1
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Dash PK, Gupta P, Sreevathsa R, Pradhan SK, Sanjay TD, Mohanty MR, Roul PK, Singh NK, Rai R. Phylogenomic Analysis of micro-RNA Involved in Juvenile to Flowering-Stage Transition in Photophilic Rice and Its Sister Species. Cells 2023; 12:1370. [PMID: 37408207 DOI: 10.3390/cells12101370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 07/07/2023] Open
Abstract
Vegetative to reproductive phase transition in phototropic plants is an important developmental process and is sequentially mediated by the expression of micro-RNA MIR172. To obtain insight into the evolution, adaptation, and function of MIR172 in photophilic rice and its wild relatives, we analyzed the genescape of a 100 kb segment harboring MIR172 homologs from 11 genomes. The expression analysis of MIR172 revealed its incremental accumulation from the 2-leaf to 10-leaf stage, with maximum expression coinciding with the flag-leaf stage in rice. Nonetheless, the microsynteny analysis of MIR172s revealed collinearity within the genus Oryza, but a loss of synteny was observed in (i) MIR172A in O. barthii (AA) and O. glaberima (AA); (ii) MIR172B in O. brachyantha (FF); and (iii) MIR172C in O. punctata (BB). Phylogenetic analysis of precursor sequences/region of MIR172 revealed a distinct tri-modal clade of evolution. The genomic information generated in this investigation through comparative analysis of MIRNA, suggests mature MIR172s to have evolved in a disruptive and conservative mode amongst all Oryza species with a common origin of descent. Further, the phylogenomic delineation provided an insight into the adaptation and molecular evolution of MIR172 to changing environmental conditions (biotic and abiotic) of phototropic rice through natural selection and the opportunity to harness untapped genomic regions from rice wild relatives (RWR).
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Affiliation(s)
- Prasanta K Dash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Payal Gupta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | | | | | - Mihir Ranjan Mohanty
- Department of Genetics & Plant Breeding (RRTTS, Jeypore), Odisha University of Agriculture and Technology, Bhubaneswar 751003, India
| | - Pravat K Roul
- Department of Genetics & Plant Breeding (RRTTS, Jeypore), Odisha University of Agriculture and Technology, Bhubaneswar 751003, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rhitu Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
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2
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Li Y, Liu H, Steenwyk JL, LaBella AL, Harrison MC, Groenewald M, Zhou X, Shen XX, Zhao T, Hittinger CT, Rokas A. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Curr Biol 2022; 32:5335-5343.e4. [PMID: 36334587 PMCID: PMC10615371 DOI: 10.1016/j.cub.2022.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
Examination of the changes in order and arrangement of homologous genes is key for understanding the mechanisms of genome evolution in eukaryotes. Previous comparisons between eukaryotic genomes have revealed considerable conservation across species that diverged hundreds of millions of years ago (e.g., vertebrates,1,2,3 bilaterian animals,4,5 and filamentous fungi6). However, understanding how genome organization evolves within and between eukaryotic major lineages remains underexplored. We analyzed high-quality genomes of 120 representative budding yeast species (subphylum Saccharomycotina) spanning ∼400 million years of eukaryotic evolution to examine how their genome organization evolved and to compare it with the evolution of animal and plant genome organization.7 We found that the decay of both macrosynteny (the conservation of homologous chromosomes) and microsynteny (the conservation of local gene content and order) was strongly associated with evolutionary divergence across budding yeast major clades. However, although macrosynteny decayed very fast, within ∼100 million years, the microsynteny of many genes-especially genes in metabolic clusters (e.g., in the GAL gene cluster8)-was much more deeply conserved both within major clades and across the subphylum. We further found that when genomes with similar evolutionary divergence times were compared, budding yeasts had lower macrosynteny conservation than animals and filamentous fungi but higher conservation than angiosperms. In contrast, budding yeasts had levels of microsynteny conservation on par with mammals, whereas angiosperms exhibited very low conservation. Our results provide new insight into the tempo and mode of the evolution of gene and genome organization across an entire eukaryotic subphylum.
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Affiliation(s)
- Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China.
| | - Hongyue Liu
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, 483 Wushan Road, Guangzhou 520643, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Taicheng Road 3, Yangling 712100, China
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, 1552 University Avenue, University of Wisconsin-Madison, Madison, WI 53726-4084, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
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3
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Kiyosawa A, Yonemaru JI, Mizuno H, Kanamori H, Wu J, Kawahigashi H, Goto K. Fine mapping of Rf5 region for a sorghum fertility restorer gene and microsynteny analysis across grass species. Breed Sci 2022; 72:141-149. [PMID: 36275935 PMCID: PMC9522528 DOI: 10.1270/jsbbs.21057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/20/2021] [Indexed: 06/16/2023]
Abstract
Cytoplasmic male sterility (CMS) is widely used to control pollination in the production of commercial F1 hybrid seed in sorghum. So far, 6 major fertility restorer genes, Rf1 to Rf6, have been reported in sorghum. Here, we fine-mapped the Rf5 locus on sorghum chromosome 5 using descendant populations of a 'Nakei MS-3A' × 'JN43' cross. The Rf5 locus was narrowed to a 140-kb region in BTx623 genome (161-kb in JN43) with 16 predicted genes, including 6 homologous to the rice fertility restorer Rf1 (PPR.1 to PPR.6). These 6 homologs have tandem pentatricopeptide repeat (PPR) motifs. Many Rf genes encode PPR proteins, which bind RNA transcripts and modulate gene expression at the RNA level. No PPR genes were detected at the Rf5 locus on the corresponding homologous chromosome of rice, foxtail millet, or maize, so this gene cluster may have originated by chromosome translocation and duplication after the divergence of sorghum from these species. Comparison of the sequences of these genes between fertile and CMS lines identified PPR.4 as the most plausible candidate gene for Rf5.
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Affiliation(s)
- Atsushi Kiyosawa
- Nagano Animal Industry Experiment Station, 10931-1 Kataoka, Shiojiri, Nagano 399-0711, Japan
| | - Jun-ichi Yonemaru
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Kawahigashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kazumi Goto
- Nagano Animal Industry Experiment Station, 10931-1 Kataoka, Shiojiri, Nagano 399-0711, Japan
- Nagano Agricultural Development Public Corporation, Kami-Ina Branch, 3497 Arai, Ina, Nagano 396-8666, Japan
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4
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Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MJM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BM, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol 2021; 12:1099-1188. [PMID: 32442304 PMCID: PMC7455281 DOI: 10.1093/gbe/evaa106] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
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Affiliation(s)
- Jan Philip Oeyen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Lead Contact
| | | | | | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | | | - Anja Buttstedt
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Germany
| | - Federica Calevro
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Elizabeth I Cash
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University.,Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Hubert Charles
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | | | - Andrew G Cridge
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Daniel Dowling
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Elizabeth Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Biology, Georgia Southern University, Statesboro.,Department of Entomology, Purdue University, West Lafayette
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Ewald Große-Wilde
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CULS), Praha 6-Suchdol, Czech Republic
| | - Cameron Gudobba
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Frank Hauser
- Department of Biology, University of Copenhagen, Denmark
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Emmanuelle Jacquin-Joly
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Versailles, France
| | | | - Jeffery W Jones
- Department of Biological Sciences, Oakland University, Rochester
| | - Steffen Klasberg
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Peter Lesný
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | - Mackenzie Lovegrove
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Sebastian Martin
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | | | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Nicolas Montagné
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Victoria C Moris
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Monica Munoz-Torres
- Berkeley Bioinformatics Open-source Projects (BBOP), Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Shwetha Canchi Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, Kansas
| | - Nicolas Parisot
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Thomas Pauli
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Ralph S Peters
- Arthropoda Department, Center for Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Emma Persyn
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Björn Marcus von Reumont
- Institute for Insect Biotechnology, University of Gießen, Germany.,Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | | | - Felipe A Simao
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - John Skelly
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | | | - Aaron L Stahl
- Department of Biological Sciences, University of Cincinnati.,Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida
| | - Megumi Sumitani
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Owashi, Tsukuba, Japan
| | - Elise M Szuter
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University
| | - Olivia Tidswell
- Biochemistry Department, University of Otago, Dunedin, New Zealand.,Zoology Department, University of Cambridge, United Kingdom
| | | | - Lucia Vedder
- Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Daisuke S Yamamoto
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Yakushiji, Shimotsuke, Japan
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Tanja Ziesmann
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Masatsugu Hatakeyama
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
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5
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Jiang L, Song C, Zhu X, Yang J. SWEET Transporters and the Potential Functions of These Sequences in Tea ( Camellia sinensis). Front Genet 2021; 12:655843. [PMID: 33868386 PMCID: PMC8044585 DOI: 10.3389/fgene.2021.655843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/15/2021] [Indexed: 01/04/2023] Open
Abstract
Tea (Camellia sinensis) is an important economic beverage crop. Its flowers and leaves could be used as healthcare tea for its medicinal value. SWEET proteins were recently identified in plants as sugar transporters, which participate in diverse physiological processes, including pathogen nutrition, seed filling, nectar secretion, and phloem loading. Although SWEET genes have been characterized and identified in model plants, such as Arabidopsis thaliana and Oryza sativa, there is very little knowledge of these genes in C. sinensis. In this study, 28 CsSWEETs were identified in C. sinensis and further phylogenetically divided into four subfamilies with A. thaliana. These identified CsSWEETs contained seven transmembrane helixes (TMHs) which were generated by an ancestral three-TMH unit with an internal duplication experience. Microsynteny analysis revealed that the large-scale duplication events were the main driving forces for members from CsSWEET family expansion in C. sinensis. The expression profiles of the 28 CsSWEETs revealed that some genes were highly expressed in reproductive tissues. Among them, CsSWEET1a might play crucial roles in the efflux of sucrose, and CsSWEET17b could control fructose content as a hexose transporter in C. sinensis. Remarkably, CsSWEET12 and CsSWEET17c were specifically expressed in flowers, indicating that these two genes might be involved in sugar transport during flower development. The expression patterns of all CsSWEETs were differentially regulated under cold and drought treatments. This work provided a systematic understanding of the members from the CsSWEET gene family, which would be helpful for further functional studies of CsSWEETs in C. sinensis.
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Affiliation(s)
- Lan Jiang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, China
| | - Xi Zhu
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Jianke Yang
- School of Preclinical Medicine, Wannan Medical College, Wuhu, China
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6
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Ferguson KB, Pannebakker BA, Centurión A, van den Heuvel J, Nieuwenhuis R, Becker FFM, Schijlen E, Thiel A, Zwaan BJ, Verhulst EC. Bracon brevicornis Genome Showcases the Potential of Linked-Read Sequencing in Identifying a Putative Complementary Sex Determiner Gene. Genes (Basel) 2020; 11:E1390. [PMID: 33255162 PMCID: PMC7759789 DOI: 10.3390/genes11121390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 01/24/2023] Open
Abstract
Bracon brevicornis is an ectoparasitoid of a wide range of larval-stage Lepidopterans, including several pests of important crops, such as the corn borer, Ostrinia nubilalis. It is also one of the earliest documented cases of complementary sex determination in Hymenoptera. Here, we present the linked-read-based genome of B. brevicornis, complete with an ab initio-derived annotation and protein comparisons with fellow braconids, Fopius arisanus and Diachasma alloeum. We demonstrate the potential of linked-read assemblies in exploring regions of heterozygosity and search for structural and homology-derived evidence of the complementary sex determiner gene (csd).
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Affiliation(s)
- Kim B. Ferguson
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Bart A. Pannebakker
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Alejandra Centurión
- Population and Evolutionary Ecology Group, Institute of Ecology, FB02, University of Bremen, 28359 Bremen, Germany; (A.C.); (A.T.)
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Ronald Nieuwenhuis
- Bioscience, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (R.N.); (E.S.)
| | - Frank F. M. Becker
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Elio Schijlen
- Bioscience, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (R.N.); (E.S.)
| | - Andra Thiel
- Population and Evolutionary Ecology Group, Institute of Ecology, FB02, University of Bremen, 28359 Bremen, Germany; (A.C.); (A.T.)
| | - Bas J. Zwaan
- Laboratory of Genetics, Wageningen University & Research, 6708PB Wageningen, The Netherlands; (B.A.P.); (J.v.d.H.); (F.F.M.B.); (B.J.Z.)
| | - Eveline C. Verhulst
- Laboratory of Entomology, Wageningen University & Research, 6708PB Wageningen, The Netherlands;
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7
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Abstract
The GLIS family transcription factors, GLIS1 and GLIS3, potentiate generation of induced pluripotent stem cells (iPSCs). In contrast, another GLIS family member, GLIS2, suppresses cell reprograming. To understand how these disparate roles arose, we examined evolutionary origins and genomic organization of GLIS genes. Comprehensive phylogenetic analysis shows that GLIS1 and GLIS3 originated during vertebrate whole genome duplication, whereas GLIS2 is a sister group to the GLIS1/3 and GLI families. This result is consistent with their opposing functions in cell reprograming. Glis1 evolved faster than Glis3, losing many protein-interacting motifs. This suggests that Glis1 acquired new functions under weakened evolutionary constraints. In fact, GLIS1 induces induced pluripotent stem cells more strongly. Transcriptomic data from various animal embryos demonstrate that glis1 is maternally expressed in some tetrapods, whereas vertebrate glis3 and invertebrate glis1/3 genes are rarely expressed in oocytes, suggesting that vertebrate (or tetrapod) Glis1 acquired a new expression domain and function as a maternal factor. Furthermore, comparative genomic analysis reveals that glis1/3 is part of a bilaterian-specific gene cluster, together with rfx3, ndc1, hspb11, and lrrc42. Because known functions of these genes are related to cilia formation and function, the last common ancestor of bilaterians may have acquired this cluster by shuffling gene order to establish more sophisticated epithelial tissues involving cilia. This evolutionary study highlights the significance of GLIS1/3 for cell reprograming, development, and diseases in ciliated organs such as lung, kidney, and pancreas.
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Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahito Matsumoto
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Advanced Diabetic Therapeutics, Department of Metabolic Endocrinology, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Yagi
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasushi Okazaki
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
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8
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Cao Y, Meng D, Li X, Wang L, Cai Y, Jiang L. A Chinese White Pear ( Pyrus bretschneideri) BZR Gene PbBZR1 Act as a Transcriptional Repressor of Lignin Biosynthetic Genes in Fruits. Front Plant Sci 2020; 11:1087. [PMID: 32765567 PMCID: PMC7379032 DOI: 10.3389/fpls.2020.01087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/01/2020] [Indexed: 05/08/2023]
Abstract
BZR transcription factors play essential roles in plant growth and environmental stimuli, and they are also the positive regulators of Brassinosteroid (BR) signal transduction in diverse plants. In addition, BZR TFs, as crucial regulators of BR synthesis, may have multiple stress-resistance functions and their related regulatory mechanisms have been well illustrated in model plants. Here, we carried out a genome-wide identification of BZR members in Chinese pear (Pyrus bretschneideri) and identified 13 members. By comparative analysis in five Rosaceae genomes, BZR members in the pear genome may have undergone large-scale duplication events during evolution. Purifying selection played an important role in almost all of the orthologous and paralogous gene pairs. According to the expression analysis of the PbBZRs during fruit development, three PbBZRs were selected for detailed analysis. Transcriptional activation assays presented that PbBZR1 repressed the promoters of P. bretschneideri lignin biosynthetic genes, such as PbCES9, PbCOMT3, and PbHCT6. Our study traces the evolution of BZR gene family members in Rosaceae genomes and illustrates that the rates of gene loss and gain are far from equilibrium in different species. At the same time, our results suggest that PbBZR1 may be involved in the negative regulation of lignin biosynthesis.
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Affiliation(s)
- Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaoxu Li
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
- *Correspondence: Lihu Wang, ; Yongping Cai, ; Lan Jiang,
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- *Correspondence: Lihu Wang, ; Yongping Cai, ; Lan Jiang,
| | - Lan Jiang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China
- *Correspondence: Lihu Wang, ; Yongping Cai, ; Lan Jiang,
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9
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Abdullah M, Cao Y, Cheng X, Shakoor A, Su X, Gao J, Cai Y. Genome-Wide Analysis Characterization and Evolution of SBP Genes in Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume. Front Genet 2018; 9:64. [PMID: 29552026 PMCID: PMC5841269 DOI: 10.3389/fgene.2018.00064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/12/2018] [Indexed: 12/04/2022] Open
Abstract
The SQUAMOSA promoter binding protein (SBP)-box proteins are plant-specific transcriptional factors in plants. SBP TFs are known to play important functions in a diverse development process and also related in the process of evolutionary novelties. SBP gene family has been characterized in several plant species, but little is known about molecular evolution, functional divergence and comprehensive study of SBP gene family in Rosacea. We carried out genome-wide investigations and identified 14, 32, 17, and 17 SBP genes from four Rosacea species (Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume, respectively). According to phylogenetic analysis arranged the SBP protein sequences in seven groups. Localization of SBP genes presented an uneven distribution on corresponding chromosomes of Rosacea species. Our analyses designated that the SBP genes duplication events (segmental and tandem) and divergence. In addition, due to highly conserved structure pattern of SBP genes, recommended that highly conserved region of microsyneteny in the Rosacea species. Type I and II functional divergence was detected among various amino acids in SBP proteins, while there was no positive selection according to substitutional model analysis using PMAL software. These results recommended that the purifying selection might be leading force during the evolution process and dominate conservation of SBP genes in Rosacea species according to environmental selection pressure analysis. Our results will provide basic understanding and foundation for future research insights on the evolution of the SBP genes in Rosacea.
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Affiliation(s)
- Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yunpeng Cao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Awais Shakoor
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Xueqiang Su
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Junshan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
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10
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Cao Y, Han Y, Meng D, Li G, Li D, Abdullah M, Jin Q, Lin Y, Cai Y. Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca. Front Genet 2017; 8:78. [PMID: 28663757 PMCID: PMC5471313 DOI: 10.3389/fgene.2017.00078] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022] Open
Abstract
WUSCHEL-related homeobox (WOX) family is one of the largest group of transcription factors (TFs) specifically found in plant kingdom. WOX TFs play an important role in plant development processes and evolutionary novelties. Although the roles of WOXs in Arabidopsis and rice have been well-studied, however, little are known about the relationships among the main clades in the molecular evolution of these genes in Rosaceae. Here, we carried out a genome-wide analysis and identified 14, 10, 10, and 9 of WOX genes from four Rosaceae species (Fragaria vesca, Prunus persica, Prunus mume, and Pyrus bretschneideri, respectively). According to evolutionary analysis, as well as amino acid sequences of their homodomains, these genes were divided into three clades with nine subgroups. Furthermore, due to the conserved structural patterns among these WOX genes, it was proposed that there should exist some highly conserved regions of microsynteny in the four Rosaceae species. Moreover, most of WOX gene pairs were presented with the conserved orientation among syntenic genome regions. In addition, according to substitution models analysis using PMAL software, no significant positive selection was detected, but type I functional divergence was identified among certain amino acids in WOX protein. These results revealed that the relaxed purifying selection might be the main driving force during the evolution of WOX genes in the tested Rosaceae species. Our result will be useful for further precise research on evolution of the WOX genes in family Rosaceae.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Guohui Li
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Dahui Li
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Muhammad Abdullah
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
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11
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Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton JM, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M, Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE. Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple. Front Plant Sci 2017; 8:1923. [PMID: 29176988 PMCID: PMC5686452 DOI: 10.3389/fpls.2017.01923] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 05/17/2023]
Abstract
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
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Affiliation(s)
- Jorge Urrestarazu
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
- Department of Agricultural Sciences, Public University of Navarre, Pamplona, Spain
- *Correspondence: Jorge Urrestarazu
| | - Hélène Muranty
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Caroline Denancé
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Diane Leforestier
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Elisa Ravon
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Arnaud Guyader
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Rémi Guisnel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Laurence Feugey
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Sébastien Aubourg
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Marc Lateur
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Patrick Houben
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | | | - Jiri Sedlak
- Research and Breeding Institute of Pomology Holovousy Ltd., Horice, Czechia
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | | | | | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | - Charles Poncet
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Anthony Théron
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Shigeki Moriya
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Marco C. A. M. Bink
- Wageningen UR, Biometris, Wageningen, Netherlands
- Hendrix Genetics, Boxmeer, Netherlands
| | - François Laurens
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Charles-Eric Durel
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12
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Cao Y, Han Y, Jin Q, Lin Y, Cai Y. Comparative Genomic Analysis of the GRF Genes in Chinese Pear ( Pyrus bretschneideri Rehd), Poplar ( Populous), Grape ( Vitis vinifera), Arabidopsis and Rice ( Oryza sativa). Front Plant Sci 2016; 7:1750. [PMID: 27933074 PMCID: PMC5121280 DOI: 10.3389/fpls.2016.01750] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/07/2016] [Indexed: 05/20/2023]
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species), Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and Chinese pear (one of the economical fruit crops). In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa), 8 genes in grape (Vitis vinifera), 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa) and 10 genes in Chinese pear (Pyrus bretschneideri). The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection plays an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
- *Correspondence: Yongping Cai,
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13
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Cao Y, Han Y, Meng D, Li D, Jin Q, Lin Y, Cai Y. Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear ( Pyrus bretschneideri). Front Plant Sci 2016; 7:1874. [PMID: 28018406 PMCID: PMC5145892 DOI: 10.3389/fpls.2016.01874] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/28/2016] [Indexed: 05/22/2023]
Abstract
Peroxidases (PRXs) are widely existed in various organisms and could be divided into different types according to their structures and functions. Specifically, the Class III Peroxidase, a plant-specific multi-gene family, involves in many physiological processes, such as the metabolism of auxin, the extension and thickening of cell wall, as well as the formation of lignin. By searching the pear genome database, 94 non-redundant PRXs from Pyrus bretschneideri (PbPRXs) were identified. Subsequently, analysis of phylogenetic relationships, gene structures, conserved motifs, and microsynteny was performed. These PbPRXs were unevenly distributed among 17 chromosomes of pear. In addition, 26 segmental duplication events but only one tandem duplication were occurred in these PbPRXs, implying segmental duplication was the main contributor to the expansion of the PbPRX family. By the Ka/Ks analysis, 26 out of 27 duplicated PbPRXs has experienced purifying selection. Twenty motifs were identified in PbPRXs based on the MEME analysis, 11 of which were enriched in pear. A total of 41 expressed genes were identified from ESTs of pear fruit. According to qRT-PCR, the expression trends of five PbPRXs in subgroup C were consistent with the change of lignin content during pear fruit development. So we inferred that the five PbPRXs were candidate genes involved in the lignin synthesis pathway. These results provided useful information for further researches of PRX genes in pear.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University Hefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Dahui Li
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University Hefei, China
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14
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Suwabe K, Suzuki G, Nunome T, Hatakeyama K, Mukai Y, Fukuoka H, Matsumoto S. Microstructure of a Brassica rapa genome segment homoeologous to the resistance gene cluster on Arabidopsis chromosome 4. Breed Sci 2012; 62:170-7. [PMID: 23136528 PMCID: PMC3405966 DOI: 10.1270/jsbbs.62.170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 03/28/2012] [Indexed: 05/23/2023]
Abstract
Genome evolution is a continuous process and genomic rearrangement occurs both within and between species. With the sequencing of the Arabidopsis thaliana genome, comparative genetics and genomics offer new insights into plant biology. The genus Brassica offers excellent opportunities with which to compare genomic synteny so as to reveal genome evolution. During a previous genetic analysis of clubroot resistance in Brassica rapa, we identified a genetic region that is highly collinear with Arabidopsis chromosome 4. This region corresponds to a disease resistance gene cluster in the A. thaliana genome. Relying on synteny with Arabidopsis, we fine-mapped the region and found that the location and order of the markers showed good correspondence with those in Arabidopsis. Microsynteny on a physical map indicated an almost parallel correspondence, with a few rearrangements such as inversions and insertions. The results show that this genomic region of Brassica is conserved extensively with that of Arabidopsis and has potential as a disease resistance gene cluster, although the genera diverged 20 million years ago.
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Affiliation(s)
- Keita Suwabe
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan
| | - Tsukasa Nunome
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Katsunori Hatakeyama
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Yasuhiko Mukai
- Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Satoru Matsumoto
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
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15
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Figueira TRES, Okura V, Rodrigues da Silva F, Jose da Silva M, Kudrna D, Ammiraju JSS, Talag J, Wing R, Arruda P. A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome. BMC Res Notes 2012; 5:185. [PMID: 22524198 PMCID: PMC3419638 DOI: 10.1186/1756-0500-5-185] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 04/23/2012] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Sugarcane breeding has significantly progressed in the last 30 years, but achieving additional yield gains has been difficult because of the constraints imposed by the complex ploidy of this crop. Sugarcane cultivars are interspecific hybrids between Saccharum officinarum and Saccharum spontaneum. S. officinarum is an octoploid with 2n = 80 chromosomes while S. spontaneum has 2n = 40 to 128 chromosomes and ploidy varying from 5 to 16. The hybrid genome is composed of 70-80% S. officinaram and 5-20% S. spontaneum chromosomes and a small proportion of recombinants. Sequencing the genome of this complex crop may help identify useful genes, either per se or through comparative genomics using closely related grasses. The construction and sequencing of a bacterial artificial chromosome (BAC) library of an elite commercial variety of sugarcane could help assembly the sugarcane genome. RESULTS A BAC library designated SS_SBa was constructed with DNA isolated from the commercial sugarcane variety SP80-3280. The library contains 36,864 clones with an average insert size of 125 Kb, 88% of which has inserts larger than 90 Kb. Based on the estimated genome size of 760-930 Mb, the library exhibits 5-6 times coverage the monoploid sugarcane genome. Bidirectional BAC end sequencing (BESs) from a random sample of 192 BAC clones sampled genes and repetitive elements of the sugarcane genome. Forty-five per cent of the total BES nucleotides represents repetitive elements, 83% of which belonging to LTR retrotransposons. Alignment of BESs corresponding to 42 BACs to the genome sequence of the 10 sorghum chromosomes revealed regions of microsynteny, with expansions and contractions of sorghum genome regions relative to the sugarcane BAC clones. In general, the sampled sorghum genome regions presented an average 29% expansion in relation to the sugarcane syntenic BACs. CONCLUSION The SS_SBa BAC library represents a new resource for sugarcane genome sequencing. An analysis of insert size, genome coverage and orthologous alignment with the sorghum genome revealed that the library presents whole genome coverage. The comparison of syntenic regions of the sorghum genome to 42 SS_SBa BES pairs revealed that the sorghum genome is expanded in relation to the sugarcane genome.
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Affiliation(s)
- Thais Rezende e Silva Figueira
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | - Vagner Okura
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | | | - Marcio Jose da Silva
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Jetty SS Ammiraju
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Rod Wing
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
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16
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Ren XY, Stiekema WJ, Nap JP. Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains. Plant Mol Biol 2007; 65:205-17. [PMID: 17641976 PMCID: PMC2039854 DOI: 10.1007/s11103-007-9209-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 07/06/2007] [Indexed: 05/16/2023]
Abstract
Chromosomal coexpression domains are found in a number of different genomes under various developmental conditions. The size of these domains and the number of genes they contain vary. Here, we define local coexpression domains as adjacent genes where all possible pair-wise correlations of expression data are higher than 0.7. In rice, such local coexpression domains range from predominantly two genes, up to 4, and make up approximately 5% of the genomic neighboring genes, when examining different expression platforms from the public domain. The genes in local coexpression domains do not fall in the same ontology category significantly more than neighboring genes that are not coexpressed. Duplication, orientation or the distance between the genes does not solely explain coexpression. The regulation of coexpression is therefore thought to be regulated at the level of chromatin structure. The characteristics of the local coexpression domains in rice are strikingly similar to such domains in the Arabidopsis genome. Yet, no microsynteny between local coexpression domains in Arabidopsis and rice could be identified. Although the rice genome is not yet as extensively annotated as the Arabidopsis genome, the lack of conservation of local coexpression domains may indicate that such domains have not played a major role in the evolution of genome structure or in genome conservation.
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Affiliation(s)
- Xin-Ying Ren
- Applied Bioinformatics, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Laboratory of Bioinformatics, Plant Sciences Group, Wageningen University and Research Centre, 6703 HA Wageningen, The Netherlands
| | - Willem J. Stiekema
- Laboratory of Bioinformatics, Plant Sciences Group, Wageningen University and Research Centre, 6703 HA Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
| | - Jan-Peter Nap
- Applied Bioinformatics, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
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17
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Armstrong MR, Whisson SC, Pritchard L, Bos JIB, Venter E, Avrova AO, Rehmany AP, Böhme U, Brooks K, Cherevach I, Hamlin N, White B, Fraser A, Lord A, Quail MA, Churcher C, Hall N, Berriman M, Huang S, Kamoun S, Beynon JL, Birch PRJ. An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci U S A 2005; 102:7766-71. [PMID: 15894622 PMCID: PMC1140420 DOI: 10.1073/pnas.0500113102] [Citation(s) in RCA: 361] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2005] [Indexed: 01/23/2023] Open
Abstract
The oomycete Phytophthora infestans causes late blight, the potato disease that precipitated the Irish famines in 1846 and 1847. It represents a reemerging threat to potato production and is one of >70 species that are arguably the most devastating pathogens of dicotyledonous plants. Nevertheless, little is known about the molecular bases of pathogenicity in these algae-like organisms or of avirulence molecules that are perceived by host defenses. Disease resistance alleles, products of which recognize corresponding avirulence molecules in the pathogen, have been introgressed into the cultivated potato from a wild species, Solanum demissum, and R1 and R3a have been identified. We used association genetics to identify Avr3a and show that it encodes a protein that is recognized in the host cytoplasm, where it triggers R3a-dependent cell death. Avr3a resides in a region of the P. infestans genome that is colinear with the locus containing avirulence gene ATR1(NdWsB) in Hyaloperonospora parasitica, an oomycete pathogen of Arabidopsis. Remarkably, distances between conserved genes in these avirulence loci were often similar, despite intervening genomic variation. We suggest that Avr3a has undergone gene duplication and that an allele evading recognition by R3a arose under positive selection.
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Affiliation(s)
- Miles R Armstrong
- Plant Pathogen Interactions Programme, Scottish Crop Research Institute, Invergowrie, DD2 5DA Dundee, UK
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