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Cao S, Chen ZJ. Transgenerational epigenetic inheritance during plant evolution and breeding. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00112-2. [PMID: 38806375 DOI: 10.1016/j.tplants.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/12/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024]
Abstract
Plants can program and reprogram their genomes to create genetic variation and epigenetic modifications, leading to phenotypic plasticity. Although consequences of genetic changes are comprehensible, the basis for transgenerational inheritance of epigenetic variation is elusive. This review addresses contributions of external (environmental) and internal (genomic) factors to the establishment and maintenance of epigenetic memory during plant evolution, crop domestication, and modern breeding. Dynamic and pervasive changes in DNA methylation and chromatin modifications provide a diverse repertoire of epigenetic variation potentially for transgenerational inheritance. Elucidating and harnessing epigenetic inheritance will help us develop innovative breeding strategies and biotechnological tools to improve crop yield and resilience in the face of environmental challenges. Beyond plants, epigenetic principles are shared across sexually reproducing organisms including humans with relevance to medicine and public health.
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Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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2
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Ren Z, Gou R, Zhuo W, Chen Z, Yin X, Cao Y, Wang Y, Mi Y, Liu Y, Wang Y, Fan LM, Deng XW, Qian W. The MBD-ACD DNA methylation reader complex recruits MICRORCHIDIA6 to regulate ribosomal RNA gene expression in Arabidopsis. THE PLANT CELL 2024; 36:1098-1118. [PMID: 38092516 PMCID: PMC10980342 DOI: 10.1093/plcell/koad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/11/2023] [Indexed: 04/01/2024]
Abstract
DNA methylation is an important epigenetic mark implicated in selective rRNA gene expression, but the DNA methylation readers and effectors remain largely unknown. Here, we report a protein complex that reads DNA methylation to regulate variant-specific 45S ribosomal RNA (rRNA) gene expression in Arabidopsis (Arabidopsis thaliana). The complex, consisting of METHYL-CpG-BINDING DOMAIN PROTEIN5 (MBD5), MBD6, ALPHA-CRYSTALLIN DOMAIN PROTEIN15.5 (ACD15.5), and ACD21.4, directly binds to 45S rDNA. While MBD5 and MBD6 function redundantly, ACD15.5 and ACD21.4 are indispensable for variant-specific rRNA gene expression. These 4 proteins undergo phase separation in vitro and in vivo and are interdependent for their phase separation. The α-crystallin domain of ACD15.5 and ACD21.4, which is essential for their function, enables phase separation of the complex, likely by mediating multivalent protein interactions. The effector MICRORCHIDIA6 directly interacts with ACD15.5 and ACD21.4, but not with MBD5 and MBD6, and is recruited to 45S rDNA by the MBD-ACD complex to regulate variant-specific 45S rRNA expression. Our study reveals a pathway in Arabidopsis through which certain 45S rRNA gene variants are silenced, while others are activated.
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Affiliation(s)
- Zhitong Ren
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Runyu Gou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wanqing Zhuo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaochang Yin
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yuxin Cao
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingjie Mi
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yannan Liu
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- College of Life Sciences, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Liu-Min Fan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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Fultz D, McKinlay A, Enganti R, Pikaard CS. Sequence and epigenetic landscapes of active and silent nucleolus organizer regions in Arabidopsis. SCIENCE ADVANCES 2023; 9:eadj4509. [PMID: 37910609 PMCID: PMC10619934 DOI: 10.1126/sciadv.adj4509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023]
Abstract
Arabidopsis thaliana has two ribosomal RNA (rRNA) gene loci, nucleolus organizer regions NOR2 and NOR4, whose complete sequences are missing in current genome assemblies. Ultralong DNA sequences assembled using an unconventional approach yielded ~5.5- and 3.9-Mbp sequences for NOR2 and NOR4 in the reference strain, Col-0. The distinct rRNA gene subtype compositions of the NORs enabled the positional mapping of their active and inactive regions, using RNA sequencing to identify subtype-specific transcripts and DNA sequencing to identify subtypes associated with flow-sorted nucleoli. Comparisons of wild-type and silencing-defective plants revealed that most rRNA gene activity occurs in the central region of NOR4, whereas most, but not all, genes of NOR2 are epigenetically silenced. Intervals of low CG and CHG methylation overlap regions where gene activity and gene subtype homogenization are high. Collectively, the data reveal the genetic and epigenetic landscapes underlying nucleolar dominance (differential NOR activity) and implicate transcription as a driver of rRNA gene concerted evolution.
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Affiliation(s)
- Dalen Fultz
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Anastasia McKinlay
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Ramya Enganti
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Craig S. Pikaard
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
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Pikaard CS, Chandrasekhara C, McKinlay A, Enganti R, Fultz D. Reaching for the off switch in nucleolar dominance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1185-1192. [PMID: 37228042 PMCID: PMC10524600 DOI: 10.1111/tpj.16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023]
Abstract
Nucleolus organizer regions (NORs) are eukaryotic chromosomal loci where ribosomal RNA (rRNA) genes are clustered, typically in hundreds to thousands of copies. Transcription of these rRNA genes by RNA polymerase I and processing of their transcripts results in the formation of the nucleolus, the sub-nuclear domain in which ribosomes are assembled. Approximately 90 years ago, cytogenetic observations revealed that NORs inherited from the different parents of an interspecific hybrid sometimes differ in morphology at metaphase. Fifty years ago, those chromosomal differences were found to correlate with differences in rRNA gene transcription and the phenomenon became known as nucleolar dominance. Studies of the past 30 years have revealed that nucleolar dominance results from selective rRNA gene silencing, involving repressive chromatin modifications, and occurs in pure species as well as hybrids. Recent evidence also indicates that silencing depends on the NOR in which an rRNA gene is located, and not on the gene's sequence. In this perspective, we discuss how our thinking about nucleolar dominance has shifted over time from the kilobase scale of individual genes to the megabase scale of NORs and chromosomes and questions that remain unanswered in the search for a genetic and biochemical understanding of the off switch.
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Affiliation(s)
- Craig S Pikaard
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Chinmayi Chandrasekhara
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| | - Anastasia McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Ramya Enganti
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Dalen Fultz
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
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Katche EI, Schierholt A, Schiessl SV, He F, Lv Z, Batley J, Becker HC, Mason AS. Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus. G3 (BETHESDA, MD.) 2023; 13:jkad136. [PMID: 37313757 PMCID: PMC10411605 DOI: 10.1093/g3journal/jkad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
Established allopolyploids are known to be genomically stable and fertile. However, in contrast, most newly resynthesized allopolyploids are infertile and meiotically unstable. Identifying the genetic factors responsible for genome stability in newly formed allopolyploid is key to understanding how 2 genomes come together to form a species. One hypothesis is that established allopolyploids may have inherited specific alleles from their diploid progenitors which conferred meiotic stability. Resynthesized Brassica napus lines are often unstable and infertile, unlike B. napus cultivars. We tested this hypothesis by characterizing 41 resynthesized B. napus lines produced by crosses between 8 Brassica rapa and 8 Brassica oleracea lines for copy number variation resulting from nonhomologous recombination events and fertility. We resequenced 8 B. rapa and 5 B. oleracea parent accessions and analyzed 19 resynthesized lines for allelic variation in a list of meiosis gene homologs. SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 3 individuals per line. Self-pollinated seed set and genome stability (number of copy number variants) were significantly affected by the interaction between both B. rapa and B. oleracea parental genotypes. We identified 13 putative meiosis gene candidates which were significantly associated with frequency of copy number variants and which contained putatively harmful mutations in meiosis gene haplotypes for further investigation. Our results support the hypothesis that allelic variants inherited from parental genotypes affect genome stability and fertility in resynthesized rapeseed.
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Affiliation(s)
- Elizabeth Ihien Katche
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Antje Schierholt
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Sarah-Veronica Schiessl
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main D-60325, Germany
| | - Fei He
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
| | - Zhenling Lv
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Heiko C Becker
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
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Joshi P, Ansari H, Dickson R, Ellison NW, Skema C, Tate JA. Polyploidy on islands - concerted evolution and gene loss amid chromosomal stasis. ANNALS OF BOTANY 2023; 131:33-44. [PMID: 35390127 PMCID: PMC9904340 DOI: 10.1093/aob/mcac051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/04/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Polyploidy is an important process that often generates genomic diversity within lineages, but it can also cause changes that result in loss of genomic material. Island lineages, while often polyploid, typically show chromosomal stasis but have not been investigated in detail regarding smaller-scale gene loss. Our aim was to investigate post-polyploidization genome dynamics in a chromosomally stable lineage of Malvaceae endemic to New Zealand. METHODS We determined chromosome numbers and used fluorescence in situ hybridization to localize 18S and 5S rDNA. Gene sequencing of 18S rDNA, the internal transcribed spacers (ITS) with intervening 5.8S rDNA, and a low-copy nuclear gene, GBSSI-1, was undertaken to determine if gene loss occurred in the New Zealand lineage following polyploidy. KEY RESULTS The chromosome number for all species investigated was 2n = 42, with the first published report for the monotypic Australian genus Asterotrichion. The five species investigated all had two 5S rDNA signals localized interstitially on the long arm of one of the largest chromosome pairs. All species, except Plagianthus regius, had two 18S rDNA signals localized proximally on the short arm of one of the smallest chromosome pairs. Plagianthus regius had two additional 18S rDNA signals on a separate chromosome, giving a total of four. Sequencing of nuclear ribosomal 18S rDNA and the ITS cistron indicated loss of historical ribosomal repeats. Phylogenetic analysis of a low-copy nuclear gene, GBSSI-1, indicated that some lineages maintained three copies of the locus, while others have lost one or two copies. CONCLUSIONS Although island endemic lineages show chromosomal stasis, with no additional changes in chromosome number, they may undergo smaller-scale processes of gene loss and concerted evolution ultimately leading to further genome restructuring and downsizing.
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Affiliation(s)
- Prashant Joshi
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Helal Ansari
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Rowan Dickson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Cynthia Skema
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Morris Arboretum of the University of Pennsylvania, Philadelphia, PA, USA
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7
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Kuhl H, Du K, Schartl M, Kalous L, Stöck M, Lamatsch DK. Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp. Nat Commun 2022; 13:4092. [PMID: 35835759 PMCID: PMC9283417 DOI: 10.1038/s41467-022-31515-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/21/2022] [Indexed: 11/08/2022] Open
Abstract
Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries-IGB (Forschungsverbund Berlin), Müggelseedamm 301, D-12587, Berlin, Germany
| | - Kang Du
- University of Würzburg, Developmental Biochemistry, Biocenter, D-97074, Würzburg, Germany
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, 78666, USA
| | - Manfred Schartl
- University of Würzburg, Developmental Biochemistry, Biocenter, D-97074, Würzburg, Germany
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, 78666, USA
| | - Lukáš Kalous
- Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries-IGB (Forschungsverbund Berlin), Müggelseedamm 301, D-12587, Berlin, Germany.
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan.
| | - Dunja K Lamatsch
- Research Department for Limnology, Mondsee, University of Innsbruck, A-5310, Mondsee, Austria.
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He J, Zhao Y, Zhang S, He Y, Jiang J, Chen S, Fang W, Guan Z, Liao Y, Wang Z, Chen F, Wang H. Uneven Levels of 5S and 45S rDNA Site Number and Loci Variations across Wild Chrysanthemum Accessions. Genes (Basel) 2022; 13:894. [PMID: 35627279 PMCID: PMC9141308 DOI: 10.3390/genes13050894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/30/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
Ribosomal DNA (rDNA) is an excellent cytogenetic marker owing to its tandem arrangement and high copy numbers. However, comparative studies have focused more on the number of rDNA site variations within the Chrysanthemum genus, and studies on the types of rDNA sites with the same experimental procedures at the species levels are lacking. To further explore the number and types of rDNA site variations, we combined related data to draw ideograms of the rDNA sites of Chrysanthemum accessions using oligonucleotide fluorescence in situ hybridization (Oligo-FISH). Latent variations (such as polymorphisms of 45S rDNA sites and co-localized 5S-45S rDNA) also occurred among the investigated accessions. Meanwhile, a significant correlation was observed between the number of 5S rDNA sites and chromosome number. Additionally, the clumped and concentrated geographical distribution of different ploidy Chrysanthemum accessions may significantly promote the karyotype evolution. Based on the results above, we identified the formation mechanism of rDNA variations. Furthermore, these findings may provide a reliable method to examine the sites and number of rDNA variations among Chrysanthemum and its related accessions and allow researchers to further understand the evolutionary and phylogenetic relationships of the Chrysanthemum genus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (J.H.); (Y.Z.); (S.Z.); (Y.H.); (J.J.); (S.C.); (W.F.); (Z.G.); (Y.L.); (Z.W.); (F.C.)
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9
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Zhao C, Zhang Y, Qin H, Wang C, Huang X, Yang L, Yu T, Xu X, Luo X, Qin Q, Liu S. Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus. BMC Ecol Evol 2021; 21:201. [PMID: 34740327 PMCID: PMC8569995 DOI: 10.1186/s12862-021-01918-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Background Autotetraploid Carassius auratus (4n = 200, RRRR) (abbreviated as 4nRR) is derived from whole genome duplication of Carassius auratus red var. (2n = 100, RR) (abbreviated as RCC). Ribosome DNA (rDNA) is often used to study molecular evolution of repeated sequences because it has high copy number and special conserved coding regions in genomes. In this study, we analysed the sequences (5S, ITS1-5.8S-ITS2 region), structure, methylation level (NTS and IGS), and expression level (5S and 18S) of 5S and 45S ribosomal RNA (rRNA) genes in 4nRR and RCC in order to elucidate the effects of autotetraploidization on rDNA in fish. Results Results showed that there was high sequence similarity of 5S, 5.8S and ITS1 region between 4nRR and RCC. This study also identified two different types of ITS2 region in 4nRR and predicted the secondary structure of ITS2. It turns out that both secondary structures are functional. Compared with RCC, there was no significant difference in NTS (5S rRNA) methylation level, but the expression level of 5S rRNA was lower in 4nRR, indicating that methylation had little effect on the expression level in 4nRR. IGS (45S rRNA) was hypermethylated in 4nRR compared to RCC, but the expression of 18S rRNA gene was no significantly different from that in RCC, indicating that methylation regulation affected gene expression in 4nRR. Conclusion The above studies initially revealed the effects of autotetraploidization on the structure and function of 5S and 45S rRNA in Carassius auratus, and provided a theoretical support for the systematic study of the evolution pattern and characteristics of rDNA in vertebrates.
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Affiliation(s)
- Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yuxin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xidan Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xiang Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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10
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Vázquez ML. Molecular evolution of the internal transcribed spacers in red oaks (Quercus sect. Lobatae). Comput Biol Chem 2019; 83:107117. [PMID: 31581032 DOI: 10.1016/j.compbiolchem.2019.107117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/09/2019] [Accepted: 08/26/2019] [Indexed: 10/26/2022]
Abstract
Previous studies of the Internal Transcribed Spacers of the nuclear ribosomal DNA (ITS) in sections Quercus (white oaks), Protobalanus (intermediate or golden cup oaks), Cerris (Cerris oaks), and Ilex (Ilex oaks) suggest that ITS regions undergo full concerted evolution in oaks; however, ITS evolution patterns in red oaks (section Lobatae) are unknown due to scant representation in published work. To determine whether full concerted evolution occurs in red oaks, the purpose of this study was to examine ITS sequences from 40 red oak species. The results show incomplete concerted evolution and the presence of three ITS ribotypes of lengths 505, 609, 601 bp, hereafter referred to as ITS-S (small), I ITS-M (medium), and ITS-L (large), respectively. Thirty species had only one ribotype (ITS-M), nine species had two ribotypes (different combinations of ITS-L, ITS-M, and ITS-S), and only one species had all three ribotypes. Furthermore, examination of these three ribotypes showed that only ITS-M is putatively functional and ITS-L and ITS-S are pseudogenes. Bayesian analysis strongly supported (100%) two pseudogenes clades but provided weak support for the monophyly of a putative functional clade (ITS-M); moreover, within the "functional" clade, species relationships were uncertain and, in most cases, sequences from the same species failed to group together. The results of the current study suggest that ITS may not be appropriate for phylogeny reconstruction of red oaks due to low levels of interspecific variation and incomplete concerted evolution.
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Affiliation(s)
- M Lucía Vázquez
- Biology Department, University of Illinois Springfield, One University Plaza, Springfield, IL, 62794-9243, USA.
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Nomaguchi T, Maeda Y, Yoshino T, Asahi T, Tirichine L, Bowler C, Tanaka T. Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris. BMC Genomics 2018; 19:330. [PMID: 29728068 PMCID: PMC5935921 DOI: 10.1186/s12864-018-4691-0] [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: 10/26/2017] [Accepted: 04/17/2018] [Indexed: 11/27/2022] Open
Abstract
Background Allopolyploidy is a genomic structure wherein two or more sets of chromosomes derived from divergent parental species coexist within an organism. It is a prevalent genomic configuration in plants, as an important source of genetic variation, and also frequently confers environmental adaptability and increased crop productivity. We previously reported the oleaginous marine diatom Fistulifera solaris JPCC DA0580 to be a promising host for biofuel production and that its genome is allopolyploid, which had never previously been reported in eukaryotic microalgae. However, the study of allopolyploidy in F. solaris was hindered by the difficulty in classifying the homoeologous genes based on their progenitor origins, owing to the shortage of diatom genomic references. Results In this study, the allopolyploid genome of F. solaris was tentatively classified into two pseudo-parental subgenomes using sequence analysis based on GC content and codon frequency in each homoeologous gene pair. This approach clearly separated the genome into two distinct fractions, subgenome Fso_h and Fso_l, which also showed the potency of codon usage analysis to differentiate the allopolyploid subgenome. Subsequent homoeolog expression bias analysis revealed that, although both subgenomes appear to contribute to global transcription, there were subgenomic preferences in approximately 61% of homoeologous gene pairs, and the majority of these genes showed continuous bias towards a specific subgenome during lipid accumulation. Additional promoter analysis indicated the possibility of promoter motifs involved in biased transcription of homoeologous genes. Among these subgenomic preferences, genes involved in lipid metabolic pathways showed interesting patterns in that biosynthetic and degradative pathways showed opposite subgenomic preferences, suggesting the possibility that the oleaginous characteristics of F. solaris derived from one of its progenitors. Conclusions We report the detailed genomic structure and expression patterns in the allopolyploid eukaryotic microalga F. solaris. The allele-specific patterns reported may contribute to the oleaginous characteristics of F. solaris and also suggest the robust oleaginous characteristics of one of its progenitors. Our data reveal novel aspects of allopolyploidy in a diatom that is not only important for evolutionary studies but may also be advantageous for biofuel production in microalgae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4691-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tatsuhiro Nomaguchi
- Department of Advanced Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Toru Asahi
- Department of Advanced Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Leila Tirichine
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Ding M, Chen ZJ. Epigenetic perspectives on the evolution and domestication of polyploid plant and crops. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:37-48. [PMID: 29502038 PMCID: PMC6058195 DOI: 10.1016/j.pbi.2018.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 05/19/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.
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Affiliation(s)
- Mingquan Ding
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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Wang T, Huang D, Chen B, Mao N, Qiao Y, Ji M. Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp. Genes Genomics 2018; 40:321-331. [DOI: 10.1007/s13258-018-0647-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/04/2018] [Indexed: 12/26/2022]
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14
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Novikova PY, Tsuchimatsu T, Simon S, Nizhynska V, Voronin V, Burns R, Fedorenko OM, Holm S, Säll T, Prat E, Marande W, Castric V, Nordborg M. Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica. Mol Biol Evol 2017; 34:957-968. [PMID: 28087777 PMCID: PMC5400380 DOI: 10.1093/molbev/msw299] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-of-function allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.
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Affiliation(s)
- Polina Yu Novikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.,Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | - Takashi Tsuchimatsu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Samson Simon
- Université de Lille CNRS, UMR 8198 - Evo-Eco-Paleo, Villeneuve d'Ascq, France
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Viktor Voronin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Robin Burns
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Olga M Fedorenko
- Institute of Biology, Karelian Research Center of the Russian Academy of Sciences, Republic of Karelia, Petrozavodsk, Russia
| | - Svante Holm
- Faculty of Science, Technology and Media, Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Torbjörn Säll
- Department of Biology, Lund University, Lund, Sweden
| | - Elisa Prat
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, Castanet-Tolosan, France
| | - William Marande
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, Castanet-Tolosan, France
| | - Vincent Castric
- Université de Lille CNRS, UMR 8198 - Evo-Eco-Paleo, Villeneuve d'Ascq, France
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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15
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Padmanaban S, Zhang P, Hare RA, Sutherland MW, Martin A. Pentaploid Wheat Hybrids: Applications, Characterisation, and Challenges. FRONTIERS IN PLANT SCIENCE 2017; 8:358. [PMID: 28367153 PMCID: PMC5355473 DOI: 10.3389/fpls.2017.00358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/01/2017] [Indexed: 05/09/2023]
Abstract
Interspecific hybridisation between hexaploid and tetraploid wheat species leads to the development of F1 pentaploid hybrids with unique chromosomal constitutions. Pentaploid hybrids derived from bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum spp. durum Desf.) crosses can improve the genetic background of either parent by transferring traits of interest. The genetic variability derived from bread and durum wheat and transferred into pentaploid hybrids has the potential to improve disease resistance, abiotic tolerance, and grain quality, and to enhance agronomic characters. Nonetheless, pentaploid wheat hybrids have not been fully exploited in breeding programs aimed at improving crops. There are several potential barriers for efficient pentaploid wheat production, such as low pollen compatibility, poor seed set, failed seedling establishment, and frequent sterility in F1 hybrids. However, most of the barriers can be overcome by careful selection of the parental genotypes and by employing the higher ploidy level genotype as the maternal parent. In this review, we summarize the current research on pentaploid wheat hybrids and analyze the advantages and pitfalls of current methods used to assess pentaploid-derived lines. Furthermore, we discuss current and potential applications in commercial breeding programs and future directions for research into pentaploid wheat.
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Affiliation(s)
- Sriram Padmanaban
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Peng Zhang
- Plant Breeding Institute, The University of Sydney, SydneyNSW, Australia
| | - Ray A. Hare
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Mark W. Sutherland
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
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Winterfeld G, Wölk A, Röser M. Genome evolution in alpine oat-like grasses through homoploid hybridization and polyploidy. AOB PLANTS 2016; 8:plw039. [PMID: 27255513 PMCID: PMC4940509 DOI: 10.1093/aobpla/plw039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 05/07/2016] [Indexed: 05/17/2023]
Abstract
Hybridization and polyploidization can radically impact genome organization from sequence level to chromosome structure. As a result, often in response to environmental change and species isolation, the development of novel traits can arise and will tend to result in the formation of homoploid or polyploid hybrid species. In this study we focus on evidence of hybridization and polyploidization by ascertaining the species parentage of the endemic alpine Helictotrichon parlatorei group. This group comprises five taxa; the diploids H. parlatorei, Helictotrichon setaceum subsp. setaceum and subsp. petzense, their putative hybrid Helictotrichon ×krischae and the hexaploid Helictotrichon sempervirens. For molecular analyses, cloned nuclear Topoisomerase VI genes of H. sempervirens and H. ×krischae were sequenced and compared with sequences of the diploids to estimate the evolutionary history in this group. In addition, detailed chromosome studies were carried out including fluorescence in situ hybridization (FISH) with 5S and 45S ribosomal and satellite DNA probes, and fluorochrome staining with chromomycin and DAPI. Two distinct types of Topoisomerase VI sequences were identified. One of them (SET) occurs in both subspecies of H. setaceum, the other (PAR) in H. parlatorei. Both types were found in H. ×krischae and H. sempervirens Karyotypes of H. parlatorei and H. setaceum could be distinguished by chromosomes with a clearly differentiated banding pattern of ribosomal DNAs. Both patterns occurred in the hybrid H. ×krischae Hexaploid H. sempervirens shares karyotype features with diploid H. parlatorei, but lacks the expected chromosome characteristics of H. setaceum, possibly an example of beginning diploidization after polyploidization. The geographic origin of the putative parental species and their hybrids and the possible biogeographical spread through the Alps are discussed.
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Affiliation(s)
- Grit Winterfeld
- Institute of Biology, Martin Luther University Halle-Wittenberg, Neuwerk 21, 06099 Halle, Germany
| | - Alexandra Wölk
- Institute of Biology, Martin Luther University Halle-Wittenberg, Neuwerk 21, 06099 Halle, Germany
| | - Martin Röser
- Institute of Biology, Martin Luther University Halle-Wittenberg, Neuwerk 21, 06099 Halle, Germany
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17
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Soltis DE, Misra BB, Shan S, Chen S, Soltis PS. Polyploidy and the proteome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:896-907. [PMID: 26993527 DOI: 10.1016/j.bbapap.2016.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 03/06/2016] [Accepted: 03/11/2016] [Indexed: 12/23/2022]
Abstract
Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.
| | - Biswapriya B Misra
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Shengchen Shan
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.
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18
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Nath S, Jha TB, Mallick SK, Jha S. Karyological relationships in Indian species of Drimia based on fluorescent chromosome banding and nuclear DNA amount. PROTOPLASMA 2015; 252:283-299. [PMID: 25052711 DOI: 10.1007/s00709-014-0679-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/08/2014] [Indexed: 06/03/2023]
Abstract
The genus Drimia (syn. Urginea), commonly called squill, represents a species complex, infrageneric delimitation being ill-defined due to morphological variability, population variation within species and polyploidy. In the present study, fluorescent chromosome banding and measurements of nuclear DNA content by flow cytometry were performed in five Indian species of Drimia: Drimia indica, Drimia polyantha, Drimia razii, Drimia wightii and Drimia coromandeliana to elucidate taxonomic relationship and obtain possible insights into the evolutionary processes within this group. All taxa analyzed exhibited similar karyomorphology with subtle differences accounted by nucleolar chromosomes. Nuclear DNA content ranged from 20.41 pg/2C in D. polyantha to 40.80 pg/2C in D. coromandeliana and was positively correlated with chromosome number (r = 0.67, P = 0.02) and total diploid chromatin length (r = 0.59, P = 0.06). Fluorescent chromosome banding revealed the presence of CMA(+ve)/DAPI(-ve) signals associated with nucleolar chromosomes presumably coincident with NOR in all species and unique CMA(+ve) signals in diploid populations of D. indica. Satellite polymorphism between homologous NOR-bearing chromosomes was observed which supports hybrid origin of the taxon. UPGMA dendrogram and scatter diagrams based on karyological parameters indicated a close relationship of D. indica, D. razii and D. polyantha while D. wightii and D. coromandeliana appeared distant. D. wightii appeared more close to D. indica than to all other species based on genome size and karyomorphology. As a whole, D. indica showed high intra-specific variability with populations exhibiting intergrading characters with other species. In conclusion, it is likely that hybridization followed by reproductive isolation of polymorphic forms arising by adaptation to different ecological niches resulted in species diversification of Drimia in India, probably from a common ancestor similar to D. indica.
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Affiliation(s)
- Sayantani Nath
- Centre of Advanced study, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700 019, West Bengal, India
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Methylation-sensitive amplified polymorphism (MSAP) marker to investigate drought-stress response in Montepulciano and Sangiovese grape cultivars. Methods Mol Biol 2014. [PMID: 24478013 DOI: 10.1007/978-1-62703-773-0_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Methylation-sensitive amplified polymorphism (MSAP) is a technique developed for assessing the extent and pattern of cytosine methylation and has been applied to genomes of several species (Arabidopsis, grape, maize, tomato, and pepper). The technique relies on the use of isoschizomers that differ in their sensitivity to methylation.
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Kitanova M, Georgiev S. Transcriptional Activity of Translocated NORs in Barley (Hordeum Vulgare L.). BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Meglena Kitanova
- Sofia University “St. Kliment Ohridski”, Faculty of Biology, Sofia, Bulgaria
| | - Sevdalin Georgiev
- Sofia University “St. Kliment Ohridski”, Faculty of Biology, Sofia, Bulgaria
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Jung Y, Kawaura K, Mishina K, Sakuma S, Kishii M, Ogihara Y. Changes in genome-wide gene expression during allopolyploidization and genome stabilization in hexaploid wheat. Genes Genet Syst 2014; 89:215-25. [PMID: 25832748 DOI: 10.1266/ggs.89.215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Allopolyploidization is an important evolutionary event in plants, but its genome-wide effects are not fully understood. Common wheat, Triticum aestivum (AABBDD), evolved through amphidiploidization between T. turgidum (AABB) and Aegilops tauschii (DD). Here, global gene expression patterns in the seedlings of a synthetic triploid wheat line (ABD), its chromosome-doubled hexaploid (AABBDD) and stable synthetic hexaploid (AABBDD), and the parental lines T. turgidum (AABB) and Ae. tauschii (DD) were compared using an oligo-DNA microarray to identify metabolic pathways affected by the genome conflict that occurs during allopolyploidization and genome stabilization. Characteristic gene expression patterns of non-additively expressed genes were detected in the newly synthesized triploid and hexaploid, and in the stable synthetic hexaploid. Hierarchical clustering of all differentially expressed and non-additively expressed genes revealed that the gene expression patterns of the triploid (ABD) were similar to those of the maternal parent (AABB), and that expression patterns in successive generations arising from self-pollination became closer to that of the pollen parent (DD). The non-additive gene expression profiles markedly differed between the triploid (ABD) and chromosome-doubled hexaploid (AABBDD), as supported by Gene Ontology (GOSlim) analysis. Four hundred and nineteen non-additively expressed genes were commonly detected in all three generations. GOSlim analysis indicated that these non-additively expressed genes were predominantly involved in "biological pathways". Notably, four of 11 genes related to sugar metabolism displayed elevated expression throughout allopolyploidization. These may be useful candidates for promoting heterosis and adaptation in plants.
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Affiliation(s)
- Yeonju Jung
- Kihara Institute for Biological Research and Department of Life and Environmental System Science, Yokohama City University
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Pizzaia D, Oliveira VM, Martins AR, Appezzato-da-Glória B, Forni-Martins E, Aguiar-Perecin MLR. Karyotype characterization reveals active 45S rDNA sites located on chromosome termini in Smilax rufescens (Smilacaceae). GENETICS AND MOLECULAR RESEARCH 2013; 12:1303-10. [PMID: 23661453 DOI: 10.4238/2013.april.25.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The genus Smilax (Smilacaceae) includes species of medicinal interest; consequently, their identification is important for the control of raw material used in the manufacture of phytotherapeutic products. We investigated the karyotype of Smilax rufescens in order to look for patterns that would be useful for comparative studies of this genus. To accomplish this, we developed procedures to grow plants and optimize root pretreatment with mitotic fuse inhibitors to obtain metaphase spreads showing clear chromosome morphology. The karyotype, analyzed in Feulgen-stained preparations, was asymmetric, with N = 16 chromosomes gradually decreasing in size; the larger ones were subtelocentric and the smaller chromosomes were submetacentric or metacentric. Nearly terminal secondary constrictions were visualized on the short arm of chromosome pairs 7, 11, and 14, but they were clearly detected only in one of the homologues of each pair. The nucleolus organizer regions (NORs) were mapped by silver staining and fluorescent in situ hybridization of 45S rDNA probes. Silver signals (Ag-NORs) colocalized with rDNA loci were detected at the termini of the short arm of 6 chromosomes. The secondary constriction heteromorphism observed in Feulgen-stained metaphases suggests that differential rRNA gene expression between homologous rDNA loci can occur, resulting in different degrees of chromatin decondensation. In addition, a heteromorphic chromosome pair was identified and was interpreted as being a sex chromosome pair in this dioecious species.
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Affiliation(s)
- D Pizzaia
- Departamento de Genética, ESALQ, Universidade de São Paulo, Piracicaba, SP, Brasil
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Xiao Z, Wang C, Mo D, Li J, Chen Y, Zhang Z, Cong P. Promoter CpG methylation status in porcine Lyn is associated with its expression levels. Gene 2012; 511:73-8. [PMID: 23000019 DOI: 10.1016/j.gene.2012.08.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 08/07/2012] [Accepted: 08/28/2012] [Indexed: 11/26/2022]
Abstract
Resistance to disease and improvement of product quality are important goals in pig farming. Tyrosine Protein Kinase Lyn (LYN) is one of several Src-family tyrosine kinases in immune cells. This protein functions both as a positive and negative regulator of B cell activation, and regulates signaling pathways through phosphorylation of inhibitory receptors, enzymes and adaptors, which suggested that LYN could be correlated with immunity and can be considered as a candidate gene to study in disease resistance. Until now, the profiles of expression and transcriptional regulation of the LYN gene in pig breeds different in immune capacity remain unclear. Using real-time PCR, it indicated that porcine LYN mRNA expressed mainly in immune organs including the spleen, duodenum and liver. Furthermore, Dahuabai pigs (a kind of Chinese indigenous pig breeds with higher immune capacity) showed significant higher LYN mRNA expression levels than that in Landrace. Methylation analysis indicates that LYN expression levels were associated with the methylation status of the LYN promoter, and methylation of the novel CpG site at -1268C/-1267G generated by transposition at -1267 (A→G) results in up-regulating transcriptional activity of this gene. Interestingly, the base A located in -1267 mainly exhibited in landrace while the base G mainly in Dahuabai pigs. These results might contribute to study the function of this gene in pig breeding for disease resistance.
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Affiliation(s)
- Zhengzhong Xiao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
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Kalinka A, Achrem M, Rogalska SM. Cytomixis-like chromosomes/chromatin elimination from pollen mother cells (PMCs) in wheat-rye allopolyploids. THE NUCLEUS 2010. [DOI: 10.1007/s13237-010-0002-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Hegarty MJ, Batstone T, Barker GL, Edwards KJ, Abbott RJ, Hiscock SJ. Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae). Mol Ecol 2010; 20:105-13. [PMID: 21073590 DOI: 10.1111/j.1365-294x.2010.04926.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The merger of two or more divergent genomes within an allopolyploid nucleus can facilitate speciation and adaptive evolution in flowering plants. Widespread changes to gene expression have been shown to result from interspecific hybridisation and polyploidy in a number of plant species, and attention has now shifted to determining the epigenetic processes that drive these changes. We present here an analysis of cytosine methylation patterns in triploid F(1) Senecio (ragwort) hybrids and their allohexaploid derivatives. We observe that, in common with similar studies in Arabidopsis, Spartina and Triticum, a small but significant proportion of loci display nonadditive methylation in the hybrids, largely resulting from interspecific hybridisation. Despite this, genome duplication results in a secondary effect on methylation, with reversion to additivity at some loci and novel methylation status at others. We also observe differences in methylation state between different allopolyploid generations, predominantly in cases of additive methylation with regard to which parental methylation state is dominant. These changes to methylation state in both F(1) triploids and their allohexaploid derivatives largely mirror the overall patterns of nonadditive gene expression observed in our previous microarray analyses and may play a causative role in generating those expression changes. These similar global changes to DNA methylation resulting from hybridisation and genome duplication may serve as a source of epigenetic variation in natural populations, facilitating adaptive evolution. Our observations that methylation state can also vary between different generations of polyploid hybrids suggests that newly formed allopolyploid species may display a high degree of epigenetic diversity upon which natural selection can act.
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Affiliation(s)
- Matthew J Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK.
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Bártová E, Horáková AH, Uhlírová R, Raska I, Galiová G, Orlova D, Kozubek S. Structure and epigenetics of nucleoli in comparison with non-nucleolar compartments. J Histochem Cytochem 2009; 58:391-403. [PMID: 20026667 DOI: 10.1369/jhc.2009.955435] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The nucleolus is a nuclear compartment that plays an important role in ribosome biogenesis. Some structural features and epigenetic patterns are shared between nucleolar and non-nucleolar compartments. For example, the location of transcriptionally active mRNA on extended chromatin loop species is similar to that observed for transcriptionally active ribosomal DNA (rDNA) genes on so-called Christmas tree branches. Similarly, nucleolus organizer region-bearing chromosomes located a distance from the nucleolus extend chromatin fibers into the nucleolar compartment. Specific epigenetic events, such as histone acetylation and methylation and DNA methylation, also regulate transcription of both rRNA- and mRNA-encoding loci. Here, we review the epigenetic mechanisms and structural features that regulate transcription of ribosomal and mRNA genes. We focus on similarities in epigenetic and structural regulation of chromatin in nucleoli and the surrounding non-nucleolar region and discuss the role of proteins, such as heterochromatin protein 1, fibrillarin, nucleolin, and upstream binding factor, in rRNA synthesis and processing.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i. Královopolská 135, CZ-612 65, Brno, Czech Republic.
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Bassene JB, Froelicher Y, Dubois C, Ferrer RM, Navarro L, Ollitrault P, Ancillo G. Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm. Heredity (Edinb) 2009; 105:299-308. [PMID: 19953121 DOI: 10.1038/hdy.2009.162] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Polyploid plants often produce new phenotypes, exceeding the range of variability existing in the diploid gene pool. Several hundred citrus allotetraploid hybrids have been created by somatic hybridization. These genotypes are interesting models to study the immediate effects of allopolyploidization on the regulation of gene expression. Here, we report genome-wide gene expression analysis in fruit pulp of a Citrus interspecific somatic allotetraploid between C. reticulata cv 'Willowleaf mandarin'+C. limon cv 'Eureka lemon', using a Citrus 20K cDNA microarray. Around 4% transcriptome divergence was observed between the two parental species, and 212 and 160 genes were more highly expressed in C. reticulata and C. limon, respectively. Differential expression of certain genes was confirmed by quantitative real-time RT-PCR. A global downregulation of the allotetraploid hybrid transcriptome was observed, as compared with a theoretical mid parent, for the genes displaying interspecific expression divergence between C. reticulata and C. limon. The genes underexpressed in mandarin, as compared with lemon, were also systematically repressed in the allotetraploid. When genes were overexpressed in C. reticulata compared with C. limon, the distribution of allotetraploid gene expression was far more balanced. Cluster analysis on the basis of gene expression clearly indicated the hybrid was much closer to C. reticulata than to C. limon. These results suggest there is a global dominance of the mandarin transcriptome, in consistence with our previous studies on aromatic compounds and proteomics. Interspecific differentiation of gene expression and non-additive gene regulation involved various biological pathways and different cellular components.
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Affiliation(s)
- J B Bassene
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UPR amélioration génétique des espèces à multiplication végétative, Montpellier, France
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31
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Allopolyploid origin of Mediterranean species inHelictotrichon(Poaceae) and its consequences for karyotype repatterning and homogenisation of rDNA repeat units. SYST BIODIVERS 2009. [DOI: 10.1017/s1477200009003041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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Chromosome banding and essential oils composition of Brazilian accessions of Lippia alba (Verbenaceae). Biologia (Bratisl) 2009. [DOI: 10.2478/s11756-009-0066-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Blevins T, Pontes O, Pikaard CS, Meins F. Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis. PLoS One 2009; 4:e5932. [PMID: 19529764 PMCID: PMC2691480 DOI: 10.1371/journal.pone.0005932] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 05/11/2009] [Indexed: 12/22/2022] Open
Abstract
5S ribosomal RNA gene repeats are arranged in heterochromatic arrays (5S rDNA) situated near the centromeres of Arabidopsis chromosomes. The chromatin remodeling factor DDM1 is known to maintain 5S rDNA methylation patterns while silencing transcription through 5S rDNA intergenic spacers (IGS). We mapped small-interfering RNAs (siRNA) to a composite 5S rDNA repeat, revealing a high density of siRNAs matching silenced IGS transcripts. IGS transcript repression requires proteins of the heterochromatic siRNA pathway, including RNA polymerase IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). Using molecular and cytogenetic approaches, we show that the DDM1 and siRNA-dependent silencing effects are genetically independent. DDM1 suppresses production of the siRNAs, however, thereby limiting RNA-directed DNA methylation at 5S rDNA repeats. We conclude that DDM1 and siRNA-dependent silencing are overlapping processes that both repress aberrant 5S rDNA transcription and contribute to the heterochromatic state of 5S rDNA arrays.
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MESH Headings
- Arabidopsis/metabolism
- Arabidopsis Proteins/metabolism
- Chromatin/chemistry
- Computational Biology/methods
- Crosses, Genetic
- DNA, Intergenic
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/metabolism
- Gene Silencing
- Genes, Plant
- In Situ Hybridization, Fluorescence
- Models, Biological
- RNA, Ribosomal, 5S/metabolism
- RNA, Small Interfering/metabolism
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Todd Blevins
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Olga Pontes
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Craig S. Pikaard
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Frederick Meins
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- * E-mail:
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34
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Chromatin: linking structure and function in the nucleolus. Chromosoma 2008; 118:11-23. [PMID: 18925405 DOI: 10.1007/s00412-008-0184-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 09/17/2008] [Accepted: 09/18/2008] [Indexed: 01/07/2023]
Abstract
The nucleolus is an informative model structure for studying how chromatin-regulated transcription relates to nuclear organisation. In this review, we describe how chromatin controls nucleolar structure through both the modulation of rDNA activity by convergently-evolved remodelling complexes and by direct effects upon rDNA packaging. This packaging not only regulates transcription but may also be important for suppressing internal recombination between tandem rDNA repeats. The identification of nucleolar histone chaperones and novel chromatin proteins by mass spectrometry suggests that structure-specific chromatin components remain to be characterised and may regulate the nucleolus in novel ways. However, it also suggests that there is considerable overlap between nucleolar and non-nucleolar-chromatin components. We conclude that a fuller understanding of nucleolar chromatin will be essential for understanding how gene organisation is linked with nuclear architecture.
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35
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Zhao Y, Yu S, Xing C, Fan S, Song M. Analysis of DNA methylation in cotton hybrids and their parents. Mol Biol 2008. [DOI: 10.1134/s0026893308020015] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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37
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Wu Y, Zhu Z, Ma L, Chen M. The preferential retention of starch synthesis genes reveals the impact of whole-genome duplication on grass evolution. Mol Biol Evol 2008; 25:1003-6. [PMID: 18296698 DOI: 10.1093/molbev/msn052] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Gene duplication is a major force in evolution. Here, we analyzed the fate of duplicated genes following the ancient whole-genome duplication (WGD) in rice. Polyploidy-derived duplicated genes were found to be preferentially lost from one of each pair of duplicated chromosomal segments, suggesting that the asymmetric gene loss may result from transcriptome dominance of the ancestral allotetraploid genome. Genes involved in synthesis and catabolism of saccharides were found to be preferentially retained in rice, reflecting different trajectories of duplicated genes formed by polyploidy between rice and Arabidopsis. Further studies demonstrated all 3 catalyzing steps in the starch biosynthesis pathway have polyploidy-derived duplicated genes and one copy in each step forms a dominant pathway in the grain filling-stage rice. The new starch biosynthesis pathway reflects one aspect of the impact of WGD on grass evolution.
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38
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Ansari HA, Ellison NW, Williams WM. Molecular and cytogenetic evidence for an allotetraploid origin of Trifolium dubium (Leguminosae). Chromosoma 2007; 117:159-67. [PMID: 18058119 DOI: 10.1007/s00412-007-0134-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 10/18/2007] [Accepted: 10/23/2007] [Indexed: 11/28/2022]
Abstract
Suckling clover, Trifolium dubium Sibth., is a European grassland legume that has spread to many parts of the world. The present work shows that it is an allotetraploid (2n = 4x = 30) combining the genomes of T. campestre Schreb. (2n = 2x = 14) and T. micranthum Viv. (2n = 2x = 16), two diploid species of similar geographic distribution. T. dubium has two nuclear ITS sequences that closely match those of T. campestre and T. micranthum. Genomic in situ hybridisation using genomic DNA of T. campestre and T. micranthum as probes has differentiated the ancestral sets of chromosomes in T. dubium cells. Comparative fluorescence in situ hybridisation analyses of 5S and 18S-26S rDNA loci were also consistent with an allotetraploid structure of the T. dubium genome. A marked preponderance of ITS repeats from T. campestre over those from T. micranthum indicated that concerted evolution has resulted in partial homogenisation of these sequences by depletion of the T. micranthum-derived 18S-26S rDNA repeats. In parallel with this, the epigenetic phenomenon of nucleolar dominance has been observed in T. dubium such that the chromatin associated with the 18S-26S rDNA loci derived from T. campestre is decondensed (transcriptionally active), whilst that from T. micranthum remains highly condensed throughout the cell cycle. T. dubium, therefore, appears to have arisen by way of hybridisation between forms of the diploid species T. campestre and T. micranthum accompanied by chromosome doubling. The observed genomic changes in rDNA resulting from interspecific hybridisation provide evidence for the process of genome diploidisation in T. dubium.
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Affiliation(s)
- Helal A Ansari
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand.
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39
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de Freitas DV, Carvalho CR, Filho FJDN, Astolfi-Filho S. Karyotype with 210 chromosomes in guaraná (Paullinia cupana 'Sorbilis'). JOURNAL OF PLANT RESEARCH 2007; 120:399-404. [PMID: 17387431 DOI: 10.1007/s10265-007-0073-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Accepted: 12/30/2006] [Indexed: 05/14/2023]
Abstract
The genus Paullinia includes the economically important P. cupana, known as guaraná in Brazil and more recently in the world market. Native Americans of the Maué and Andirá tribes cultivated P. cupana 'Sorbilis' in central Amazon, and the Barés cultivated the 'Typica' variety in the upper Negro River (Brazil). Cytological studies in the Sapindaceae family have concentrated on the diversity in number (from 2n = 14 to 96) and size of the chromosomes. In Paullinia, seven species have been karyotyped and all show 2n = 24. Meristem maceration, cellular dissociation and air-drying techniques were used for cytogenetic preparations and DNA content was determined by flow cytometry. Chromosome characterization and DNA content of Paullinia cupana Kunth 'Sorbilis' (Mart.) Ducke (Sapindaceae) were studied. The high chromosome number (2n = 210) fall into two cytomorphological groups: (a) a metacentric and submetacentric group showing 25 sets of three pairs of chromosomes (2-76); (b) a group containing only acrocentric showing 12 sets of two pairs of chromosomes (82-105), a homologous submetacentric pair (1) and an acrocentric pair (81). Mean nuclear DNA content of guaraná was 2C = 22.8 pg. A karyogram was set up showing a high chromosome number complement.
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Affiliation(s)
- Danival Vieira de Freitas
- Instituto de Ciências Biológicas, Laboratório de Tecnologia de DNA, Universidade Federal do Amazonas, Manaus, AM, Brazil.
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40
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Li X, Cong Y, Yang G, Shi Y, Qu S, Li Z, Wang G, Zhang Z, Luo S, Dai H, Xie J, Jiang G, Liu J, Wang T. Trait evaluation and trial cultivation of Dongfang No. 2, the hybrid of a male gametophyte clone of Laminaria longissima (Laminariales, Phaeophyta) and a female one of L. japonica. JOURNAL OF APPLIED PHYCOLOGY 2007; 19:139-151. [PMID: 19396352 PMCID: PMC2668635 DOI: 10.1007/s10811-006-9120-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 07/09/2006] [Indexed: 05/07/2023]
Abstract
Direct cultivation of the first filial generation of gametophyte clones from different Laminaria species is a highly effective way of utilizing kelp heterozygous vigor (heterosis). A male gametophyte clone of L. longissima Miyabe and a female one of L. japonica Areschoug were hybridized, generating Dongfang No. 2 hybrid kelp. This hybrid kelp was used directly in trial cultivation, and its agronomical traits were evaluated. L. longissima and L. japonica are obviously different and complement each other in their morphological characteristics and ecological performances. The hybrid of their gametophyte clones, Dongfang No. 2, showed 56.8% heterozygous vigor in yield. It also showed increased yields of 41.0 and 76.4% compared to the widely used commercial kelps Variety 1 and Variety 2, respectively. In large-scale cultivation trials at different locations and in different years, Dongfang No. 2 attained significantly higher yields than Varieties 1 and 2, increasing yield by 26.4% on average over Variety 1 and by 65.0% over the other. Dongfang No. 2 has a robust holdfast and a wide, long and deep-brown uniform blade, which shows a distinct middle groove. In addition to yield, Dongfang No. 2 also demonstrates obvious heterozygous vigor in other agronomic traits. It is resistant to strong irradiance, as the two commercial varieties are, has an appropriate vegetative maturation time, and adapts well to a range of different culture conditions. The parentage analysis using AFLP of total DNA and SNP of the ITS region of ribosomal RNA transcription unit showed that Dongfang No. 2 is the real hybrid of L. japonica and L. longissima.
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Affiliation(s)
- Xiaojie Li
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
- College of Marine Life Science, Ocean University of China, 5 Yushanlu Road, Qingdao, Shandong 266003 People’s Republic of China
| | - Yizhou Cong
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Guanpin Yang
- College of Marine Life Science, Ocean University of China, 5 Yushanlu Road, Qingdao, Shandong 266003 People’s Republic of China
| | - Yuanyuan Shi
- College of Marine Life Science, Ocean University of China, 5 Yushanlu Road, Qingdao, Shandong 266003 People’s Republic of China
| | - Shancun Qu
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Zhiling Li
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Guowen Wang
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Zhuangzhi Zhang
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Shiju Luo
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Hongliang Dai
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Jianzu Xie
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Guangliang Jiang
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Jialiang Liu
- Shandong Oriental Ocean Sci-tec Co., Ltd., Yantai, Shandong 264003 People’s Republic of China
| | - Tongyong Wang
- Wendeng Fishery Technique Popularization Station of Shandong Province, Wendeng, Shandong 264400 People’s Republic of China
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41
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Mondin M, Santos-Serejo JA, Aguiar-Perecin ML. Karyotype characterization of Crotalaria juncea (L.) by chromosome banding and physical mapping of 18S-5.8S-26S and 5S rRNA gene sites. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000100013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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42
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Chen ZJ. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. ANNUAL REVIEW OF PLANT BIOLOGY 2007; 58:377-406. [PMID: 17280525 PMCID: PMC1949485 DOI: 10.1146/annurev.arplant.58.032806.103835] [Citation(s) in RCA: 590] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Polyploidy, or whole-genome duplication (WGD), is an important genomic feature for all eukaryotes, especially many plants and some animals. The common occurrence of polyploidy suggests an evolutionary advantage of having multiple sets of genetic material for adaptive evolution. However, increased gene and genome dosages in autopolyploids (duplications of a single genome) and allopolyploids (combinations of two or more divergent genomes) often cause genome instabilities, chromosome imbalances, regulatory incompatibilities, and reproductive failures. Therefore, new allopolyploids must establish a compatible relationship between alien cytoplasm and nuclei and between two divergent genomes, leading to rapid changes in genome structure, gene expression, and developmental traits such as fertility, inbreeding, apomixis, flowering time, and hybrid vigor. Although the underlying mechanisms for these changes are poorly understood, some themes are emerging. There is compelling evidence that changes in DNA sequence, cis- and trans-acting effects, chromatin modifications, RNA-mediated pathways, and regulatory networks modulate differential expression of homoeologous genes and phenotypic variation that may facilitate adaptive evolution in polyploid plants and domestication in crops.
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Affiliation(s)
- Z Jeffrey Chen
- Department of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
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43
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Keyte AL, Percifield R, Liu B, Wendel JF. Infraspecific DNA Methylation Polymorphism in Cotton (Gossypium hirsutum L.). J Hered 2006; 97:444-50. [PMID: 16987937 DOI: 10.1093/jhered/esl023] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cytosine methylation is important in the epigenetic regulation of gene expression and development in plants and has been implicated in silencing duplicate genes after polyploid formation in several plant groups. Relatively little information exists, however, on levels and patterns of methylation polymorphism (MP) at homologous loci within species. Here we explored the levels and patterns of methylation-polymorphism diversity at CCGG sites within allotetraploid cotton, Gossypium hirsutum, using a methylation-sensitive amplified fragment length polymorphism screen and a selected set of 20 G. hirsutum accessions for which we have information on genetic polymorphism levels and relationships. Methylation and MP exist at high levels within G. hirsutum: of 150 HpaII/MspI sites surveyed, 48 were methylated at the inner cytosine (32%) and 32 of these were polymorphic (67%). Both these values are higher than comparable measures of genetic diversity using restriction fragment length polymorphisms. The high percentage of methylation-polymorphic sites and potential relationship to gene expression underscore the potential significance of MP within and among populations. We speculate that biased correlation of methylation-polymorphic sites and genes in cotton may be a consequence of polyploidy and the attendant doubling of all genes.
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Affiliation(s)
- Anna L Keyte
- Department of Biology, Duke University, Durham, NC 27710, USA
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44
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Wang J, Tian L, Lee HS, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Chen ZJ. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 2006; 172:507-17. [PMID: 16172500 PMCID: PMC1456178 DOI: 10.1534/genetics.105.047894] [Citation(s) in RCA: 390] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 09/19/2005] [Indexed: 12/21/2022] Open
Abstract
Polyploidy has occurred throughout the evolutionary history of all eukaryotes and is extremely common in plants. Reunification of the evolutionarily divergent genomes in allopolyploids creates regulatory incompatibilities that must be reconciled. Here we report genomewide gene expression analysis of Arabidopsis synthetic allotetraploids, using spotted 70-mer oligo-gene microarrays. We detected >15% transcriptome divergence between the progenitors, and 2105 and 1818 genes were highly expressed in Arabidopsis thaliana and A. arenosa, respectively. Approximately 5.2% (1362) and 5.6% (1469) genes displayed expression divergence from the midparent value (MPV) in two independently derived synthetic allotetraploids, suggesting nonadditive gene regulation following interspecific hybridization. Remarkably, the majority of nonadditively expressed genes in the allotetraploids also display expression changes between the parents, indicating that transcriptome divergence is reconciled during allopolyploid formation. Moreover, >65% of the nonadditively expressed genes in the allotetraploids are repressed, and >94% of the repressed genes in the allotetraploids match the genes that are expressed at higher levels in A. thaliana than in A. arenosa, consistent with the silencing of A. thaliana rRNA genes subjected to nucleolar dominance and with overall suppression of the A. thaliana phenotype in the synthetic allotetraploids and natural A. suecica. The nonadditive gene regulation is involved in various biological pathways, and the changes in gene expression are developmentally regulated. In contrast to the small effects of genome doubling on gene regulation in autotetraploids, the combination of two divergent genomes in allotetraploids by interspecific hybridization induces genomewide nonadditive gene regulation, providing a molecular basis for de novo variation and allopolyploid evolution.
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Affiliation(s)
- Jianlin Wang
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706, USA
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GRANT-DOWNTON RT, DICKINSON HG. Epigenetics and its implications for plant biology. 1. The epigenetic network in plants. ANNALS OF BOTANY 2005; 96:1143-64. [PMID: 16254022 PMCID: PMC4247072 DOI: 10.1093/aob/mci273] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND Epigenetics has rapidly evolved in the past decade to form an exciting new branch of biology. In modern terms, 'epigenetics' studies molecular pathways regulating how the genes are packaged in the chromosome and expressed, with effects that are heritable between cell divisions and even across generations. CONTEXT Epigenetic mechanisms often conflict with Mendelian models of genetics, and many components of the epigenetic systems in plants appeared anomalous. However, it is now clear that these systems govern how the entire genome operates and evolves. SCOPE In the first part of a two-part review, how epigenetic systems in plants were elucidated is addressed. Also there is a discussion on how the different components of the epigenetic system--regulating DNA methylation, histones and their post-translational modification, and pathways recognizing aberrant transcripts--may work together.
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Neves N, Delgado M, Silva M, Caperta A, Morais-Cecílio L, Viegas W. Ribosomal DNA heterochromatin in plants. Cytogenet Genome Res 2005; 109:104-11. [PMID: 15753565 DOI: 10.1159/000082388] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 02/19/2004] [Indexed: 11/19/2022] Open
Abstract
The aim of this review is to integrate earlier results and recent findings to present the current state-of-the-art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene expression patterns. Correlations between several heterochromatin fractions and rDNA arrays demonstrate the heterochromatic nature of the rDNA and reveal the importance of the genomic environment and of developmental controls in modulating its dynamics.
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Affiliation(s)
- N Neves
- Secção de Genética, Centro de Botânica Aplicada à Agricultura, Instituto Superior de Agronomia, Lisboa, Portugal
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Ma XF, Gustafson JP. Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res 2005; 109:236-49. [PMID: 15753583 DOI: 10.1159/000082406] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Accepted: 03/09/2004] [Indexed: 11/19/2022] Open
Abstract
Allopolyploidy is a prominent mode of speciation in higher plants. Due to the coexistence of closely related genomes, a successful allopolyploid must have the ability to invoke and maintain diploid-like behavior, both cytologically and genetically. Recent studies on natural and synthetic allopolyploids have raised many discrepancies. Most species have displayed non-Mendelian behavior in the allopolyploids, but others have not. Some species have demonstrated rapid genome changes following allopolyploid formation, while others have conserved progenitor genomes. Some have displayed directed, non-random genome changes, whereas others have shown random changes. Some of the genomic changes have appeared in the F1 hybrids, which have been attributed to the union of gametes from different progenitors, while other changes have occurred during or after genome doubling. Although these observations provide significant novel insights into the evolution of allopolyploids, the overall mechanisms of the event are still elusive. It appears that both genetic and epigenetic operations are involved in the diploidization process of allopolyploids. Overall, genetic and epigenetic variations are often associated with the activities of repetitive sequences and transposon elements. Specifically, genomic sequence elimination and chromosome rearrangement are probably the major forces guiding cytological diploidization. Gene non-functionalization, sub-functionalization, neo-functionalization, as well as other kinds of epigenetic modifications, are likely the leading factors promoting genetic diploidization.
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Affiliation(s)
- X-F Ma
- Department of Agronomy, University of Missouri-Columbia, MO 65211, USA
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Hasterok R, Wolny E, Kulak S, Zdziechiewicz A, Maluszynska J, Heneen WK. Molecular cytogenetic analysis of Brassica rapa-Brassica oleracea var. alboglabra monosomic addition lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:196-205. [PMID: 15756535 DOI: 10.1007/s00122-005-1942-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 01/25/2005] [Indexed: 05/24/2023]
Abstract
Interspecific alien chromosome addition lines can be very useful for gene mapping and studying chromosome homoeology between closely related species. In this study we demonstrate a simple but robust manner of identifying individual C-genome chromosomes (C5, C8 and C9) in the A-genome background through the simultaneous use of 5S and 25S ribosomal probes on mitotic and meiotic chromosomes of three different Brassica rapa-B. oleracea var. alboglabra monosomic addition lines. Sequential silver staining and fluorescence in situ hybridisation indicated that 18S-5.8S-25S rRNA genes on the additional chromosome C9 are expressed in the A-genome background. Meiotic behaviour of the additional chromosomes was studied in pollen mother cells at diakinesis and metaphase I. In all of the addition lines the alien chromosome was most frequently observed as a univalent. The alien chromosome C5, which carries an intercalary 5S rDNA locus, occasionally formed trivalents that involved either rDNA- or non rDNA-carrying chromosomes from the A genome. In the case of chromosomes C8 and C9, the most frequently observed intergenomic associations involved the regions occupied by 18S-5.8S-25S ribosomal RNA genes. It is possible that not all such associations represent true pairing but are remnants of nucleolar associations from the preceding interphase. Variations in the numbers and distribution of 5S and 25S rDNA sites between cultivars of B. oleracea, B. oleracea var. alboglabra and B. rapa are discussed.
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Affiliation(s)
- Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, Katowice, Poland.
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Law RD, Suttle JC. Chromatin remodeling in plant cell culture: patterns of DNA methylation and histone H3 and H4 acetylation vary during growth of asynchronous potato cell suspensions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2005; 43:527-34. [PMID: 15922608 DOI: 10.1016/j.plaphy.2005.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Accepted: 03/09/2005] [Indexed: 05/02/2023]
Abstract
Changes in DNA cytosine methylation and core histone multi-acetylation were determined in cell suspension cultures of potato (Solanum tuberosum L. cv. Russet Burbank) during 15 days of in vitro culture. Cell subculture induced a transient 33% decrease in genome-wide 5-methylcytosine (5mC) content and a transient threefold increase in transcription rates that were most evident at 6 and 9 days after subculture, respectively. In contrast to the global reduction in 5mC content, subculture resulted in a transient twofold increase in 5mC levels within 5'-CCGG-3' sequences and no detectable change in 5'-CG-3' methylation. Multi-acetylation of histones H3.1, H3.2 and H4 rose 2-, 1.5- and 3-fold by 9, 9 and 12 days after subculture, respectively. All observed epigenetic changes were reset during aging of cell cultures. Inclusion of the histone deacetylase inhibitor trichostatin A (TSA) and/or the cytosine methylation inhibitor 5-azacytidine (5AC) in culture sequentially decreased genome-wide 5mC levels by approximately 25% at day 9, then decreased 5'-mCmCGG-3' by 30-50% and increased H3 and H4 multi-acetylation by 30-60% at day 15, compared to controls. Treatment with 5AC or TSA alone or in combination had no effect on RNA synthesis at day 9. At day 15, 5AC treatment remained ineffective, while de novo RNA synthesis was approximately twofold higher in cells grown in both inhibitors or in TSA alone. Collectively, these results demonstrate that in potato suspension cultures, rapid, reversible changes in 5mC levels precede regulatory post-translational acetylation of core histones, and suggest that interactions between these epigenetic processes appear to be necessary to power transcription and growth induction in potato cells.
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Affiliation(s)
- R David Law
- United States Department of Agriculture, Agricultural Research Service, Northern Crop Science Laboratory, Sugarbeet and Potato Research, Post Office Box 5677, State University Station, Fargo, ND 58105-5677, USA
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Wang J, Tian L, Madlung A, Lee HS, Chen M, Lee JJ, Watson B, Kagochi T, Comai L, Chen ZJ. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 2005; 167:1961-73. [PMID: 15342533 PMCID: PMC1471021 DOI: 10.1534/genetics.104.027896] [Citation(s) in RCA: 279] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Polyploidization is an abrupt speciation mechanism for eukaryotes and is especially common in plants. However, little is known about patterns and mechanisms of gene regulation during early stages of polyploid formation. Here we analyzed differential expression patterns of the progenitors' genes among successive selfing generations and independent lineages. The synthetic Arabidopsis allotetraploid lines were produced by a genetic cross between A. thaliana and A. arenosa autotetraploids. We found that some progenitors' genes are differentially expressed in early generations, whereas other genes are silenced in late generations or among different siblings within a selfing generation, suggesting that the silencing of progenitors' genes is rapidly and/or stochastically established. Moreover, a subset of genes is affected in autotetraploid and multiple independent allotetraploid lines and in A. suecica, a natural allotetraploid derived from A. thaliana and A. arenosa, indicating locus-specific susceptibility to ploidy-dependent gene regulation. The role of DNA methylation in silencing progenitors' genes is tested in DNA-hypomethylation transgenic lines of A. suecica using RNA interference (RNAi). Two silenced genes are reactivated in both ddm1- and met1-RNAi lines, consistent with the demethylation of centromeric repeats and gene-specific regions in the genome. A rapid and stochastic process of differential gene expression is reinforced by epigenetic regulation during polyploid formation and evolution.
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Affiliation(s)
- Jianlin Wang
- Genetics Program, Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843-2474, USA
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