1
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Thatcher S, Jung M, Panangipalli G, Fengler K, Sanyal A, Li B, Llaca V, Habben J. The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence-absence variation, integrated domain diversity, and mobility. MOLECULAR PLANT PATHOLOGY 2023; 24:742-757. [PMID: 36929631 PMCID: PMC10257044 DOI: 10.1111/mpp.13319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 06/11/2023]
Abstract
Plant pathogens cause significant crop loss worldwide, and new resistance genes deployed to combat diseases can be overcome quickly. Understanding the existing resistance gene diversity within the germplasm of major crops, such as maize, is crucial for the development of new disease-resistant varieties. We analysed the nucleotide-binding leucine-rich repeat receptors (NLRs) of 26 recently sequenced diverse founder lines from the maize nested association mapping (NAM) population and compared them to the R gene complement present in a wild relative of maize, Zea luxurians. We found that NLRs in both species contain a large diversity of atypical integrated domains, including many domains that have not previously been found in the NLRs of other species. Additionally, the single Z. luxurians genome was found to have greater integrated atypical domain diversity than all 26 NAM founder lines combined, indicating that this species may represent a rich source of novel resistance genes. NLRs were also found to have very high sequence diversity and presence-absence variation among the NAM founder lines, with a large NLR cluster on Chr10 representing a diversity hotspot. Additionally, NLRs were shown to be mobile within maize genomes, with several putative interchromosomal translocations identified.
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2
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Liu J, Dawe RK. Large haplotypes highlight a complex age structure within the maize pan-genome. Genome Res 2023; 33:359-370. [PMID: 36854668 PMCID: PMC10078284 DOI: 10.1101/gr.276705.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other nongenic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad timescale with peaks at ∼16 and 300 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.
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Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
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3
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Huang Y, Wang H, Zhu Y, Huang X, Li S, Wu X, Zhao Y, Bao Z, Qin L, Jin Y, Cui Y, Ma G, Xiao Q, Wang Q, Wang J, Yang X, Liu H, Lu X, Larkins BA, Wang W, Wu Y. THP9 enhances seed protein content and nitrogen-use efficiency in maize. Nature 2022; 612:292-300. [PMID: 36385527 DOI: 10.1038/s41586-022-05441-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
Abstract
Teosinte, the wild ancestor of maize (Zea mays subsp. mays), has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms that are responsible for this trait are unknown1,2. Here we use trio binning to create a contiguous haplotype DNA sequence of a teosinte (Zea mays subsp. parviglumis) and, through map-based cloning, identify a major high-protein quantitative trait locus, TEOSINTE HIGH PROTEIN 9 (THP9), on chromosome 9. THP9 encodes an asparagine synthetase 4 enzyme that is highly expressed in teosinte, but not in the B73 inbred, in which a deletion in the tenth intron of THP9-B73 causes incorrect splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 significantly increased the seed protein content. Introgression of THP9-teosinte into modern maize inbreds and hybrids greatly enhanced the accumulation of free amino acids, especially asparagine, throughout the plant, and increased seed protein content without affecting yield. THP9-teosinte seems to increase nitrogen-use efficiency, which is important for promoting a high yield under low-nitrogen conditions.
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Affiliation(s)
- Yongcai Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China
| | - Haihai Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China
| | - Yidong Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Xing Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shuai Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xingguo Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yao Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Zhigui Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Li Qin
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, China
| | - Yongbo Jin
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yahui Cui
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guangjin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Qiao Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Qiong Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China
| | - Jiechen Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China
| | - Xuerong Yang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, China
| | - Brian A Larkins
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Wenqin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.
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4
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The maize abnormal chromosome 10 meiotic drive haplotype: a review. Chromosome Res 2022; 30:205-216. [PMID: 35652970 DOI: 10.1007/s10577-022-09693-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
The maize abnormal chromosome 10 (Ab10) haplotype encodes a meiotic drive system that converts heterochromatic knobs into centromere-like bodies that are preferentially segregated through female meiosis. Ab10 was first described in the 1940s and has been intensively studied. Here I provide a comprehensive review of the literature, starting from the discovery of knobs and Ab10, preceding through the classic literature, and finishing with molecular structure and mechanisms. The defining features of the Ab10 haplotype are its two specialized kinesins, Kinesin driver and TR-1 kinesin, that activate neocentromeres at knobs containing different classes of the tandem repeat. In most Ab10 haplotypes, the two kinesin/knob systems cooperate to promote maximum meiotic drive. However, recent interpretations suggest that each kinesin/knob system can function as an independent meiotic driver and that in some cases they compete with each other. Ab10 is present at low frequencies throughout the genus Zea and has significantly expanded genome size by promoting the formation of knobs throughout the genome.
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5
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Ansari HA, Ellison N, Stewart AV, Williams WM. Distribution patterns of rDNA loci in the Schedonorus- Lolium complex (Poaceae). COMPARATIVE CYTOGENETICS 2022; 16:39-54. [PMID: 35437460 PMCID: PMC8971122 DOI: 10.3897/compcytogen.v16.i1.79056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The Schedonorus-Lolium complex of the subtribe Loliinae (Poaceae) includes several economically important forage and turf grasses. This complex encompasses Lolium Linnaeus, 1753, Festuca Linnaeus, 1753 subgenus Schedonorus (P. Beauvois, 1824) Petermann, 1849 and Micropyropsis Romero Zarco et Cabezudo, 1983. New FISH results of 5S and 18S-26S rDNA sequences are presented for three species and the results are interpreted in a review of distribution patterns of 5S and 18S-26S rDNA sequences among other species in the complex. Micropyropsistuberosa Romero Zarco et Cabezudo, 1983 (2n = 2x = 14) displayed a distribution pattern of rDNA sequences identical to that of F.pratensis Hudson, 1762, supporting a close phylogenetic relationship at the bottom of the phylogenetic tree. "Loliummultiflorum" Lamarck, 1779 accessions sourced from Morocco showed a different pattern from European L.multiflorum and could be a unique and previously uncharacterised taxon. North African Festucasimensis Hochstetter ex A. Richard, 1851 had a marker pattern consistent with allotetraploidy and uniparental loss of one 18S-26S rDNA locus. This allotetraploid has previously been suggested to have originated from a hybrid with Festucaglaucescens (Festucaarundinaceavar.glaucescens Boissier, 1844). However, the distribution patterns of the two rDNA sequences in this allotetraploid do not align with F.glaucescens, suggesting that its origin from this species is unlikely. Furthermore, comparisons with other higher alloploids in the complex indicate that F.simensis was a potential donor of two sub-genomes of allohexaploid Festucagigantea (Linnaeus) Villars, 1787. In the overall complex, the proximal locations of both rDNA markers were conserved among the diploid species. Two types of synteny of the two markers could, to a considerable extent, distinguish allo- and autogamous Lolium species. The ancestral parentage of the three Festuca allotetraploids has not yet been determined, but all three appear to have been sub-genome donors to the higher allopolypoids of sub-genus Schedonorus. Terminal locations of both the markers were absent from the diploids but were very frequently observed in the polyploids.
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Affiliation(s)
- Helal Ahmad Ansari
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Nicholas Ellison
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Alan Vincent Stewart
- PGG Wrightson Seeds, Kimihia Research Centre, 1375 Springs Road, RD4, Lincoln 7674, New ZealandKimihia Research CentreLincolnNew Zealand
| | - Warren Mervyn Williams
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
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6
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Carvalho RF, Aguiar-Perecin MLR, Clarindo WR, Fristche-Neto R, Mondin M. A Heterochromatic Knob Reducing the Flowering Time in Maize. Front Genet 2022; 12:799681. [PMID: 35280927 PMCID: PMC8908004 DOI: 10.3389/fgene.2021.799681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Maize flowering time is an important agronomic trait, which has been associated with variations in the genome size and heterochromatic knobs content. We integrated three steps to show this association. Firstly, we selected inbred lines varying for heterochromatic knob composition at specific sites in the homozygous state. Then, we produced homozygous and heterozygous hybrids for knobs. Second, we measured the genome size and flowering time for all materials. Knob composition did not affect the genome size and flowering time. Finally, we developed an association study and identified a knob marker on chromosome 9 showing the strongest association with flowering time. Indeed, modelling allele substitution and dominance effects could offer only one heterochromatic knob locus that could affect flowering time, making it earlier rather than the knob composition.
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Affiliation(s)
- Renata Flávia Carvalho
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
| | | | | | - Roberto Fristche-Neto
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
- International Rice Research Institute (IRRI) - Breeding Analytics and Data, Management Unit, Laguna, Philippines
| | - Mateus Mondin
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
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7
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Abstract
The supernumerary B chromosome of maize is dispensable, containing no vital genes, and thus is variable in number and presence in lines of maize. In order to be maintained in populations, it has a drive mechanism consisting of nondisjunction at the pollen mitosis that produces the two sperm cells, and then the sperm with the two B chromosomes has a preference for fertilizing the egg as opposed to the central cell in the process of double fertilization. The sequence of the B chromosome coupled with B chromosomal aberrations has localized features involved with nondisjunction and preferential fertilization, which are present at the centromeric region. The predicted genes from the sequence have paralogues dispersed across all A chromosomes and have widely different divergence times suggesting that they have transposed to the B chromosome over evolutionary time followed by degradation or have been co-opted for the selfish functions of the supernumerary chromosome.
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Affiliation(s)
- James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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8
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Garrido-Ramos MA. The Genomics of Plant Satellite DNA. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:103-143. [PMID: 34386874 DOI: 10.1007/978-3-030-74889-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.
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9
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Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DW, Zeng Y, O'Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, Portwood JL, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 2021; 373:655-662. [PMID: 34353948 PMCID: PMC8733867 DOI: 10.1126/science.abg5289] [Citation(s) in RCA: 233] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022]
Abstract
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
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Affiliation(s)
- Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | - Margaret R Woodhouse
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | | | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Tingting Guo
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Silas Tittes
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Asher I Hudson
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | | | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Rebecca D Piri
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Dong Won Kim
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Amanda M Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Erin Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - John L Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Ethalinda K S Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David E Hufnagel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Qiuhan Jiang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Michael L Syring
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Jeffrey Ross-Ibarra
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Doreen Ware
- USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - R Kelly Dawe
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
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10
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Wang N, Liu J, Ricci WA, Gent JI, Dawe RK. Maize centromeric chromatin scales with changes in genome size. Genetics 2021; 217:iyab020. [PMID: 33857306 PMCID: PMC8049547 DOI: 10.1093/genetics/iyab020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/30/2021] [Indexed: 11/14/2022] Open
Abstract
Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.
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Affiliation(s)
- Na Wang
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
- Department of Genetics, University of Georgia, Athens GA 30602, USA
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11
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Kwiatek MT, Drozdowska Z, Kurasiak-Popowska D, Noweiska A, Nawracała J. Cytomolecular analysis of mutants, breeding lines, and varieties of camelina (Camelina sativa L. Crantz). J Appl Genet 2021; 62:199-205. [PMID: 33409934 DOI: 10.1007/s13353-020-00600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 10/22/2022]
Abstract
Camelina sativa L. Crantz (Brassicaceae family), known as camelina, has gained new attention as a re-emerging oil seed crop. With a unique seed oil profile, with the majority of the fatty acids consisting of linolenic (C18:3), oleic (C18:1), linoleic (C18:2), and eicosenoic (C20:1), camelina oil is reported to be useful as a food oil and biofuel. However, there are still many unknown factors about the structure and genetic variability of this crop. Chromosomal localization of ribosomal DNA was performed using fluorescence in situ hybridization (FISH) with 5S rDNA and 25S rDNA sequences as molecular probes on mitotic chromosomes of enzymatically digested root-tip meristematic cells. Here, we present for the first time a comparative analysis of selected genotypes (cultivars, breeding lines and mutants) of C. sativa with the use of cytogenetic techniques. The main aim of the study was to determine the intraspecific and interspecific polymorphisms in the structure of chromosomes of selected accessions using conserved 5S and 25S rDNA repetitive sequences as molecular probes. The results were compared with C. microcarpa (closely related to C. sativa) rDNA gene loci distribution. The presence of minor rDNA sites was discussed and compared with other Brassicaceae species. In addition, demonstration karyograms of C. sativa and C. microcarpa mapped with rDNA probes were prepared based on the cv. "Przybrodzka" and GE2011-02 genotype, respectively. The use of 5S and 25S rDNA probes provided an insight on the genome structure of C. sativa at the cytogenetic level and can help to understand the genome organization of this crop. The putative role of cytogenetic markers in phylogenetic analyses of camelina was discussed, as well.
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Affiliation(s)
- Michał T Kwiatek
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland.
| | - Zofia Drozdowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland
| | - Danuta Kurasiak-Popowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland
| | - Aleksandra Noweiska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland
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12
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Yao H, Srivastava S, Swyers N, Han F, Doerge RW, Birchler JA. Inbreeding Depression in Genotypically Matched Diploid and Tetraploid Maize. Front Genet 2020; 11:564928. [PMID: 33329701 PMCID: PMC7734256 DOI: 10.3389/fgene.2020.564928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023] Open
Abstract
The genetic and molecular basis of heterosis has long been studied but without a consensus about mechanism. The opposite effect, inbreeding depression, results from repeated self-pollination and leads to a reduction in vigor. A popular explanation for this reaction is the homozygosis of recessive, slightly deleterious alleles upon inbreeding. However, extensive studies in alfalfa indicated that inbreeding between diploids and autotetraploids was similar despite the fact that homozygosis of alleles would be dramatically different. The availability of tetraploid lines of maize generated directly from various inbred lines provided the opportunity to examine this issue in detail in perfectly matched diploid and tetraploid hybrids and their parallel inbreeding regimes. Identical hybrids at the diploid and tetraploid levels were inbred in triplicate for seven generations. At the conclusion of this regime, F1 hybrids and selected representative generations (S1, S3, S5, S7) were characterized phenotypically in randomized blocks during the same field conditions. Quantitative measures of the multiple generations of inbreeding provided little evidence for a distinction in the decline of vigor between the diploids and the tetraploids. The results suggest that the homozygosis of completely recessive, slightly deleterious alleles is an inadequate hypothesis to explain inbreeding depression in general.
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Affiliation(s)
- Hong Yao
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Sanvesh Srivastava
- Department of Statistics and Actuarial Science, University of Iowa, Iowa City, IA, United States
| | - Nathan Swyers
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Fangpu Han
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Rebecca W Doerge
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, United States
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
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13
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Wear EE, Song J, Zynda GJ, Mickelson-Young L, LeBlanc C, Lee TJ, Deppong DO, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF. Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots. PLoS Genet 2020; 16:e1008623. [PMID: 33052904 PMCID: PMC7588055 DOI: 10.1371/journal.pgen.1008623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 10/26/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022] Open
Abstract
Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed. In traditional cell division, or mitosis, a cell’s genetic material is duplicated and then split between two daughter cells. In contrast, in some specialized cell types, the DNA is duplicated a second time without an intervening division step, resulting in cells that carry twice as much DNA. This phenomenon, which is called the endocycle, is common during plant development. At each step, DNA replication follows an ordered program in which highly compacted DNA is unraveled and replicated in sections at different times during the synthesis (S) phase. In plants, it is unclear whether traditional and endocycle programs are the same, especially since endocycling cells are typically in the process of differentiation. Using root tips of maize, we found that in comparison to replication in the mitotic cell cycle, there is a small portion of the genome whose replication in the endocycle is shifted in time, usually to later in S phase. Some of these regions are scattered around the genome and mostly coincide with active genes. However, the most prominent shifts occur in centromeres. The shift to later replication in centromeres is noteworthy because they orchestrate the process of separating duplicated chromosomes into daughter cells, a function that is not needed in the endocycle.
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Affiliation(s)
- Emily E. Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Gregory J. Zynda
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chantal LeBlanc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - David O. Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - George C. Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - William F. Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
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14
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Liu Y, Su H, Zhang J, Shi L, Liu Y, Zhang B, Bai H, Liang S, Gao Z, Birchler JA, Han F. Rapid Birth or Death of Centromeres on Fragmented Chromosomes in Maize. THE PLANT CELL 2020; 32:3113-3123. [PMID: 32817254 PMCID: PMC7534475 DOI: 10.1105/tpc.20.00389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/17/2020] [Accepted: 08/18/2020] [Indexed: 05/04/2023]
Abstract
Comparative genomics has revealed common occurrences in karyotype evolution such as chromosomal end-to-end fusions and insertions of one chromosome into another near the centromere, as well as many cases of de novo centromeres that generate positional polymorphisms. However, how rearrangements such as dicentrics and acentrics persist without being destroyed or lost remains unclear. Here, we sought experimental evidence for the frequency and timeframe for inactivation and de novo formation of centromeres in maize (Zea mays). The pollen from plants with supernumerary B chromosomes was gamma-irradiated and then applied to normal maize silks of a line without B chromosomes. In ∼8,000 first-generation seedlings, we found many B-A translocations, centromere expansions, and ring chromosomes. We also found many dicentric chromosomes, but a fraction of these show only a single primary constriction, which suggests inactivation of one centromere. Chromosomal fragments were found without canonical centromere sequences, revealing de novo centromere formation over unique sequences; these were validated by immunolocalization with Thr133-phosphorylated histone H2A, a marker of active centromeres, and chromatin immunoprecipitation-sequencing with the CENH3 antibody. These results illustrate the regular occurrence of centromere birth and death after chromosomal rearrangement during a narrow window of one to potentially only a few cell cycles for the rearranged chromosomes to be recognized in this experimental regime.
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Affiliation(s)
- Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Lindan Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Han Bai
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuang Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi Gao
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211-7400
| | - James A Birchler
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211-7400
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Swentowsky KW, Gent JI, Lowry EG, Schubert V, Ran X, Tseng KF, Harkess AE, Qiu W, Dawe RK. Distinct kinesin motors drive two types of maize neocentromeres. Genes Dev 2020; 34:1239-1251. [PMID: 32820038 PMCID: PMC7462060 DOI: 10.1101/gad.340679.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022]
Abstract
A maize chromosome variant called abnormal chromosome 10 (Ab10) converts knobs on chromosome arms into neocentromeres, causing their preferential segregation to egg cells in a process known as meiotic drive. We previously demonstrated that the gene Kinesin driver (Kindr) on Ab10 encodes a kinesin-14 required to mobilize neocentromeres made up of the major tandem repeat knob180. Here we describe a second kinesin-14 gene, TR-1 kinesin (Trkin), that is required to mobilize neocentromeres made up of the minor tandem repeat TR-1. Trkin lies in a 4-Mb region of Ab10 that is not syntenic with any other region of the maize genome and shows extraordinary sequence divergence from Kindr and other kinesins in plants. Despite its unusual structure, Trkin encodes a functional minus end-directed kinesin that specifically colocalizes with TR-1 in meiosis, forming long drawn out neocentromeres. TRKIN contains a nuclear localization signal and localizes to knobs earlier in prophase than KINDR. The fact that TR-1 repeats often co-occur with knob180 repeats suggests that the current role of the TRKIN/TR-1 system is to facilitate the meiotic drive of the KINDR/knob180 system.
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Affiliation(s)
- Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Elizabeth G Lowry
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Veit Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Seeland, Germany
| | - Xia Ran
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Kuo-Fu Tseng
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Alex E Harkess
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA.,Department of Genetics, University of Georgia, Athens Georgia 30602, USA
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16
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Silva JC, Soares FAF, Sattler MC, Clarindo WR. Repetitive sequences and structural chromosome alterations promote intraspecific variations in Zea mays L. karyotype. Sci Rep 2020; 10:8866. [PMID: 32483238 PMCID: PMC7264354 DOI: 10.1038/s41598-020-65779-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/07/2020] [Indexed: 12/02/2022] Open
Abstract
LTR-retrotransposons, knobs and structural chromosome alterations contribute to shape the structure and organization of the Zea mays karyotype. Our initial nuclear DNA content data of Z. mays accessions revealed an intraspecific variation (2 C = 2.00 pg to 2 C = 6.10 pg), suggesting differences in their karyotypes. We aimed to compare the karyotypes of three Z. mays accessions in search of the differences and similarities among them. Karyotype divergences were demonstrated among the accessions, despite their common chromosome number (2n = 20) and ancestral origin. Cytogenomic analyses showed that repetitive sequences and structural chromosome alterations play a significant role in promoting intraspecific nuclear DNA content variation. In addition, heterozygous terminal deletion in chromosome 3 was pointed out as a cause of lower nuclear 2 C value. Besides this, translocation was also observed in the short arm of chromosome 1. Differently, higher 2 C value was associated with the more abundant distribution of LTR-retrotransposons from the family Grande in the karyotype. Moreover, heteromorphism involving the number and position of the 180-bp knob sequence was found among the accessions. Taken together, we provide insights on the pivotal role played by repetitive sequences and structural chromosome alterations in shaping the karyotype of Z. mays.
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Affiliation(s)
- Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil.
| | - Fernanda Aparecida Ferrari Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| | - Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
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17
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Liu J, Seetharam AS, Chougule K, Ou S, Swentowsky KW, Gent JI, Llaca V, Woodhouse MR, Manchanda N, Presting GG, Kudrna DA, Alabady M, Hirsch CN, Fengler KA, Ware D, Michael TP, Hufford MB, Dawe RK. Gapless assembly of maize chromosomes using long-read technologies. Genome Biol 2020; 21:121. [PMID: 32434565 PMCID: PMC7238635 DOI: 10.1186/s13059-020-02029-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.
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Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Victor Llaca
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | | | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gernot G Presting
- Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Magdy Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Georgia Genomics and Bioinformatics Core Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Kevin A Fengler
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, 14853, USA
| | - Todd P Michael
- Informatics Department, J. Craig Venter Institute, La Jolla, CA, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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18
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Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam AS, Stein JC, Llaca V, Manchanda N, Gilbert AM, Wei S, Chin CS, Hufnagel DE, Pedersen S, Snodgrass SJ, Fengler K, Woodhouse M, Walenz BP, Koren S, Phillippy AM, Hannigan BT, Dawe RK, Hirsch CN, Hufford MB, Ware D. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nat Commun 2020; 11:2288. [PMID: 32385271 PMCID: PMC7211024 DOI: 10.1038/s41467-020-16037-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 04/09/2020] [Indexed: 01/23/2023] Open
Abstract
Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11-21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.
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Affiliation(s)
- Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Kapeel M Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | | | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
- Genome Informatics Facility, Iowa State University, Ames, Iowa, 50011, USA
| | - Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Victor Llaca
- Genomics Technologies, Applied Science and Technology, Corteva Agriscience TM, Johnston, Iowa, 50131, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Amanda M Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Chen-Shan Chin
- DNAnexus, Inc., Mountain View, San Francisco, California, 94040, USA
| | - David E Hufnagel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Kevin Fengler
- Genomics Technologies, Applied Science and Technology, Corteva Agriscience TM, Johnston, Iowa, 50131, USA
| | - Margaret Woodhouse
- USDA ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa, 50011, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Brett T Hannigan
- DNAnexus, Inc., Mountain View, San Francisco, California, 94040, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA.
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108, USA.
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA.
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA.
- USDA ARS Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, New York, 14853, USA.
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19
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A universal chromosome identification system for maize and wild Zea species. Chromosome Res 2020; 28:183-194. [PMID: 32219602 DOI: 10.1007/s10577-020-09630-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022]
Abstract
Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared with other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species.
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20
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Bhowmick BK, Jha S. Differences in Karyotype and Fluorochrome Banding Patterns among Variations of Trichosanthes cucumerina with Different Fruit Size. CYTOLOGIA 2019. [DOI: 10.1508/cytologia.84.237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Biplab Kumar Bhowmick
- Department of Botany, Scottish Church College
- CAS, Department of Botany, University of Calcutta
| | - Sumita Jha
- CAS, Department of Botany, University of Calcutta
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21
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Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF. Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize. Genetics 2019; 213:143-160. [PMID: 31320409 PMCID: PMC6727801 DOI: 10.1534/genetics.119.302378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 11/18/2022] Open
Abstract
In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1 plants appear similar to typical maize × teosinte F1s. However, upon backcrossing to maize, the BC1 and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set, and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. A de novo assembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 upregulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation, and small RNAs are similar between sickly plants and normal controls, although a few upregulated transcripts and transposable elements are associated with altered small RNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon "hybrid decay" and present ideas on the mechanism that may underlie it.
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Affiliation(s)
- Wei Xue
- College of Agronomy, Shenyang Agricultural University, 110866 Liaoning Province, China
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, 518060 Guangdong Province, China
| | - Liyan Yang
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- Life Science College, Shanxi Normal University, 041004 Shanxi Province, China
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Qing Li
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jaclyn Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Paul Bilinski
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Michelle C Stitzer
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Sherry Flint-Garcia
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
- Agricultural Research Service, United States Department of Agriculture, Columbia, Missouri 65211
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, 518060 Guangdong Province, China
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. Proc Natl Acad Sci U S A 2019; 116:1679-1685. [PMID: 30655344 PMCID: PMC6358699 DOI: 10.1073/pnas.1813957116] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Whole-chromosome painting probes were developed for each of the 10 chromosomes of maize by producing amplifiable libraries of unique sequences of oligonucleotides that can generate labeled probes through transcription reactions. These paints allow identification of individual homologous chromosomes for many applications as demonstrated in somatic root tip metaphase cells, in the pachytene stage of meiosis, and in interphase nuclei. Several chromosomal aberrations were examined as proof of concept for study of various rearrangements using probes that cover the entire chromosome and that label diverse varieties. The relationship of the supernumerary B chromosome and the normal chromosomes was examined with the finding that there is no detectable homology between any of the normal A chromosomes and the B chromosome. Combined with other chromosome-labeling techniques, a complete set of whole-chromosome oligonucleotide paints lays the foundation for future studies of the structure, organization, and evolution of genomes.
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Easterling KA, Pitra NJ, Jones RJ, Lopes LG, Aquino JR, Zhang D, Matthews PD, Bass HW. 3D Molecular Cytology of Hop ( Humulus lupulus) Meiotic Chromosomes Reveals Non-disomic Pairing and Segregation, Aneuploidy, and Genomic Structural Variation. FRONTIERS IN PLANT SCIENCE 2018; 9:1501. [PMID: 30443259 PMCID: PMC6221928 DOI: 10.3389/fpls.2018.01501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/25/2018] [Indexed: 05/31/2023]
Abstract
Hop (Humulus lupulus L.) is an important crop worldwide, known as the main flavoring ingredient in beer. The diversifying brewing industry demands variation in flavors, superior process properties, and sustainable agronomics, which are the focus of advanced molecular breeding efforts in hops. Hop breeders have been limited in their ability to create strains with desirable traits, however, because of the unusual and unpredictable inheritance patterns and associated non-Mendelian genetic marker segregation. Cytogenetic analysis of meiotic chromosome behavior has also revealed conspicuous and prevalent occurrences of multiple, atypical, non-disomic chromosome complexes, including those involving autosomes in late prophase. To explore the role of meiosis in segregation distortion, we undertook 3D cytogenetic analysis of hop pollen mother cells stained with DAPI and FISH. We used telomere FISH to demonstrate that hop exhibits a normal telomere clustering bouquet. We also identified and characterized a new sub-terminal 180 bp satellite DNA tandem repeat family called HSR0, located proximal to telomeres. Highly variable 5S rDNA FISH patterns within and between plants, together with the detection of anaphase chromosome bridges, reflect extensive departures from normal disomic signal composition and distribution. Subsequent FACS analysis revealed variable DNA content in a cultivated pedigree. Together, these findings implicate multiple phenomena, including aneuploidy, segmental aneuploidy, or chromosome rearrangements, as contributing factors to segregation distortion in hop.
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Affiliation(s)
- Katherine A. Easterling
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
- Hopsteiner, S.S. Steiner, Inc., New York, NY, United States
| | | | | | - Lauren G. Lopes
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Jenna R. Aquino
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Dong Zhang
- Hopsteiner, S.S. Steiner, Inc., New York, NY, United States
| | | | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
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Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers. Genes (Basel) 2018; 9:genes9090433. [PMID: 30158460 PMCID: PMC6162735 DOI: 10.3390/genes9090433] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 12/02/2022] Open
Abstract
The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses.
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Bilinski P, Albert PS, Berg JJ, Birchler JA, Grote MN, Lorant A, Quezada J, Swarts K, Yang J, Ross-Ibarra J. Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays. PLoS Genet 2018; 14:e1007162. [PMID: 29746459 PMCID: PMC5944917 DOI: 10.1371/journal.pgen.1007162] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/20/2017] [Indexed: 12/03/2022] Open
Abstract
While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes. Genome size in plants can vary by orders of magnitude, but this variation has long been considered to be of little functional consequence. Studying three independent adaptations to high altitude in Zea mays, we find that genome size experiences parallel pressures from natural selection, causing a reduction in genome size with increasing altitude. Though reductions in overall repetitive content are responsible for the genome size change, we find that only those individual loci contributing most to the variation in genome size are individually targeted by selection. To identify the phenotype influenced by genome size, we study how variation in genome size within a single wild population impacts leaf growth and cell division. We find that genome size variation correlates negatively with the rate of cell division, suggesting that individuals with larger genomes require longer to complete a mitotic cycle. Finally, we reanalyze data from maize inbreds to show that faster cell division is correlated with earlier flowering, connecting observed variation in genome size to an important adaptive phenotype.
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Affiliation(s)
- Paul Bilinski
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
- * E-mail: (PB); (JRI)
| | - Patrice S. Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jeremy J. Berg
- Center for Population Biology, University of California, Davis, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Mark N. Grote
- Department of Anthropology, University of California, Davis, Davis, California, United States of America
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Juvenal Quezada
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Kelly Swarts
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Jinliang Yang
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Center for Population Biology, University of California, Davis, Davis, California, United States of America
- Genome Center, University of California, Davis, Davis, California, United States of America
- * E-mail: (PB); (JRI)
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Bilinski P, Albert PS, Berg JJ, Birchler JA, Grote MN, Lorant A, Quezada J, Swarts K, Yang J, Ross-Ibarra J. Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays. PLoS Genet 2018; 14:e1007162. [PMID: 29746459 DOI: 10.1371/journal.pgen.1007162.g001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/20/2017] [Indexed: 05/23/2023] Open
Abstract
While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.
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Affiliation(s)
- Paul Bilinski
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jeremy J Berg
- Center for Population Biology, University of California, Davis, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Mark N Grote
- Department of Anthropology, University of California, Davis, Davis, California, United States of America
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Juvenal Quezada
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Kelly Swarts
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Jinliang Yang
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Center for Population Biology, University of California, Davis, Davis, California, United States of America
- Genome Center, University of California, Davis, Davis, California, United States of America
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27
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Presting GG. Centromeric retrotransposons and centromere function. Curr Opin Genet Dev 2018; 49:79-84. [DOI: 10.1016/j.gde.2018.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/05/2018] [Accepted: 03/08/2018] [Indexed: 12/17/2022]
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Silva JC, Carvalho CR, Clarindo WR. Updating the maize karyotype by chromosome DNA sizing. PLoS One 2018; 13:e0190428. [PMID: 29293613 PMCID: PMC5749775 DOI: 10.1371/journal.pone.0190428] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/14/2017] [Indexed: 12/20/2022] Open
Abstract
The karyotype is a basic concept regarding the genome, fundamentally described by the number and morphological features of all chromosomes. Chromosome class, centromeric index, intra- and interchromosomal asymmetry index, and constriction localization are important in clinical, systematic and evolutionary approaches. In spite of the advances in karyotype characterization made over the last years, new data about the chromosomes can be generated from quantitative methods, such as image cytometry. Therefore, using Zea mays L., this study aimed to update the species' karyotype by supplementing information on chromosome DNA sizing. After adjustment of the procedures, chromosome morphometry and class as well as knob localization enabled describing the Z. mays karyotype. In addition, applying image cytometry, DNA sizing was unprecedentedly measured for the arms and satellite of all chromosomes. This way, unambiguous identification of the chromosome pairs, and hence the assembly of 51 karyograms, were only possible after the DNA sizing of each chromosome, their arms and satellite portions. These accurate, quantitative and reproducible data also enabled determining the distribution and variation of DNA content in each chromosome. From this, a correlation between DNA amount and total chromosome length evidenced that the mean DNA content of chromosome 9 was higher than that of chromosome 8. The chromosomal DNA sizing updated the Z. mays karyotype, providing insights into its dynamic genome with regards to the organization of the ten chromosomes and their respective portions. Considering the results and the relevance of cytogenetics in the current scenario of comparative sequencing and genomics, chromosomal DNA sizing should be incorporated as an additional parameter for karyotype definition. Based on this study, it can be affirmed that cytogenetic approaches go beyond the simple morphological description of chromosomes.
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Affiliation(s)
- Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa–MG, Brazil
| | - Carlos Roberto Carvalho
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa–MG, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética, Departamento de Biologia, Campus Alegre, Universidade Federal do Espírito Santo, Alegre–ES, Brazil
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30
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Gent JI, Wang N, Dawe RK. Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives. Genome Biol 2017. [PMID: 28637491 PMCID: PMC5480163 DOI: 10.1186/s13059-017-1249-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere positioning because many of its large (~2 Mb) centromeres are not dominated by satellite DNA. These centromeres, which we call complex centromeres, allow for both assembly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric histone H3 (cenH3). Results We found frequent complex centromeres in maize and its wild relatives Z. mays parviglumis, Z. mays mexicana, and particularly Z. mays huehuetenangensis. Analysis of individual plants reveals minor variation in the positions of complex centromeres among siblings. However, such positional shifts are stochastic and not heritable, consistent with prior findings that centromere positioning is stable at the population level. Centromeres are also stable in multiple F1 hybrid contexts. Analysis of repeats in Z. mays and other species (Zea diploperennis, Zea luxurians, and Tripsacum dactyloides) reveals tenfold differences in abundance of the major satellite CentC, but similar high levels of sequence polymorphism in individual CentC copies. Deviation from the CentC consensus has little or no effect on binding of cenH3. Conclusions These data indicate that complex centromeres are neither a peculiarity of cultivation nor inbreeding in Z. mays. While extensive arrays of CentC may be the norm for other Zea and Tripsacum species, these data also reveal that a wide diversity of DNA sequences and multiple types of genetic elements in and near centromeres support centromere function and constrain centromere positions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1249-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, USA. .,Department of Genetics, University of Georgia, Athens, USA.
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31
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Bilinski P, Han Y, Hufford MB, Lorant A, Zhang P, Estep MC, Jiang J, Ross-Ibarra J. Genomic abundance is not predictive of tandem repeat localization in grass genomes. PLoS One 2017; 12:e0177896. [PMID: 28570674 PMCID: PMC5453492 DOI: 10.1371/journal.pone.0177896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/04/2017] [Indexed: 11/25/2022] Open
Abstract
Highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Previous research has investigated variation in centromere repeats across eukaryotes, positing that the highest abundance tandem repeat in a genome is often the centromeric repeat. To test this assumption, we used shotgun sequencing and a bioinformatic pipeline to identify common tandem repeats across a number of grass species. We find that de novo assembly and subsequent abundance ranking of repeats can successfully identify tandem repeats with homology to known tandem repeats. Fluorescent in-situ hybridization shows that de novo assembly and ranking of repeats from non-model taxa identifies chromosome domains rich in tandem repeats both near pericentromeres and elsewhere in the genome.
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Affiliation(s)
- Paul Bilinski
- Dept. of Plant Sciences, University of California, Davis, Davis, CA, United States of America
- * E-mail: (PB); (JRI)
| | - Yonghua Han
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Dept. of Horticulture, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States of America
| | - Anne Lorant
- Dept. of Plant Sciences, University of California, Davis, Davis, CA, United States of America
| | - Pingdong Zhang
- Dept. of Horticulture, University of Wisconsin-Madison, Madison, WI, United States of America
- College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, China
| | - Matt C. Estep
- Dept. of Biology, Appalachian State University, Boone, NC, United States of America
| | - Jiming Jiang
- Dept. of Horticulture, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Jeffrey Ross-Ibarra
- Dept. of Plant Sciences, University of California, Davis, Davis, CA, United States of America
- Genome Center and Center for Population Biology, University of California, Davis, Davis, CA, United States of America
- * E-mail: (PB); (JRI)
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Zhu M, Du P, Zhuang L, Chu C, Zhao H, Qi Z. A simple and efficient non-denaturing FISH method for maize chromosome differentiation using single-strand oligonucleotide probes. Genome 2017; 60:657-664. [PMID: 28472606 DOI: 10.1139/gen-2016-0167] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Single-strand oligonucleotides (SSONs hereafter) as probes are becoming a powerful method of chromosome painting in many species. In this study, nine SSONs ((ACT)10, (ACT)19, Knob-1, Knob-2, Knob-3, CentC69-1, MR68-3, K10-72-1, and TR1-357-2) were developed and used for chromosome identification in 16 maize (Zea mays L., 2n = 20) inbred lines and hybrids by non-denaturing fluorescence in situ hybridization (ND-FISH). Each SSON produced clear signals on 2-10 chromosomes of inbred lines B73 and Mo17. A multiplex probe set containing four SSONs ((ACT)10, Knob-2, CentC69-1, and MR68-3) clearly characterized all maize chromosomes in the 16 lines by a single round of ND-FISH and revealed genetic variation at a chromosome level. For example, unique signals on chromosome 6 clearly distinguished all 16 genotypes. The SSONs and multiplex probe developed in this research will facilitate genotype identification and chromosome research in maize.
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Affiliation(s)
- Minqiu Zhu
- a Agriculture College, Nanjing Agricultural University, Nanjing 210095, China
| | - Pei Du
- a Agriculture College, Nanjing Agricultural University, Nanjing 210095, China
| | - Lifang Zhuang
- a Agriculture College, Nanjing Agricultural University, Nanjing 210095, China
| | - Chenggen Chu
- b Monsanto Company, 21120 Hwy 30, Filer, ID 83301, USA
| | - Han Zhao
- c Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zengjun Qi
- a Agriculture College, Nanjing Agricultural University, Nanjing 210095, China
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33
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Findley SD, Birchler JA, Stacey G. Metaphase Chromosome Preparation from Soybean (Glycine max) Root Tips. ACTA ACUST UNITED AC 2017; 2:78-88. [PMID: 31725978 DOI: 10.1002/cppb.20046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit presents a highly reliable protocol to produce and screen metaphase chromosome spreads from root tip cell suspensions of soybean (Glycine max), or other legumes. The procedures represent soybean-optimized versions of protocols developed for maize. The use of pressurized nitrous oxide to reliably generate metaphase-arrested chromosomes is crucial to overcoming one of the challenges of working with tiny and numerous soybean chromosomes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Seth D Findley
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
| | - James A Birchler
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Gary Stacey
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
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34
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Findley SD, Birchler JA, Stacey G. Fluorescence In Situ Hybridization for Glycine max Metaphase Chromosomes. CURRENT PROTOCOLS IN PLANT BIOLOGY 2017; 2:89-107. [PMID: 31725974 DOI: 10.1002/cppb.20045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This article presents protocols for fluorescence in situ hybridization (FISH) in the cultivated soybean, Glycine max. The protocols represent soybean-optimized versions developed for maize. We describe the use of two different probes types: genomic-repeat-based fluorescently-tagged oligonucleotides and bacterial artificial chromosomes (BACs). The two probe types can be used either individually or together, depending on the experimental questions. The article also includes starting points for executing FISH in additional legume species. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Seth D Findley
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
| | - James A Birchler
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Gary Stacey
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
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Liu S, Zheng J, Migeon P, Ren J, Hu Y, He C, Liu H, Fu J, White FF, Toomajian C, Wang G. Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. Sci Rep 2017; 7:42444. [PMID: 28186206 PMCID: PMC5301235 DOI: 10.1038/srep42444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/10/2017] [Indexed: 12/15/2022] Open
Abstract
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jun Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Cheng He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Taian 271018, P.R. China.,College of Life Sciences, Shandong Agricultural University, Taian 271018, P.R. China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
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Kirov IV, Kiseleva AV, Van Laere K, Van Roy N, Khrustaleva LI. Tandem repeats of Allium fistulosum associated with major chromosomal landmarks. Mol Genet Genomics 2017; 292:453-464. [PMID: 28150039 DOI: 10.1007/s00438-016-1286-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 12/30/2016] [Indexed: 01/22/2023]
Abstract
Tandem repeats are often associated with important chromosomal landmarks, such as centromeres, telomeres, subtelomeric, and other heterochromatic regions, and can be good candidates for molecular cytogenetic markers. Tandem repeats present in many plant species demonstrate dramatic differences in unit length, proportion in the genome, and chromosomal organization. Members of genus Allium with their large genomes represent a challenging task for current genetics. Using the next generation sequencing data, molecular, and cytogenetic methods, we discovered two tandemly organized repeats in the Allium fistulosum genome (2n = 2C = 16), HAT58 and CAT36. Together, these repeats comprise 0.25% of the bunching onion genome with 160,000 copies/1 C of HAT58 and 93,000 copies/1 C of CAT36. Fluorescent in situ hybridization (FISH) and C-banding showed that HAT58 and CAT36 associated with the interstitial and pericentromeric heterochromatin of the A. fistulosum chromosomes 5, 6, 7, and 8. FISH with HAT58 and CAT36 performed on A. cepa (2n = 2C = 16) and A. wakegi (2n = 2C = 16), a natural allodiploid hybrid between A. fistulosum and A. cepa, revealed that these repeats are species specific and produced specific hybridization patterns only on A. fistulosum chromosomes. Thus, the markers can be used in interspecific breeding programs for monitoring of alien genetic material. We applied Non-denaturing FISH that allowed detection of the repeat bearing chromosomes within 3 h. A polymorphism of the HAT58 chromosome location was observed. This finding suggests that the rapid evolution of the HAT58 repeat is still ongoing.
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Affiliation(s)
- Ilya V Kirov
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium.
| | - Anna V Kiseleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Katrijn Van Laere
- Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium
| | - Nadine Van Roy
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Ludmila I Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.
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McCaw M, Graham N, Cody J, Swyers N, Zhao C, Birchler J. Fluorescence In Situ Hybridization to Maize (Zea mays) Chromosomes. CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:530-545. [PMID: 31725962 DOI: 10.1002/cppb.20033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fluorescence In Situ Hybridization (FISH) is the annealing of fluorescent DNA probes to their complementary sequences on prepared chromosomes and subsequent visualization with a fluorescent microscope. In maize, FISH is useful for distinguishing each of the ten chromosomes in different accessions (karyotyping), roughly mapping single genes, transposable elements, transgene insertions, and identifying various chromosomal alterations. FISH can also be used to distinguish chromosomes between different Zea species in interspecific hybrids by use of retroelement painting. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Morgan McCaw
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Nathaniel Graham
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Jon Cody
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Nathan Swyers
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Changzeng Zhao
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - James Birchler
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
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Waminal NE, Choi HI, Kim NH, Jang W, Lee J, Park JY, Kim HH, Yang TJ. A refined Panax ginseng karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs. J Ginseng Res 2016; 41:469-476. [PMID: 29021693 PMCID: PMC5628329 DOI: 10.1016/j.jgr.2016.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 07/25/2016] [Accepted: 08/03/2016] [Indexed: 12/29/2022] Open
Abstract
Background Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4′,6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.
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Affiliation(s)
- Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, Republic of Korea
- Corresponding authors. Hyun Hee Kim, Department of Life Science, Plant Biotechnology Institute, Sahmyook University, 2nd Science Building Room 408, Gongneung 2-dong, Nowon-gu, Seoul 01795, Republic of Korea; Tae-Jin Yang, Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Gwanangno, Gwanak-gu, Seoul National University 200-4119, Seoul 08826, Republic of Korea.
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Corresponding authors. Hyun Hee Kim, Department of Life Science, Plant Biotechnology Institute, Sahmyook University, 2nd Science Building Room 408, Gongneung 2-dong, Nowon-gu, Seoul 01795, Republic of Korea; Tae-Jin Yang, Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Gwanangno, Gwanak-gu, Seoul National University 200-4119, Seoul 08826, Republic of Korea.
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Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives. G3-GENES GENOMES GENETICS 2016; 6:1013-22. [PMID: 26865698 PMCID: PMC4825637 DOI: 10.1534/g3.115.024984] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.
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Abstract
Functional centromeres, the chromosomal sites of spindle attachment during cell division, are marked epigenetically by the centromere-specific histone H3 variant cenH3 and typically contain long stretches of centromere-specific tandem DNA repeats (∼1.8 Mb in maize). In 23 inbreds of domesticated maize chosen to represent the genetic diversity of maize germplasm, partial or nearly complete loss of the tandem DNA repeat CentC precedes 57 independent cenH3 relocation events that result in neocentromere formation. Chromosomal regions with newly acquired cenH3 are colonized by the centromere-specific retrotransposon CR2 at a rate that would result in centromere-sized CR2 clusters in 20,000-95,000 y. Three lines of evidence indicate that CentC loss is linked to inbreeding, including (i) CEN10 of temperate lineages, presumed to have experienced a genetic bottleneck, contain less CentC than their tropical relatives; (ii) strong selection for centromere-linked genes in domesticated maize reduced diversity at seven of the ten maize centromeres to only one or two postdomestication haplotypes; and (iii) the centromere with the largest number of haplotypes in domesticated maize (CEN7) has the highest CentC levels in nearly all domesticated lines. Rare recombinations introduced one (CEN2) or more (CEN5) alternate CEN haplotypes while retaining a single haplotype at domestication loci linked to these centromeres. Taken together, this evidence strongly suggests that inbreeding, favored by postdomestication selection for centromere-linked genes affecting key domestication or agricultural traits, drives replacement of the tandem centromere repeats in maize and other crop plants. Similar forces may act during speciation in natural systems.
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Wolfgruber TK, Nakashima MM, Schneider KL, Sharma A, Xie Z, Albert PS, Xu R, Bilinski P, Dawe RK, Ross-Ibarra J, Birchler JA, Presting GG. High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events. FRONTIERS IN PLANT SCIENCE 2016; 7:308. [PMID: 27047500 PMCID: PMC4806543 DOI: 10.3389/fpls.2016.00308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/27/2016] [Indexed: 05/02/2023]
Abstract
The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR) has presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here, we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 × 10(-6) and 5 × 10(-5) for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb from the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length CR from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB) repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. In many cases examined here, DSB repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to efficiently repair frequent DSBs in centromeres.
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Affiliation(s)
- Thomas K. Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Megan M. Nakashima
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Kevin L. Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Anupma Sharma
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Zidian Xie
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Patrice S. Albert
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Ronghui Xu
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Paul Bilinski
- Department of Plant Sciences, University of California DavisDavis, CA, USA
| | - R. Kelly Dawe
- Department of Plant Biology, University of GeorgiaAthens, GA, USA
| | | | - James A. Birchler
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Gernot G. Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
- *Correspondence: Gernot G. Presting
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Realini MF, Poggio L, Cámara-Hernández J, González GE. Intra-specific variation in genome size in maize: cytological and phenotypic correlates. AOB PLANTS 2015; 8:plv138. [PMID: 26644343 PMCID: PMC4742330 DOI: 10.1093/aobpla/plv138] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/07/2015] [Indexed: 05/15/2023]
Abstract
Genome size variation accompanies the diversification and evolution of many plant species. Relationships between DNA amount and phenotypic and cytological characteristics form the basis of most hypotheses that ascribe a biological role to genome size. The goal of the present research was to investigate the intra-specific variation in the DNA content in maize populations from Northeastern Argentina and further explore the relationship between genome size and the phenotypic traits seed weight and length of the vegetative cycle. Moreover, cytological parameters such as the percentage of heterochromatin as well as the number, position and sequence composition of knobs were analysed and their relationships with 2C DNA values were explored. The populations analysed presented significant differences in 2C DNA amount, from 4.62 to 6.29 pg, representing 36.15 % of the inter-populational variation. Moreover, intra-populational genome size variation was found, varying from 1.08 to 1.63-fold. The variation in the percentage of knob heterochromatin as well as in the number, chromosome position and sequence composition of the knobs was detected among and within the populations. Although a positive relationship between genome size and the percentage of heterochromatin was observed, a significant correlation was not found. This confirms that other non-coding repetitive DNA sequences are contributing to the genome size variation. A positive relationship between DNA amount and the seed weight has been reported in a large number of species, this relationship was not found in the populations studied here. The length of the vegetative cycle showed a positive correlation with the percentage of heterochromatin. This result allowed attributing an adaptive effect to heterochromatin since the length of this cycle would be optimized via selection for an appropriate percentage of heterochromatin.
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Affiliation(s)
- María Florencia Realini
- Instituto de Ecología, Genética y Evolución (IEGEBA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Lidia Poggio
- Instituto de Ecología, Genética y Evolución (IEGEBA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Julián Cámara-Hernández
- Cátedra de Botánica Agrícola, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Graciela Esther González
- Instituto de Ecología, Genética y Evolución (IEGEBA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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Mascagni F, Barghini E, Giordani T, Rieseberg LH, Cavallini A, Natali L. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes. Genome Biol Evol 2015; 7:3368-82. [PMID: 26608057 PMCID: PMC4700961 DOI: 10.1093/gbe/evv230] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes—7 wild accessions and 8 cultivars—of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower.
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Affiliation(s)
- Flavia Mascagni
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Elena Barghini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Tommaso Giordani
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Loren H Rieseberg
- The Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
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Zhao H, Zhu X, Wang K, Gent JI, Zhang W, Dawe RK, Jiang J. Gene Expression and Chromatin Modifications Associated with Maize Centromeres. G3 (BETHESDA, MD.) 2015; 6:183-92. [PMID: 26564952 PMCID: PMC4704717 DOI: 10.1534/g3.115.022764] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/09/2015] [Indexed: 12/23/2022]
Abstract
Centromeres are defined by the presence of CENH3, a variant of histone H3. Centromeres in most plant species contain exclusively highly repetitive DNA sequences, which has hindered research on structure and function of centromeric chromatin. Several maize centromeres have been nearly completely sequenced, providing a sequence-based platform for genomic and epigenomic research of plant centromeres. Here we report a high resolution map of CENH3 nucleosomes in the maize genome. Although CENH3 nucleosomes are spaced ∼190 bp on average, CENH3 nucleosomes that occupied CentC, a 156-bp centromeric satellite repeat, showed clear positioning aligning with CentC monomers. Maize centromeres contain alternating CENH3-enriched and CENH3-depleted subdomains, which account for 87% and 13% of the centromeres, respectively. A number of annotated genes were identified in the centromeres, including 11 active genes that were located exclusively in CENH3-depleted subdomains. The euchromatic histone modification marks, including H3K4me3, H3K36me3 and H3K9ac, detected in maize centromeres were associated mainly with the active genes. Interestingly, maize centromeres also have lower levels of the heterochromatin histone modification mark H3K27me2 relative to pericentromeric regions. We conclude that neither H3K27me2 nor the three euchromatic histone modifications are likely to serve as functionally important epigenetic marks of centromere identity in maize.
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Affiliation(s)
- Hainan Zhao
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Xiaobiao Zhu
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Kai Wang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
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González GE, Poggio L. Genomic affinities revealed by GISH suggests intergenomic restructuring between parental genomes of the paleopolyploid genus Zea. Genome 2015; 58:433-9. [PMID: 26506040 DOI: 10.1139/gen-2015-0081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present work compares the molecular affinities, revealed by GISH, with the analysis of meiotic pairing in intra- and interspecific hybrids between species of Zea obtained in previous works. The joint analysis of these data provided evidence about the evolutionary relationships among the species from the paleopolyploid genus Zea (maize and teosintes). GISH and meiotic pairing of intraspecific hybrids revealed high genomic affinity between maize (Zea mays subsp. mays) and both Zea mays subsp. parviglumis and Zea mays subsp. mexicana. On the other hand, when Zea mays subsp. huehuetenanguensis DNA was probed on maize chromosomes, a lower affinity was detected, and the pattern of hybridization suggested intergenomical restructuring between the parental genomes of maize. When DNA from Zea luxurians was used as probe, homogeneous hybridization signals were observed through all maize chromosomes. Lower genomic affinity was observed when DNA from Zea diploperennis was probed on maize chromosomes, especially at knob regions. Maize chromosomes hybridized with Zea perennis DNA showed hybridization signals on four chromosome pairs: two chromosome pairs presented hybridization signal in only one chromosomal arm, whereas four chromosome pairs did not show any hybridization. These results are in agreement with previous GISH studies, which have identified the genomic source of the chromosomes involved in the meiotic configurations of Z. perennis × maize hybrids. These findings allow postulating that maize has a parental genome not shared with Z. perennis, and the existence of intergenomic restructuring between the parental genomes of maize. Moreover, the absence of hybridization signals in all maize knobs indicate that these heterochromatic regions were lost during the Z. perennis genome evolution.
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Affiliation(s)
- Graciela Esther González
- Instituto de Ecología, Genética y Evolución (IEGEBA, Consejo Nacional de Investigaciones Científicas y Técnicas - CONICET); Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Int. Güiraldes N° 2620, Pabellón II, Lab. 110, 4° Piso (1428), Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Ecología, Genética y Evolución (IEGEBA, Consejo Nacional de Investigaciones Científicas y Técnicas - CONICET); Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Int. Güiraldes N° 2620, Pabellón II, Lab. 110, 4° Piso (1428), Ciudad Autónoma de Buenos Aires, Argentina
| | - Lidia Poggio
- Instituto de Ecología, Genética y Evolución (IEGEBA, Consejo Nacional de Investigaciones Científicas y Técnicas - CONICET); Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Int. Güiraldes N° 2620, Pabellón II, Lab. 110, 4° Piso (1428), Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Ecología, Genética y Evolución (IEGEBA, Consejo Nacional de Investigaciones Científicas y Técnicas - CONICET); Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Int. Güiraldes N° 2620, Pabellón II, Lab. 110, 4° Piso (1428), Ciudad Autónoma de Buenos Aires, Argentina
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Stable Patterns of CENH3 Occupancy Through Maize Lineages Containing Genetically Similar Centromeres. Genetics 2015; 200:1105-16. [PMID: 26063660 PMCID: PMC4574241 DOI: 10.1534/genetics.115.177360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/08/2015] [Indexed: 01/08/2023] Open
Abstract
While the approximate chromosomal position of centromeres has been identified in many species, little is known about the dynamics and diversity of centromere positions within species. Multiple lines of evidence indicate that DNA sequence has little or no impact in specifying centromeres in maize and in most multicellular organisms. Given that epigenetically defined boundaries are expected to be dynamic, we hypothesized that centromere positions would change rapidly over time, which would result in a diversity of centromere positions in isolated populations. To test this hypothesis, we used CENP-A/cenH3 (CENH3 in maize) chromatin immunoprecipitation to define centromeres in breeding pedigrees that included the B73 inbred as a common parent. While we found a diversity of CENH3 profiles for centromeres with divergent sequences that were not inherited from B73, the CENH3 profiles from centromeres that were inherited from B73 were indistinguishable from each other. We propose that specific genetic elements in centromeric regions favor or inhibit CENH3 accumulation, leading to reproducible patterns of CENH3 occupancy. These data also indicate that dramatic shifts in centromere position normally originate from accumulated or large-scale genetic changes rather than from epigenetic positional drift.
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Cai Z, Liu H, He Q, Pu M, Chen J, Lai J, Li X, Jin W. Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping. BMC Genomics 2014; 15:1025. [PMID: 25425126 PMCID: PMC4256728 DOI: 10.1186/1471-2164-15-1025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 11/19/2014] [Indexed: 02/07/2023] Open
Abstract
Abstract Background Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9–11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have been reported for C. aquatica Roxb. One sterile cytotype (2n = 30) closely related to C. aquatica has been recently found in Guangxi of China. This putative hybrid has been named C. aquatica HG (Hybrid Guangxi). The genome composition and the evolutionary history of C. lacryma-jobi and C. aquatica HG are largely unclear. Results About 76% of the genome of C. lacryma-jobi and 73% of the genome of C. aquatica HG are repetitive DNA sequences as shown by low coverage genome sequencing followed by similarity-based cluster analysis. In addition, long terminal repeat (LTR) retrotransposable elements are dominant repetitive sequences in these two genomes, and the proportions of many repetitive sequences in whole genome varied greatly between the two species, indicating evolutionary divergence of them. We also found that a novel 102 bp variant of centromeric satellite repeat CentX and two other satellites only appeared in C. aquatica HG. The results from FISH analysis with repeat probe cocktails and the data from chromosomes pairing in meiosis metaphase showed that C. lacryma-jobi is likely a diploidized paleotetraploid species and C. aquatica HG is possibly a recently formed hybrid. Furthermore, C. lacryma-jobi and C. aquatica HG shared more co-existing repeat families and higher sequence similarity with Sorghum than with Zea. Conclusions The composition and abundance of repetitive sequences are divergent between the genomes of C. lacryma-jobi and C. aquatica HG. The results from fine karyotyping analysis and chromosome pairing suggested diploidization of C. lacryma-jobi during evolution and C. aquatica HG is a recently formed hybrid. The genome-wide comparison of repetitive sequences indicated that the repeats in Coix were more similar to those in Sorghum than to those in Zea, which is consistent with the phylogenetic relationship reported by previous work. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1025) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Weiwei Jin
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Coordinated Research Center for Crop Biology, China Agricultural University, Beijing 100193, China.
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Mondin M, Santos-Serejo JA, Bertäo MR, Laborda P, Pizzaia D, Aguiar-Perecin MLR. Karyotype variability in tropical maize sister inbred lines and hybrids compared with KYS standard line. FRONTIERS IN PLANT SCIENCE 2014; 5:544. [PMID: 25352856 PMCID: PMC4195276 DOI: 10.3389/fpls.2014.00544] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/24/2014] [Indexed: 05/27/2023]
Abstract
Maize karyotype variability has been extensively investigated. The identification of maize somatic and pachytene chromosomes has improved with the development of fluorescence in situ hybridization (FISH) using tandemly repeated DNA sequences as probes. We identified the somatic chromosomes of sister inbred lines that were derived from a tropical flint maize population (Jac Duro [JD]), and hybrids between them, using FISH probes for the 180-bp knob repeat, centromeric satellite (CentC), centromeric satellite 4 (Cent4), subtelomeric clone 4-12-1, 5S ribosomal DNA and nucleolus organizing region DNA sequences. The observations were integrated with data based on C-banded mitotic metaphases and conventional analysis of pachytene chromosomes. Heterochromatic knobs visible at pachynema were coincident with C-bands and 180-bp FISH signals on somatic chromosomes, and most of them were large. Variation in the presence of some knobs was observed among lines. Small 180-bp knob signals were invariant on the short arms of chromosomes 1, 6, and 9. The subtelomeric 4-12-1 signal was also invariant and useful for identifying some chromosomes. The centromere location of chromosomes 2 and 4 differed from previous reports on standard maize lines. Somatic chromosomes of a JD line and the commonly used KYS line were compared by FISH in a hybrid of these lines. The pairing behavior of chromosomes 2 and 4 at pachytene stage in this hybrid was investigated using FISH with chromosome-specific probes. The homologues were fully synapsed, including the 5S rDNA and CentC sites on chromosome 2, and Cent4 and subtelomeric 4-12-1 sites on chromosome 4. This suggests that homologous chromosomes could pair through differential degrees of chromatin packaging in homologous arms differing in size. The results contribute to current knowledge of maize global diversity and also raise questions concerning the meiotic pairing of homologous chromosomes possibly differing in their amounts of repetitive DNA.
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Affiliation(s)
- Mateus Mondin
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
| | - Janay A. Santos-Serejo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Embrapa Cassava and Fruits, Brazilian Agricultural Research CorporationCruz das Almas, Brazil
| | - Mônica R. Bertäo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Department of Biological Sciences, Faculty of Sciences and Letters, São Paulo State UniversityAssis, Brazil
| | - Prianda Laborda
- Center for Molecular Biology and Genetic Engineering, State University of CampinasCampinas, Brazil
| | - Daniel Pizzaia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Herminio Ometto University Center, Herminio Ometto FoundationAraras, Brazil
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Bilinski P, Distor K, Gutierrez-Lopez J, Mendoza GM, Shi J, Dawe RK, Ross-Ibarra J. Diversity and evolution of centromere repeats in the maize genome. Chromosoma 2014; 124:57-65. [PMID: 25190528 DOI: 10.1007/s00412-014-0483-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/21/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
Abstract
Centromere repeats are found in most eukaryotes and play a critical role in kinetochore formation. Though centromere repeats exhibit considerable diversity both within and among species, little is understood about the mechanisms that drive centromere repeat evolution. Here, we use maize as a model to investigate how a complex history involving polyploidy, fractionation, and recent domestication has impacted the diversity of the maize centromeric repeat CentC. We first validate the existence of long tandem arrays of repeats in maize and other taxa in the genus Zea. Although we find considerable sequence diversity among CentC copies genome-wide, genetic similarity among repeats is highest within these arrays, suggesting that tandem duplications are the primary mechanism for the generation of new copies. Nonetheless, clustering analyses identify similar sequences among distant repeats, and simulations suggest that this pattern may be due to homoplasious mutation. Although the two ancestral subgenomes of maize have contributed nearly equal numbers of centromeres, our analysis shows that the majority of all CentC repeats derive from one of the parental genomes, with an even stronger bias when examining the largest assembled contiguous clusters. Finally, by comparing maize with its wild progenitor teosinte, we find that the abundance of CentC likely decreased after domestication, while the pericentromeric repeat Cent4 has drastically increased.
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Affiliation(s)
- Paul Bilinski
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
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Del Prete S, Arpón J, Sakai K, Andrey P, Gaudin V. Nuclear architecture and chromatin dynamics in interphase nuclei of Arabidopsis thaliana. Cytogenet Genome Res 2014; 143:28-50. [PMID: 24992956 DOI: 10.1159/000363724] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The interphase cell nucleus is extraordinarily complex, ordered, and dynamic. In the last decade, remarkable progress has been made in deciphering the functional organisation of the cell nucleus, and intricate relationships between genome functions (transcription, DNA repair, or replication) and various nuclear compartments have been revealed. In this review, we describe the architecture of the Arabidopsis thaliana interphase cell nucleus and discuss the dynamic nature of its organisation. We underline the need for further developments in quantitative and modelling approaches to nuclear organization.
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Affiliation(s)
- Stefania Del Prete
- INRA, UMR1318-AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), INRA-Centre de Versailles-Grignon, Versailles, France
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