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Legan AW, Mehl HL, Wissotski M, Adhikari BN, Callicott KA. Telomere-to-telomere genome assembly of the aflatoxin biocontrol agent Aspergillus flavus isolate La3279 isolated from maize in Nigeria. Microbiol Resour Announc 2024; 13:e0069623. [PMID: 38332494 DOI: 10.1128/mra.00696-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
Here, we report the complete genome of the non-aflatoxigenic Aspergillus flavus isolate La3279, which is an active ingredient of the aflatoxin biocontrol product Aflasafe. The chromosome-scale assembly clarifies the deletion pattern in the aflatoxin biosynthesis gene cluster and corrects a misidentified assembly previously published for this isolate.
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Affiliation(s)
- Andrew W Legan
- Arid Land Agricultural Research Center, US Department of Agriculture, Tucson, Arizona, USA
| | - Hillary L Mehl
- Arid Land Agricultural Research Center, US Department of Agriculture, Tucson, Arizona, USA
| | - Marina Wissotski
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Bishwo N Adhikari
- APHIS PPQ Plant Germplasm Quarantine Program, US Department of Agriculture, Laurel, Maryland, USA
| | - Kenneth A Callicott
- Arid Land Agricultural Research Center, US Department of Agriculture, Tucson, Arizona, USA
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2
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Legan AW, Mack BM, Mehl HL, Wissotski M, Ching’anda C, Maxwell LA, Callicott KA. Complete genome of the toxic mold Aspergillus pseudotamarii isolate NRRL 25517 reveals genomic instability of the aflatoxin biosynthesis cluster. G3 (Bethesda) 2023; 13:jkad150. [PMID: 37401423 PMCID: PMC10468309 DOI: 10.1093/g3journal/jkad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/24/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023]
Abstract
Fungi can synthesize a broad array of secondary metabolite chemicals. The genes underpinning their biosynthesis are typically arranged in tightly linked clusters in the genome. For example, ∼25 genes responsible for the biosynthesis of carcinogenic aflatoxins by Aspergillus section Flavi species are grouped in a ∼70 Kb cluster. Assembly fragmentation prevents assessment of the role of structural genomic variation in secondary metabolite evolution in this clade. More comprehensive analyses of secondary metabolite evolution will be possible by working with more complete and accurate genomes of taxonomically diverse Aspergillus species. Here, we combined short- and long-read DNA sequencing to generate a highly contiguous genome of the aflatoxigenic fungus, Aspergillus pseudotamarii (isolate NRRL 25517 = CBS 766.97; scaffold N50 = 5.5 Mb). The nuclear genome is 39.4 Mb, encompassing 12,639 putative protein-encoding genes and 74-97 candidate secondary metabolite biosynthesis gene clusters. The circular mitogenome is 29.7 Kb and contains 14 protein-encoding genes that are highly conserved across the genus. This highly contiguous A. pseudotamarii genome assembly enables comparisons of genomic rearrangements between Aspergillus section Flavi series Kitamyces and series Flavi. Although the aflatoxin biosynthesis gene cluster of A. pseudotamarii is conserved with Aspergillus flavus, the cluster has an inverted orientation relative to the telomere and occurs on a different chromosome.
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Affiliation(s)
- Andrew W Legan
- US Department of Agriculture, Arid Land Agricultural Research Center, Tucson, AZ 85701, USA
| | - Brian M Mack
- US Department of Agriculture, Food and Feed Safety Research Unit, New Orleans, LA 70124, USA
| | - Hillary L Mehl
- US Department of Agriculture, Arid Land Agricultural Research Center, Tucson, AZ 85701, USA
| | - Marina Wissotski
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Connel Ching’anda
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Lourena A Maxwell
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kenneth A Callicott
- US Department of Agriculture, Arid Land Agricultural Research Center, Tucson, AZ 85701, USA
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3
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Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JSS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KFX, Rounsley S, Wing RA. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 2014; 46:982-8. [PMID: 25064006 PMCID: PMC7036042 DOI: 10.1038/ng.3044] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Abstract
Mingsheng Chen, Klaus Mayer, Steve Rounsley, Rod Wing and colleagues report the genome sequence of African rice (Oryza glaberrima), a different species than Asian rice. The authors resequenced 20 O. glaberrima accessions and 94 Oryza barthii accessions (the putative progenitor species of O. glaberrima), and their analyses support the hypothesis that O. glaberrima was domesticated in a single region along the upper Niger river. The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.
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Affiliation(s)
- Muhua Wang
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2]
| | - Yeisoo Yu
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2]
| | - Georg Haberer
- 1] Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany. [2]
| | | | - Chuanzhu Fan
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jose Luis Goicoechea
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Xiang Song
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jetty S S Ammiraju
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] DuPont Pioneer, Johnston, Iowa, USA
| | - Rosa Maria Cossu
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Carlos Maldonado
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Nick Sisneros
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Kristi de Baynast
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Woojin Kim
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Paul Sanchez
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] US Arid Land Agricultural Research Center, Maricopa, Arizona, USA
| | | | | | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Judith Carney
- Department of Geography, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/Institut de Recherche pour le Développement/l'Université de Perpignan Via Domitia, Université de Perpignan, Perpignan, France
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
| | | | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
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4
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Febrer M, Goicoechea JL, Wright J, McKenzie N, Song X, Lin J, Collura K, Wissotski M, Yu Y, Ammiraju JSS, Wolny E, Idziak D, Betekhtin A, Kudrna D, Hasterok R, Wing RA, Bevan MW. An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PLoS One 2010; 5:e13461. [PMID: 20976139 PMCID: PMC2956642 DOI: 10.1371/journal.pone.0013461] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 08/27/2010] [Indexed: 11/18/2022] Open
Abstract
The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation.
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Affiliation(s)
| | - Jose Luis Goicoechea
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | | | | | - Xiang Song
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Jinke Lin
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Kristi Collura
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Marina Wissotski
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Yeisoo Yu
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Jetty S. S. Ammiraju
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Elzbieta Wolny
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Dominika Idziak
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Alexander Betekhtin
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Dave Kudrna
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Rod A. Wing
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
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Lin L, Pierce GJ, Bowers JE, Estill JC, Compton RO, Rainville LK, Kim C, Lemke C, Rong J, Tang H, Wang X, Braidotti M, Chen AH, Chicola K, Collura K, Epps E, Golser W, Grover C, Ingles J, Karunakaran S, Kudrna D, Olive J, Tabassum N, Um E, Wissotski M, Yu Y, Zuccolo A, ur Rahman M, Peterson DG, Wing RA, Wendel JF, Paterson AH. A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics 2010; 11:395. [PMID: 20569427 PMCID: PMC2996926 DOI: 10.1186/1471-2164-11-395] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/22/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing. RESULTS A whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences. CONCLUSION Several lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence.
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Affiliation(s)
- Lifeng Lin
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Gary J Pierce
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - John E Bowers
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - James C Estill
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Rosana O Compton
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Lisa K Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Junkang Rong
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- School of Agriculture and Food Sciences, Zhejiang Forestry University, Lin'an, Hangzhou, Zhejiang, 311300, China
| | - Haibao Tang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant and Microbiology, College of Natural Resources, University of California, Berkeley, CA, USA
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Michele Braidotti
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Amy H Chen
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Kristen Chicola
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Kristi Collura
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Ethan Epps
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Corrinne Grover
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jennifer Ingles
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | | | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Jaime Olive
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Nabila Tabassum
- National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Eareana Um
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Andrea Zuccolo
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Mehboob ur Rahman
- National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Daniel G Peterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Life Sciences & Biotechnology Institute, Mississippi State University, Mississippi State, MS 39762 USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 2009; 326:1112-5. [PMID: 19965430 DOI: 10.1126/science.1178534] [Citation(s) in RCA: 2467] [Impact Index Per Article: 164.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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7
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Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA. Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 2009; 5:e1000728. [PMID: 19936048 PMCID: PMC2773423 DOI: 10.1371/journal.pgen.1000728] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 10/16/2009] [Indexed: 12/20/2022] Open
Abstract
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
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Affiliation(s)
- Fusheng Wei
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Joshua C. Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Chengzhi Liang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Robert S. Fulton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Regina S. Baucom
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Emanuele De Paoli
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Lixing Yang
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yujun Han
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Apurva Narechania
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Cheng-Ting Yeh
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Kai Ying
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Dawn H. Nagel
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Kristi Collura
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Jennifer Currie
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Jinke Lin
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - HyeRan Kim
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Angelina Angelova
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Gabriel Scara
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Laura Courtney
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Scott Kruchowski
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tina A. Graves
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Susan M. Rock
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stephanie Adams
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda A. Fulton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catrina Fronick
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - William Courtney
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lori Spiegel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lydia Nascimento
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of America
| | - Cristian Chaparro
- Université de Perpignan Via Domitia, CNRS UMR 5096, Perpignan, France
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, CNRS UMR 5096, Perpignan, France
| | - Phillip San Miguel
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Susan R. Wessler
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Pamela J. Green
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Blake C. Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Jeffrey L. Bennetzen
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Srinivas Aluru
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Sandra W. Clifton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patrick S. Schnable
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Richard K. Wilson
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rod A. Wing
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
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8
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Kim H, Hurwitz B, Yu Y, Collura K, Gill N, SanMiguel P, Mullikin JC, Maher C, Nelson W, Wissotski M, Braidotti M, Kudrna D, Goicoechea JL, Stein L, Ware D, Jackson SA, Soderlund C, Wing RA. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol 2008; 9:R45. [PMID: 18304353 PMCID: PMC2374706 DOI: 10.1186/gb-2008-9-2-r45] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 02/12/2008] [Accepted: 02/28/2008] [Indexed: 01/31/2023] Open
Abstract
Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presented We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.
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Affiliation(s)
- HyeRan Kim
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.
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9
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Kim H, San Miguel P, Nelson W, Collura K, Wissotski M, Walling JG, Kim JP, Jackson SA, Soderlund C, Wing RA. Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics 2007; 176:379-90. [PMID: 17339227 PMCID: PMC1893071 DOI: 10.1534/genetics.106.068783] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Accepted: 02/09/2007] [Indexed: 11/18/2022] Open
Abstract
A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and 34,224 fingerprints, onto the O. sativa genome sequence. The level of conservation of each chromosome between the two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene-rich regions. Further, this characteristic enabled localization of heterochromatic and euchromatic regions for each chromosome of both species. The alignment identified 16 locations containing expansions, contractions, inversions, and transpositions. By aligning 40% of the punctata BES on the map, 87% of the punctata FPC map covered 98% of the O. sativa genome sequence. The genome size of O. punctata was estimated to be 8% larger than that of O. sativa with individual chromosome differences of 1.5-16.5%. The sum of expansions and contractions observed in regions >500 kb were similar, suggesting that most of the contractions/expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged approximately 2 million years ago.
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Affiliation(s)
- HyeRan Kim
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA
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