatory mechanism, termed Sucrose-Induced Repression of Translation (SIRT). The conservation of both C/S1 bZIP interactions and SIRT remains poorly characterized in non-model species, leaving their evolutionary origin uncertain and limiting crop research. In this work, we explored recently published plant sequencing data to establish a detailed phylogeny of C and S1 bZIPs, investigating their intertwined role in plant evolution, and the origin of SIRT. Our analyses clarified C and S1 bZIP orthology relationships in angiosperms, and identified S1 sequences in gymnosperms. We experimentally showed that the gymnosperm orthologs are regulated by SIRT, tracing back the origin of this unique regulatory mechanism to the ancestor of seed plants. Additionally, we discovered an earlier S ortholog in the charophyte algae Klebsormidium flaccidum, together with a C ortholog. This suggests that C and S groups originated by duplication from a single algal proto-C/S ancestor. Based on our observations, we propose a model wherein the C/S1 bZIP dimer network evolved in seed plants from pre-existing C/S bZIP interactions.
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Application of a modified drop method for high-resolution pachytene chromosome spreads in two Phalaenopsis species. Mol Cytogenet 2016; 9:44. [PMID: 27275186 PMCID: PMC4893830 DOI: 10.1186/s13039-016-0254-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Preparation of good chromosome spreads without cytoplasmic contamination is the crucial step in cytogenetic mapping. To date, cytogenetic research in the Orchidaceae family has been carried out solely on mitotic metaphase chromosomes. Well-spread meiotic pachytene chromosomes can provide higher resolution and fine detail for analysis of chromosomal structure and are also beneficial for chromosomal FISH (fluorescence in situ hybridization) mapping. However, an adequate method for the preparation of meiotic pachytene chromosomes in orchid species has not yet been reported. RESULTS Two Taiwanese native Phalaenopsis species were selected to test the modified drop method for preparation of meiotic pachytene chromosomes from pollinia. In this modified method, pollinia were ground and treated with an enzyme mixture to completely remove cell walls. Protoplasts were resuspended in ethanol/glacial acetic acid and dropped onto a wet inclined slide of 30° from a height of 0.5 m. The sample was then flowed down the inclined plane to spread the chromosomes. Hundreds of pachytene chromosomes with little to no cytoplasmic contamination were well spread on each slide. We also showed that the resolution of 45S rDNA-containing chromosomes at the pachytene stage was up to 20 times higher than that at metaphase. Slides prepared following this modified drop method were amenable to FISH mapping of both 45S and 5S rDNA on pachytene chromosomes and, after FISH, the chromosomal structure remained intact for further analysis. CONCLUSION This modified drop method is suitable for pachytene spreads from pollinia of Phalaenopsis orchids. The large number and high-resolution pachytene spreads, with little or no cytoplasmic contamination, prepared by the modified drop method could be used for FISH mapping of DNA fragments to accelerate the integration of cytogenetic and molecular research in Phalaenopsis orchids.
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Ribeiro T, Barrela RM, Bergès H, Marques C, Loureiro J, Morais-Cecílio L, Paiva JAP. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes. FRONTIERS IN PLANT SCIENCE 2016; 7:510. [PMID: 27148332 PMCID: PMC4840385 DOI: 10.3389/fpls.2016.00510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/31/2016] [Indexed: 05/30/2023]
Abstract
The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus.
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Affiliation(s)
- Teresa Ribeiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of LisbonLisboa, Portugal
| | - Ricardo M. Barrela
- Plant Cell Biotechnology Laboratory, Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
| | - Hélène Bergès
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques VégétalesCastanet-Tolosan, France
| | - Cristina Marques
- RAIZ, Instituto de Investigação da Floresta e PapelAveiro, Portugal
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of CoimbraCoimbra, Portugal
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of LisbonLisboa, Portugal
| | - Jorge A. P. Paiva
- Plant Cell Biotechnology Laboratory, Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
- Department of Integrative Plant Biology, Instytut Genetyki Roślin, Polskiej Akademii NaukPoznań, Poland
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Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E, Aury JM. MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data. BMC Bioinformatics 2016; 17:115. [PMID: 26936254 PMCID: PMC4776351 DOI: 10.1186/s12859-016-0969-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022] Open
Abstract
Background Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring. Results We present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a Whole Genome Profiling™ (WGP) map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the contiguity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase contiguity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency. Conclusions MaGuS is a powerful reference-free evaluator of assembly quality and a WGP map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the contiguity of large and complex genome assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0969-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohammed-Amin Madoui
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Carole Dossat
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Léo d'Agata
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Jan van Oeveren
- Keygene NV, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands.
| | | | - Jean-Marc Aury
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
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Wróblewska M, Dołzbłasz A, Zagórska-Marek B. The role of ABC genes in shaping perianth phenotype in the basal angiosperm Magnolia. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:230-238. [PMID: 26359638 DOI: 10.1111/plb.12392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
It is generally accepted that the genus Magnolia is characterised by an undifferentiated perianth, typically organised into three whorls of nearly identical tepals. In some species, however, we encountered interesting and significant perianth modifications. In Magnolia acuminata, M. liliiflora and M. stellata the perianth elements of the first whorl are visually different from the others. In M. stellata the additional, spirally arranged perianth elements are present above the first three whorls, which suggests that they have been formed within the domain of stamen primordia. In these three species, we analysed expression patterns of the key flower genes (AP1, AGL6, AP3, PI, AG) responsible for the identity of flower elements and correlated them with results of morphological and anatomical investigations. In all studied species the elements of the first whorl lacked the identity of petals (lack of AP3 and PI expression) but also that of leaves (presence of AGL6 expression), and this seems to prove their sepal character. The analysis of additional perianth elements of M. stellata, spirally arranged on the elongated floral axis, revealed overlapping and reduced activity of genes involved in specification of the identity of the perianth (AGL6) but also of generative parts (AG), even though no clear gradient of morphological changes could be observed. In conclusion, Magnolia genus is capable of forming, in some species, a perianth differentiated into a calyx (sepals) and corolla (petals). Spirally arranged, additional perianth elements of M. stellata, despite activity of AG falling basipetally, resemble petals.
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Affiliation(s)
- M Wróblewska
- Department of Plant Developmental Biology, Faculty of Biological Sciences, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | - A Dołzbłasz
- Department of Plant Developmental Biology, Faculty of Biological Sciences, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | - B Zagórska-Marek
- Department of Plant Developmental Biology, Faculty of Biological Sciences, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
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The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci Rep 2016; 6:19427. [PMID: 26786968 PMCID: PMC4726258 DOI: 10.1038/srep19427] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/11/2015] [Indexed: 12/13/2022] Open
Abstract
Globe artichoke (Cynara cardunculus var. scolymus) is an out-crossing, perennial, multi-use crop species that is grown worldwide and belongs to the Compositae, one of the most successful Angiosperm families. We describe the first genome sequence of globe artichoke. The assembly, comprising of 13,588 scaffolds covering 725 of the 1,084 Mb genome, was generated using ~133-fold Illumina sequencing data and encodes 26,889 predicted genes. Re-sequencing (30×) of globe artichoke and cultivated cardoon (C. cardunculus var. altilis) parental genotypes and low-coverage (0.5 to 1×) genotyping-by-sequencing of 163 F1 individuals resulted in 73% of the assembled genome being anchored in 2,178 genetic bins ordered along 17 chromosomal pseudomolecules. This was achieved using a novel pipeline, SOILoCo (Scaffold Ordering by Imputation with Low Coverage), to detect heterozygous regions and assign parental haplotypes with low sequencing read depth and of unknown phase. SOILoCo provides a powerful tool for de novo genome analysis of outcrossing species. Our data will enable genome-scale analyses of evolutionary processes among crops, weeds, and wild species within and beyond the Compositae, and will facilitate the identification of economically important genes from related species.
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45
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Soltis DE. Floral flexibility: Diversification of the flower. NATURE PLANTS 2016; 2:15211. [PMID: 27250754 DOI: 10.1038/nplants.2015.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA, the Department of Biology, University of Florida, Gainesville, Florida 32611, USA, and the Genetics Institute, University of Florida, Gainesville, Florida 32608, USA
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Tello-Ruiz MK, Stein J, Wei S, Youens-Clark K, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol 2016; 1374:141-63. [PMID: 26519404 DOI: 10.1007/978-1-4939-3167-5_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for economically important and research model crops, including wheat, potato, tomato, banana, grape, poplar, and Chlamydomonas. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) view a phylogenetic tree for a family of transcription factors, (2) explore genetic variation in the orthologues of a gene with a known trait association, and (3) upload, visualize, and privately share end user data into a new genome browser track.Moreover, this is the first publication describing Gramene's new web interface-intended to provide a simplified portal to the most complete and up-to-date set of plant genome and pathway annotations.
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Affiliation(s)
| | - Joshua Stein
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Ken Youens-Clark
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
- USDA-ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, 14853, USA.
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Bolser D, Staines DM, Pritchard E, Kersey P. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data. Methods Mol Biol 2016; 1374:115-40. [PMID: 26519403 DOI: 10.1007/978-1-4939-3167-5_6] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ).
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Affiliation(s)
- Dan Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Emily Pritchard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Paul Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Cao HX, Vu GTH, Wang W, Appenroth KJ, Messing J, Schubert I. The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. THE NEW PHYTOLOGIST 2016; 209:354-363. [PMID: 26305472 DOI: 10.1111/nph.13592] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/03/2015] [Indexed: 06/04/2023]
Abstract
Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. We selected physically mapped bacterial artificial chromosomes (BACs) containing Spirodela DNA inserts with little or no repetitive elements as probes for multicolor fluorescence in situ hybridization (mcFISH), using an optimized BAC pooling strategy, to validate its physical map and correlate it with its chromosome complement. By consecutive mcFISH analyses, we assigned the originally assembled 32 pseudomolecules (supercontigs) of the genomic sequences to the 20 chromosomes of S. polyrhiza. A Spirodela cytogenetic map containing 96 BAC markers with an average distance of 0.89 Mbp was constructed. Using a cocktail of 41 BACs in three colors, all chromosome pairs could be individualized simultaneously. Seven ancestral blocks emerged from duplicated chromosome segments of 19 Spirodela chromosomes. The chromosomally integrated genome of S. polyrhiza and the established prerequisites for comparative chromosome painting enable future studies on the chromosome homoeology and karyotype evolution of duckweed species.
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Affiliation(s)
- Hieu Xuan Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Giang Thi Ha Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Wenqin Wang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | | | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
- Faculty of Science and Central European Institute of Technology, Masaryk University, CZ-61137, Brno, Czech Republic
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Muggli MD, Puglisi SJ, Ronen R, Boucher C. Misassembly detection using paired-end sequence reads and optical mapping data. Bioinformatics 2015; 31:i80-8. [PMID: 26072512 PMCID: PMC4542784 DOI: 10.1093/bioinformatics/btv262] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Motivation: A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method called misSEQuel that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data. Our method also fulfills the critical need for open source computational methods for analyzing optical mapping data. We apply our method to various assemblies of the loblolly pine, Francisella tularensis, rice and budgerigar genomes. We generated and used stimulated optical mapping data for loblolly pine and F.tularensis and used real optical mapping data for rice and budgerigar. Results: Our results demonstrate that we detect more than 54% of extensively misassembled contigs and more than 60% of locally misassembled contigs in assemblies of F.tularensis and between 31% and 100% of extensively misassembled contigs and between 57% and 73% of locally misassembled contigs in assemblies of loblolly pine. Using the real optical mapping data, we correctly identified 75% of extensively misassembled contigs and 100% of locally misassembled contigs in rice, and 77% of extensively misassembled contigs and 80% of locally misassembled contigs in budgerigar. Availability and implementation:misSEQuel can be used as a post-processing step in combination with any genome assembler and is freely available at http://www.cs.colostate.edu/seq/. Contact:muggli@cs.colostate.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin D Muggli
- Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Simon J Puglisi
- Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Roy Ronen
- Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christina Boucher
- Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
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Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D. Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res 2015; 44:D1133-40. [PMID: 26553803 PMCID: PMC4702844 DOI: 10.1093/nar/gkv1179] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 10/13/2015] [Indexed: 12/21/2022] Open
Abstract
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials.
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Affiliation(s)
| | - Joshua Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Vindhya Amarasinghe
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Palitha Dharmawardhana
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joseph Mulvaney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - James Thomason
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Daniel M Bolser
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Arnaud Kerhornou
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Brandon Walts
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Nuno A Fonseca
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Laura Huerta
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Maria Keays
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Y Amy Tang
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Helen Parkinson
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Antonio Fabregat
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Sheldon McKay
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
| | - Joel Weiser
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
| | - Peter D'Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Lincoln Stein
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
| | - Robert Petryszak
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Paul J Kersey
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
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