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Masonbrink RE, Maier TR, Hudson M, Severin A, Baum T. A chromosomal assembly of the soybean cyst nematode genome. Mol Ecol Resour 2021; 21:2407-2422. [PMID: 34036752 DOI: 10.1111/1755-0998.13432] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 02/22/2021] [Revised: 04/16/2021] [Accepted: 05/13/2021] [Indexed: 01/02/2023]
Abstract
The soybean cyst nematode (Heterodera glycines) is a sedentary plant parasite that exceeds billion USD annually in yield losses. This problem is exacerbated by H. glycines populations overcoming the limited sources of natural resistance in soybean and by the lack of effective and safe alternative treatments. Although there are genetic determinants that render soybeans resistant to nematode genotypes, resistant soybeans are increasingly ineffective because their multiyear usage has selected for virulent H. glycines populations. Successful H. glycines infection relies on the comprehensive re-engineering of soybean root cells into a syncytium, as well as the long-term suppression of host defences to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms that control genomic effector acquisition, diversification, and selection are important insights needed for the development of essential novel control strategies. As a foundation to obtain this understanding, we created a nine-scaffold, 158 Mb pseudomolecule assembly of the H. glycines genome using PacBio, Chicago, and Hi-C sequencing. A Mikado consensus gene prediction produced an annotation of 22,465 genes using short- and long-read expression data. To evaluate assembly and annotation quality, we cross-examined synteny among H. glycines assemblies, and compared BUSCO across related species. To describe the predicted proteins involved in H. glycines' secretory pathway, we contrasted expression between preparasitic and parasitic stages with functional gene information. Here, we present the results from our assembly and annotation of the H. glycines genome and contribute this resource to the scientific community.
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Affiliation(s)
- Rick E Masonbrink
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA
| | - Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Matthew Hudson
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA
| | - Thomas Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
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Maier TR, Masonbrink RE, Vijayapalani P, Gardner M, Howland AD, Mitchum MG, Baum TJ. Esophageal Gland RNA-Seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode Heterodera glycines. Mol Plant Microbe Interact 2021; 34:1084-1087. [PMID: 33900122 DOI: 10.1094/mpmi-03-21-0051-a] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The soybean cyst nematode Heterodera glycines is the most economically devastating pathogen of soybean in the United States and threatens to become even more damaging through the selection of virulent nematode populations in the field that can overcome natural resistance mechanisms in soybean cultivars. This pathogen, therefore, demands intense transcriptomic/genomic research inquiries into the biology of its parasitic mechanisms. H. glycines delivers effector proteins that are produced in specialized gland cells into the soybean root to enable infection. The study of effector proteins, thus, is particularly promising when exploring novel management options against this pathogen. Here, we announce the availability of a gland cell-specific RNA-seq resource. These data represent an expression snapshot of gland cell activity during early soybean infection of a virulent and an avirulent H. glycines population, providing a unique and highly valuable resource for scientists examining effector biology and nematode virulence.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Rick E Masonbrink
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, U.S.A
| | | | - Michael Gardner
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Amanda D Howland
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, U.S.A
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
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Masonbrink RE, Alt D, Bayles DO, Boggiatto P, Edwards W, Tatum F, Williams J, Wilson-Welder J, Zimin A, Severin A, Olsen S. A pseudomolecule assembly of the Rocky Mountain elk genome. PLoS One 2021; 16:e0249899. [PMID: 33909645 PMCID: PMC8081196 DOI: 10.1371/journal.pone.0249899] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/28/2021] [Indexed: 11/20/2022] Open
Abstract
Rocky Mountain elk (Cervus canadensis) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella abortus in the Greater Yellowstone area. Vaccination attempts against intracellular bacterial diseases in elk populations have not been successful due to a negligible adaptive cellular immune response. A lack of genomic resources has impeded attempts to better understand why vaccination does not induce protective immunity. To overcome this limitation, PacBio, Illumina, and Hi-C sequencing with a total of 686-fold coverage was used to assemble the elk genome into 35 pseudomolecules. A robust gene annotation was generated resulting in 18,013 gene models and 33,422 mRNAs. The accuracy of the assembly was assessed using synteny to the red deer and cattle genomes identifying several chromosomal rearrangements, fusions and fissions. Because this genome assembly and annotation provide a foundation for genome-enabled exploration of Cervus species, we demonstrate its utility by exploring the conservation of immune system-related genes. We conclude by comparing cattle immune system-related genes to the elk genome, revealing eight putative gene losses in elk.
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Affiliation(s)
- Rick E. Masonbrink
- Genome Informatics Facility, Department of Biotech, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| | - David Alt
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Darrell O. Bayles
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Paola Boggiatto
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - William Edwards
- Wildlife Health Laboratory, Wyoming Game and Fish Department, Laramie, Wyoming, United States of America
| | - Fred Tatum
- Respiratory Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Jeffrey Williams
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Jennifer Wilson-Welder
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Aleksey Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Andrew Severin
- Genome Informatics Facility, Department of Biotech, Iowa State University, Ames, Iowa, United States of America
| | - Steven Olsen
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
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Stromberg ZR, Masonbrink RE, Mellata M. Transcriptomic Analysis of Shiga Toxin-Producing Escherichia coli during Initial Contact with Cattle Colonic Explants. Microorganisms 2020; 8:microorganisms8111662. [PMID: 33120988 PMCID: PMC7693793 DOI: 10.3390/microorganisms8111662] [Citation(s) in RCA: 5] [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: 10/07/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 01/10/2023] Open
Abstract
Foodborne pathogens are a public health threat globally. Shiga toxin-producing Escherichia coli (STEC), particularly O26, O111, and O157 STEC, are often associated with foodborne illness in humans. To create effective preharvest interventions, it is critical to understand which factors STEC strains use to colonize the gastrointestinal tract of cattle, which serves as the reservoir for these pathogens. Several colonization factors are known, but little is understood about initial STEC colonization factors. Our objective was to identify these factors via contrasting gene expression between nonpathogenic E. coli and STEC. Colonic explants were inoculated with nonpathogenic E. coli strain MG1655 or STEC strains (O26, O111, or O157), bacterial colonization levels were determined, and RNA was isolated and sequenced. STEC strains adhered to colonic explants at numerically but not significantly higher levels compared to MG1655. After incubation with colonic explants, flagellin (fliC) was upregulated (log2 fold-change = 4.0, p < 0.0001) in O157 STEC, and collectively, Lon protease (lon) was upregulated (log2 fold-change = 3.6, p = 0.0009) in STEC strains compared to MG1655. These results demonstrate that H7 flagellum and Lon protease may play roles in early colonization and could be potential targets to reduce colonization in cattle.
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Affiliation(s)
- Zachary R. Stromberg
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA;
| | - Rick E. Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA;
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA;
- Correspondence: ; Tel.: +1-515-294-9220
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Abstract
BACKGROUND Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared data science infrastructures like Boag is needed to efficiently process and parse data contained in large data repositories. The main features of Boag are inspired from existing languages for data intensive computing and can easily integrate data from biological data repositories. RESULTS As a proof of concept, Boa for genomics, Boag, has been implemented to analyze RefSeq's 153,848 annotation (GFF) and assembly (FASTA) file metadata. Boag provides a massive improvement from existing solutions like Python and MongoDB, by utilizing a domain-specific language that uses Hadoop infrastructure for a smaller storage footprint that scales well and requires fewer lines of code. We execute scripts through Boag to answer questions about the genomes in RefSeq. We identify the largest and smallest genomes deposited, explore exon frequencies for assemblies after 2016, identify the most commonly used bacterial genome assembly program, and address how animal genome assemblies have improved since 2016. Boag databases provide a significant reduction in required storage of the raw data and a significant speed up in its ability to query large datasets due to automated parallelization and distribution of Hadoop infrastructure during computations. CONCLUSIONS In order to keep pace with our ability to produce biological data, innovative methods are required. The Shared Data Science Infrastructure, Boag, provides researchers a greater access to researchers to efficiently explore data in new ways. We demonstrate the potential of a the domain specific language Boag using the RefSeq database to explore how deposited genome assemblies and annotations are changing over time. This is a small example of how Boag could be used with large biological datasets.
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Affiliation(s)
- Hamid Bagheri
- Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, 50011 USA
| | - Usha Muppirala
- Genome Informatics Facility, Iowa State University, 206 Science I, Ames, 50011 USA
| | - Rick E. Masonbrink
- Genome Informatics Facility, Iowa State University, 206 Science I, Ames, 50011 USA
| | - Andrew J. Severin
- Genome Informatics Facility, Iowa State University, 206 Science I, Ames, 50011 USA
| | - Hridesh Rajan
- Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, 50011 USA
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Barnes SN, Masonbrink RE, Maier TR, Seetharam A, Sindhu AS, Severin AJ, Baum TJ. Heterodera glycines utilizes promiscuous spliced leaders and demonstrates a unique preference for a species-specific spliced leader over C. elegans SL1. Sci Rep 2019; 9:1356. [PMID: 30718603 PMCID: PMC6362198 DOI: 10.1038/s41598-018-37857-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
Spliced leader trans-splicing (SLTS) plays a part in the maturation of pre-mRNAs in select species across multiple phyla but is particularly prevalent in Nematoda. The role of spliced leaders (SL) within the cell is unclear and an accurate assessment of SL occurrence within an organism is possible only after extensive sequencing data are available, which is not currently the case for many nematode species. SL discovery is further complicated by an absence of SL sequences from high-throughput sequencing results due to incomplete sequencing of the 5'-ends of transcripts during RNA-seq library preparation, known as 5'-bias. Existing datasets and novel methodology were used to identify both conserved SLs and unique hypervariable SLs within Heterodera glycines, the soybean cyst nematode. In H. glycines, twenty-one distinct SL sequences were found on 2,532 unique H. glycines transcripts. The SL sequences identified on the H. glycines transcripts demonstrated a high level of promiscuity, meaning that some transcripts produced as many as nine different individual SL-transcript combinations. Most uniquely, transcriptome analysis revealed that H. glycines is the first nematode to demonstrate a higher SL trans-splicing rate using a species-specific SL over well-conserved Caenorhabditis elegans SL-like sequences.
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Affiliation(s)
- Stacey N Barnes
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA, 50011, USA
| | - Rick E Masonbrink
- Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Thomas R Maier
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA, 50011, USA
| | - Arun Seetharam
- Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | | | - Andrew J Severin
- Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Thomas J Baum
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA, 50011, USA.
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Masonbrink RE, Purcell CM, Boles SE, Whitehead A, Hyde JR, Seetharam AS, Severin AJ. An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species. Genome Biol Evol 2019; 11:431-438. [PMID: 30657886 PMCID: PMC6373831 DOI: 10.1093/gbe/evz006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2019] [Indexed: 11/13/2022] Open
Abstract
Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.
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Affiliation(s)
| | - Catherine M Purcell
- Ocean Associates, Inc. Under Contract to NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California
| | - Sara E Boles
- Department of Environmental Toxicology, University of California, Davis
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis
| | - John R Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California
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Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, Masonbrink RE, Peterson DG, Wendel JF. The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. Front Plant Sci 2019; 10:1541. [PMID: 31827481 PMCID: PMC6890844 DOI: 10.3389/fpls.2019.01541] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/05/2019] [Indexed: 05/20/2023]
Abstract
One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium diploids (n = 13). Previous analysis demonstrated that the directionality of their reduced chromosome number was through large structural rearrangements. A series of structural rearrangements were identified comparing the de novo G. kirkii genome sequence to genome sequences of Gossypium, including chromosome fusions and inversions. Genome comparison between G. kirkii and Gossypium suggests that multiple steps are required to generate the extant structural differences.
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Affiliation(s)
- Joshua A. Udall
- Crop Germplasm Research, USDA, College Station, TX, United States
- *Correspondence: Joshua A. Udall, ; Jonathan F. Wendel,
| | - Evan Long
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Thiruvarangan Ramaraj
- National Center of Genome Resources, Santa Fe, NM, United States
- School of Computing, DePaul University, Chicago, IL, United States
| | | | - Daojun Yuan
- EEOB Department, Iowa State University, Ames, IA, United States
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | | | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Mark A. Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Rick E. Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA, United States
| | - Daniel G. Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Jonathan F. Wendel
- EEOB Department, Iowa State University, Ames, IA, United States
- *Correspondence: Joshua A. Udall, ; Jonathan F. Wendel,
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Han J, Masonbrink RE, Shan W, Song F, Zhang J, Yu W, Wang K, Wu Y, Tang H, Wendel JF, Wang K. Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton. Plant J 2016; 88:992-1005. [PMID: 27539015 DOI: 10.1111/tpj.13309] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/07/2016] [Accepted: 08/11/2016] [Indexed: 05/27/2023]
Abstract
Centromeric chromatin in most eukaryotes is composed of highly repetitive centromeric retrotransposons and satellite repeats that are highly variable even among closely related species. The evolutionary mechanisms that underlie the rapid evolution of centromeric repeats remain unknown. To obtain insight into the evolution of centromeric repeats following polyploidy, we studied a model diploid progenitor (Gossypium raimondii, D-genome) of the allopolyploid (AD-genome) cottons, G. hirsutum and G. barbadense. Sequence analysis of chromatin-immunoprecipitated DNA showed that the G. raimondii centromeric repeats originated from retrotransposon-related sequences. Comparative analysis showed that nine of the 10 analyzed centromeric repeats were absent from the centromeres in the A-genome and related diploid species (B-, F- and G-genomes), indicating that they colonized the centromeres of D-genome lineage after the divergence of the A- and D- ancestral species or that they were ancestrally retained prior to the origin of Gossypium. Notably, six of the nine repeats were present in both the A- and D-subgenomes in tetraploid G. hirsutum, and increased in abundance in both subgenomes. This finding suggests that centromeric repeats may spread and proliferate between genomes subsequent to polyploidization. Two repeats, Gr334 and Gr359 occurred in both the centromeres and nucleolar organizer regions (NORs) in D- and AD-genome species, yet localized to just the NORs in A-, B-, F-, and G-genome species. Contained within is a story of an established centromeric repeat that is eliminated and allopolyploidization provides an opportunity for reinvasion and reestablishment, which broadens our evolutionary understanding behind the cycles of centromeric repeat establishment and targeting.
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Affiliation(s)
- Jinlei Han
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Rick E Masonbrink
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Wenbo Shan
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Fengqin Song
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Weichang Yu
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Yufeng Wu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kai Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
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Gong L, Masonbrink RE, Grover CE, Renny-Byfield S, Wendel JF. A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in Gossypium raimondii. Plant Genome 2015; 8:eplantgenome2014.11.0088. [PMID: 33228305 DOI: 10.3835/plantgenome2014.11.0088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/06/2015] [Indexed: 06/11/2023]
Abstract
Stabilization of transposable element (TE) copy number involves the biosynthesis of short silencing RNAs (siRNAs) and further initialization of siRNA-mediated TE silencing. To gain insight into the relationship between the biosynthesis of siRNAs and their source TEs, we examined the co-evolutionary dynamics and expression of these two entities by characterizing the siRNA distribution across the genome of Gossypium raimondii Ulbr. We identified an unusual region at the 3' end of chromosome 1 with significantly enriched siRNA coverage. Analysis of the correlation pattern between uniquely mapped siRNAs and those mapping to multiple regions implicated active biogenesis of siRNAs from these potential young TEs. Furthermore, divergence estimates of TEs within this region confirmed that the majority of TEs are young. Active transcription of the source TEs and their positive correlation with expressed siRNAs indicates that sufficient expression of TEs may be necessary to generate siRNAs and maintain the silenced state of recently transposed TEs.
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Affiliation(s)
- Lei Gong
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Rick E Masonbrink
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Corrinne E Grover
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Simon Renny-Byfield
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
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11
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Masonbrink RE, Gallagher JP, Jareczek JJ, Renny-Byfield S, Grover CE, Gong L, Wendel JF. CenH3 evolution in diploids and polyploids of three angiosperm genera. BMC Plant Biol 2014; 14:383. [PMID: 25547313 PMCID: PMC4308911 DOI: 10.1186/s12870-014-0383-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/12/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification. The centromere specific histone, CenH3, evolves rapidly in many species, perhaps as a coevolutionary response to rapidly evolving centromeric DNA. To gain insight into CenH3 evolution, we characterized patterns of nucleotide and protein diversity among diploids and allopolyploids within three diverse angiosperm genera, Brassica, Oryza, and Gossypium (cotton), with a focus on evidence for diversifying selection in the various domains of the CenH3 gene. In addition, we compare expression profiles and alternative splicing patterns for CenH3 in representatives of each genus. RESULTS All three genera retain both duplicated CenH3 copies, while Brassica and Gossypium exhibit pronounced homoeologous expression level bias. Comparisons among genera reveal shared and unique aspects of CenH3 evolution, variable levels of diversifying selection in different CenH3 domains, and that alternative splicing contributes significantly to CenH3 diversity. CONCLUSIONS Since the N terminus is subject to diversifying selection but the DNA binding domains do not appear to be, rapidly evolving centromere sequences are unlikely to be the primary driver of CenH3 sequence diversification. At present, the functional explanation for the diversity generated by both conventional protein evolution in the N terminal domain, as well as alternative splicing, remains unexplained.
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Affiliation(s)
- Rick E Masonbrink
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Joseph P Gallagher
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Josef J Jareczek
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Simon Renny-Byfield
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Lei Gong
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
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Masonbrink RE, Fu S, Han F, Birchler JA. Heritable loss of replication control of a minichromosome derived from the B chromosome of maize. Genetics 2013; 193:77-84. [PMID: 23114381 PMCID: PMC3527256 DOI: 10.1534/genetics.112.146126] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 10/29/2012] [Indexed: 01/24/2023] Open
Abstract
During an accumulation regime of a small telomere-truncated B chromosome, a derivative with large variations in size and multiple punctate centromere loci exhibiting amplified copy numbers was discovered. Multiple centromere satellite loci or transgene signals were documented in amplified chromosomes, suggesting over-replication. Immunolocalization studies revealed multiple foci of biochemical markers characteristic of active centromeres such as CENP-C and phosphorylation of histones H3S10 and H2AThr133. The amplified chromosomes exhibit an absence of chromosome disjunction in meiosis I and an infrequent chromosome disjunction in meiosis II. Despite their unusual structure and behavior these chromosomes were observed in the lineage for seven generations during the course of this study. While severely truncated relative to a normal B chromosome, the progenitor minichromosome is estimated to be at least several megabases in size. Given that the centromere and transgene signals at opposite ends of the chromosome generally match in copy number, the replication control is apparently lost over several megabases.
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Affiliation(s)
- Rick E. Masonbrink
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Shulan Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese National Academy of Sciences, Beijing, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese National Academy of Sciences, Beijing, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
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Abstract
Multiple copies of B chromosomes in maize (Zea mays) can accumulate in the genome using the B chromosome's accumulation mechanism, specifically nondisjunction at the second pollen mitosis and preferential fertilization of the egg. Using this mechanism, we accumulated 4 different-sized minichromosomes derived from the B chromosome to test the chromosome limits of the cell. The accumulation of normal B chromosomes is associated with multiple phenotypes including white stripes and asymmetric leaf blades, but when minichromosomes are accumulated these symptoms are absent. We also found that multiple B chromosome-derived minichromosomes can coexist with A chromosome-derived minichromosomes. During the years that these experiments were conducted, we found many B chromosome rearrangements and fragments, 2 recoverable A chromosome fragments, and observed a minichromosome breakage-fusion-bridge cycle in roots.
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Affiliation(s)
- R E Masonbrink
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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Masonbrink RE, Gaeta RT, Birchler JA. Multiple maize minichromosomes in meiosis. Chromosome Res 2012; 20:395-402. [DOI: 10.1007/s10577-012-9283-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/09/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
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Abstract
Synthetic chromosomes provide the means to stack transgenes independently of the remainder of the genome. Combining them with haploid breeding could provide the means to transfer many transgenes more easily among varieties of the same species. The epigenetic nature of centromere formation complicates the production of synthetic chromosomes. However, telomere-mediated truncation coupled with the introduction of site-specific recombination cassettes has been used to produce minichromosomes consisting of little more than a centromere. Methods that have been developed to modify genes in vivo could be applied to minichromosomes to improve their utility and to continue to increase their length and genic content. Synthetic chromosomes establish the means to add or subtract multiple transgenes, multigene complexes, or whole biochemical pathways to plants to change their properties for agricultural applications or to use plants as factories for the production of foreign proteins or metabolites.
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Affiliation(s)
- Robert T Gaeta
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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Gaeta RT, Danilova TV, Zhao C, Masonbrink RE, McCaw ME, Birchler JA. Recovery of a telomere-truncated chromosome via a compensating translocation in maize. Genome 2011; 54:184-95. [PMID: 21423281 DOI: 10.1139/g10-108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Maize-engineered minichromosomes are easily recovered from telomere-truncated B chromosomes but are rarely recovered from A chromosomes. B chromosomes lack known genes, and their truncation products are tolerated and transmitted during meiosis. In contrast, deficiency gametes resulting from truncated A chromosomes prevent their transmission. We report here a de novo compensating translocation that permitted recovery of a large truncation of chromosome 1 in maize. The truncation (trunc-1) and translocation with chromosome 6 (super-6) occurred during telomere-mediated truncation experiments and were characterized using single-gene fluorescent in situ hybridization (FISH) probes. The truncation contained a transgene signal near the end of the broken chromosome and transmitted together with the compensating translocation as a heterozygote to approximately 41%-55% of progeny. Transmission as an addition chromosome occurred in ~15% of progeny. Neither chromosome transmitted through pollen. Transgene expression (Bar) cosegregated with trunc-1 transcriptionally and phenotypically. Meiosis in T1 plants revealed eight bivalents and one tetravalent chain composed of chromosome 1, trunc-1, chromosome 6, and super-6 in diplotene and diakinesis. Our data suggest that de novo compensating translocations allow recovery of truncated A chromosomes by compensating deficiency in female gametes and by affecting chromosome pairing and segregation. The truncated chromosome can be maintained as an extra chromosome or together with the super-6 as a heterozygote.
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Affiliation(s)
- Robert T Gaeta
- Department of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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Masonbrink RE, Birchler JA. Sporophytic nondisjunction of the maize B chromosome at high copy numbers. J Genet Genomics 2010; 37:79-84. [PMID: 20171580 DOI: 10.1016/s1673-8527(09)60027-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [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: 09/02/2009] [Revised: 10/05/2009] [Accepted: 10/15/2009] [Indexed: 01/12/2023]
Abstract
It has been known for decades that the maize B chromosome undergoes nondisjunction at the second pollen mitosis. Fluorescence in-situ hybridization (FISH) was used to undertake a quantitative study of maize plants with differing numbers of B chromosomes to observe if instability increases by increasing B dosage in root tip tissue. B chromosome nondisjunction was basically absent at low copy number, but increased at higher B numbers. Thus, B nondisjunction rates are dependent on the dosage of B's in the sporophyte. Differences in nondisjunction were also documented between odd and even doses of the B. In plants that have inherited odd numbered doses of the B chromosome, B loss is nearly twice as likely as B gain in a somatic division. When comparing plants with even doses of B's to plants with odd doses of B's, plants with even numbers had a significantly higher chance to increase in number. Therefore, the B's non-disjunctive capacity, previously thought to be primarily restricted to the gametophyte, is present in sporophytic cells.
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Affiliation(s)
- Rick E Masonbrink
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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