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Barro-Trastoy D, Köhler C. Helitrons: genomic parasites that generate developmental novelties. Trends Genet 2024; 40:437-448. [PMID: 38429198 DOI: 10.1016/j.tig.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.
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Affiliation(s)
- Daniela Barro-Trastoy
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Claudia Köhler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden.
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2
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Li C, Cong C, Liu F, Yu Q, Zhan Y, Zhu L, Li Y. Abundance of Transgene Transcript Variants Associated with Somatically Active Transgenic Helitrons from Multiple T-DNA Integration Sites in Maize. Int J Mol Sci 2023; 24:ijms24076574. [PMID: 37047545 PMCID: PMC10095026 DOI: 10.3390/ijms24076574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Helitrons, a novel type of mysterious DNA transposons discovered computationally prior to bench work confirmation, are components ubiquitous in most sequenced genomes of various eukaryotes, including plants, animals, and fungi. There is a paucity of empirical evidence to elucidate the mechanism of Helitrons transposition in plants. Here, by constructing several artificial defective Helitron (dHel) reporter systems, we aim to identify the autonomous Helitrons (aHel) in maize genetically and to demonstrate the transposition and repair mechanisms of Helitrons upon the dHel-GFP excision in maize. When crossing with various inbred lines, several transgenic lines produced progeny of segregated, purple-blotched kernels, resulting from a leaky expression of the C1 gene driven by the dHel-interrupted promoter. Transcription analysis indicated that the insertion of different dHels into the C1 promoter or exon would lead to multiple distinct mRNA transcripts corresponding to transgenes in the host genome. Simple excision products and circular intermediates of dHel-GFP transposition have been detected from the leaf tissue of the seedlings in F1 hybrids of transgenic lines with corresponding c1 tester, although they failed to be detected in all primary transgenic lines. These results revealed the transposition and repair mechanism of Helitrons in maize. It is strongly suggested that this reporter system can detect the genetic activity of autonomic Helitron at the molecular level. Sequence features of dHel itself, together with the flanking regions, impact the excision activity of dHel and the regulation of the dHel on the transcription level of the host gene.
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Affiliation(s)
- Chuxi Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunsheng Cong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fangyuan Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qian Yu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yuan Zhan
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yubin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
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Pegler JL, Oultram JMJ, Mann CWG, Carroll BJ, Grof CPL, Eamens AL. Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:1101. [PMID: 36903960 PMCID: PMC10004981 DOI: 10.3390/plants12051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Poretti M, Praz CR, Sotiropoulos AG, Wicker T. A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material. PLANT DIRECT 2023; 7:e484. [PMID: 36937792 PMCID: PMC10020141 DOI: 10.1002/pld3.484] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae-specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.
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Affiliation(s)
- Manuel Poretti
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Coraline R. Praz
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
| | | | - Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
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Wang J, Yang W, Zhang S, Hu H, Yuan Y, Dong J, Chen L, Ma Y, Yang T, Zhou L, Chen J, Liu B, Li C, Edwards D, Zhao J. A pangenome analysis pipeline provides insights into functional gene identification in rice. Genome Biol 2023; 24:19. [PMID: 36703158 PMCID: PMC9878884 DOI: 10.1186/s13059-023-02861-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking. RESULTS To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants' position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic diversity. We characterize a new locus (qPH8-1) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS). CONCLUSIONS Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.
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Affiliation(s)
- Jian Wang
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wu Yang
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shaohong Zhang
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Haifei Hu
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
- Western Crop Genetics Alliance, Murdoch University, Murdoch, Western Australia, 6150, Australia.
| | - Yuxuan Yuan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Jingfang Dong
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Luo Chen
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yamei Ma
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Tifeng Yang
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lian Zhou
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jiansong Chen
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bin Liu
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Chengdao Li
- Western Crop Genetics Alliance, Murdoch University, Murdoch, Western Australia, 6150, Australia.
| | - David Edwards
- School of Biological Sciences and Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, Australia.
| | - Junliang Zhao
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Chen Z, Guan Y, Han M, Guo Y, Zhang J, Guo Z, Sun G, Yan X. Altitudinal Patterns in Adaptive Evolution of Genome Size and Inter-Genome Hybridization Between Three Elymus Species From the Qinghai–Tibetan Plateau. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.923967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome size variation and hybridization occur frequently within or between plant species under diverse environmental conditions, which enrich species diversification and drive the evolutionary process. Elymus L. is the largest genus in Triticeae with five recognized basic genomes (St, H, P, W, and Y). However, the data on population cytogenetics of Elymus species are sparse, especially whether genome hybridization and chromosomal structure can be affected by altitude are still unknown. In order to explore the relationship between genome sizes, we studied interspecific hybridization and altitude of Elymus species at population genetic and cytological levels. Twenty-seven populations at nine different altitudes (2,800–4,300 m) of three Elymus species, namely, hexaploid E. nutans (StHY, 2n = 6x = 42), tetraploid E. burchan-buddae (StY, 2n = 4x = 28), and E. sibiricus (StH, 2n = 4x = 28), were sampled from the Qinghai–Tibetan Plateau (QTP) to estimate whether intraspecific variation could affect the genomic relationships by genomic in situ hybridization (GISH), and quantify the genome size of Elymus among different altitude ecological groups by flow cytometry. The genome size of E. nutans, E. burchan-buddae, and E. sibiricus varied from 12.38 to 22.33, 8.81 to 18.93, and 11.46 to 20.96 pg/2C with the averages of 19.59, 12.39, and 16.85 pg/2C, respectively. The curve regression analysis revealed a strong correlation between altitude and nuclear DNA content in three Elymus species. In addition, the chromosomes of the St and Y genomes demonstrated higher polymorphism than that of the H genome. Larger genome size variations occurred in the mid-altitude populations (3,900–4,300 m) compared with other-altitude populations, suggesting a notable altitudinal pattern in genome size variation, which shaped genome evolution by altitude. This result supports our former hypothesis that genetic richness center at medium altitude is useful and valuable for species adaptation to highland environmental conditions, germplasm utilization, and conservation.
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Noronha RCR, Almeida BRR, Chagas MCS, Tavares FS, Cardoso AL, Bastos CEMC, Silva NKN, Klautau AGCM, Luna FO, Attademo FLN, Lima DS, Sabioni LA, Sampaio MIC, Oliveira JM, do Nascimento LAS, Martins C, Vicari MR, Nagamachi CY, Pieczarka JC. Karyotypes of Manatees: New Insights into Hybrid Formation ( Trichechus inunguis × Trichechus m. manatus) in the Amazon Estuary. Genes (Basel) 2022; 13:1263. [PMID: 35886048 PMCID: PMC9323068 DOI: 10.3390/genes13071263] [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: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Great efforts have been made to preserve manatees. Recently, a hybrid zone was described between Trichechus inunguis (TIN) and the Trichechus manatus manatus (TMM) in the Amazon estuary. Cytogenetic data on these sirenians are limited, despite being fundamental to understanding the hybridization/introgression dynamics and genomic organization in Trichechus. We analyzed the karyotype of TMM, TIN, and two hybrid specimens ("Poque" and "Vitor") by classical and molecular cytogenetics. G-band analysis revealed that TMM (2n = 48) and TIN (2n = 56) diverge by at least six Robertsonian translocations and a pericentric inversion. Hybrids had 2n = 50, however, with Autosomal Fundamental Number (FNA) = 88 in "Poque" and FNA = 74 in "Vitor", and chromosomal distinct pairs in heterozygous; additionally, "Vitor" exhibited heteromorphisms and chromosomes whose pairs could not be determined. The U2 snDNA and Histone H3 multi genes are distributed in small clusters along TIN and TMM chromosomes and have transposable Keno and Helitron elements (TEs) in their sequences. The different karyotypes observed among manatee hybrids may indicate that they represent different generations formed by crossing between fertile hybrids and TIN. On the other hand, it is also possible that all hybrids recorded represent F1 and the observed karyotype differences must result from mechanisms of elimination.
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Affiliation(s)
- Renata C. R. Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Bruno R. R. Almeida
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
- Campus Itaituba, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Itaituba 68183-300, PA, Brazil
| | - Monique C. S. Chagas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Flávia S. Tavares
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Adauto L. Cardoso
- Laboratório Genômica Integrativa, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu 18618-970, SP, Brazil; (A.L.C.); (C.M.)
| | - Carlos E. M. C. Bastos
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Natalia K. N. Silva
- Campus Tucuruí, Universidade do Estado do Pará, Tucuruí 68455-210, PA, Brazil;
| | - Alex G. C. M. Klautau
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte, Instituto Chico Mendes de Conservação da Biodiversidade, Belém 66635-110, PA, Brazil;
| | - Fábia O. Luna
- Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Instituto Chico Mendes de Conservação de Biodiversidade, Santos 11050-031, SP, Brazil; (F.O.L.); (F.L.N.A.)
| | - Fernanda L. N. Attademo
- Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Instituto Chico Mendes de Conservação de Biodiversidade, Santos 11050-031, SP, Brazil; (F.O.L.); (F.L.N.A.)
- Departamento de Zoologia, Programa de Pós-Graduação em Biologia Animal/PPBA, Laboratório de Ecologia Comportamento e Conservação/LECC, Universidade Federal de Pernambuco/UFPE, Recife 50670-901, PE, Brazil
| | - Danielle S. Lima
- Grupo de Pesquisa em Mamíferos Aquáticos Amazônicos, Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, Tefé 69553-225, AM, Brazil; (D.S.L.); (L.A.S.)
- Rede de Pesquisa e Conservação de Sirênios no Estuário Amazônico, Macapá 68903-197, AP, Brazil
| | - Luiz A. Sabioni
- Grupo de Pesquisa em Mamíferos Aquáticos Amazônicos, Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, Tefé 69553-225, AM, Brazil; (D.S.L.); (L.A.S.)
- Rede de Pesquisa e Conservação de Sirênios no Estuário Amazônico, Macapá 68903-197, AP, Brazil
- Campus Porto Grande, Instituto Federal de Educação Ciência e Tecnologia do Amapá, Rodovia BR 210, Km 103, s/n, Zona Rural, Porto Grande 68997-000, AP, Brazil
| | - Maria I. C. Sampaio
- Instituto de Estudos Costeiros, Campus Bragança, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil;
| | - Jairo Moura Oliveira
- Zoological Park of Santarém, ZOOUNAMA, Universidade da Amazônia, Santarém 68030-150, PA, Brazil;
| | | | - Cesar Martins
- Laboratório Genômica Integrativa, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu 18618-970, SP, Brazil; (A.L.C.); (C.M.)
| | - Marcelo R. Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil;
| | - Cleusa Y. Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Julio C. Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
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8
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Birchler JA, Yang H. The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation. THE PLANT CELL 2022; 34:2466-2474. [PMID: 35253876 PMCID: PMC9252495 DOI: 10.1093/plcell/koac076] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/17/2022] [Indexed: 05/13/2023]
Abstract
Gene duplications have long been recognized as a contributor to the evolution of genes with new functions. Multiple copies of genes can result from tandem duplication, from transposition to new chromosomes, or from whole-genome duplication (polyploidy). The most common fate is that one member of the pair is deleted to return the gene to the singleton state. Other paths involve the reduced expression of both copies (hypofunctionalization) that are held in duplicate to maintain sufficient quantity of function. The two copies can split functions (subfunctionalization) or can diverge to generate a new function (neofunctionalization). Retention of duplicates resulting from doubling of the whole genome occurs for genes involved with multicomponent interactions such as transcription factors and signal transduction components. In contrast, these classes of genes are underrepresented in small segmental duplications. This complementary pattern suggests that the balance of interactors affects the fate of the duplicate pair. We discuss the different mechanisms that maintain duplicated genes, which may change over time and intersect.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
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9
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Song JM, Zhang Y, Zhou ZW, Lu S, Ma W, Lu C, Chen LL, Guo L. Oil plant genomes: current state of the science. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2859-2874. [PMID: 35560205 DOI: 10.1093/jxb/erab472] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/22/2021] [Indexed: 05/25/2023]
Abstract
Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhi-Wei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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10
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Wang Z, Zhao G, Yang Q, Gao L, Liu C, Ru Z, Wang D, Jia J, Cui D. Helitron and CACTA DNA transposons actively reshape the common bread wheat - AK58 genome. Genomics 2022; 114:110288. [DOI: 10.1016/j.ygeno.2022.110288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 12/01/2021] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
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11
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Watson AK, Lopez P, Bapteste E. Hundreds of out-of-frame remodelled gene families in the E. coli pangenome. Mol Biol Evol 2021; 39:6430988. [PMID: 34792602 PMCID: PMC8788219 DOI: 10.1093/molbev/msab329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized to have formed de novo, from noncoding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from noncoding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodeled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodeling event. These genes with out-of-frame components represent ∼2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.
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Affiliation(s)
- Andrew K Watson
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
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12
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Su Y, Huang Q, Wang Z, Wang T. High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weed Mikania micrantha. Ecol Evol 2021; 11:13501-13517. [PMID: 34646486 PMCID: PMC8495827 DOI: 10.1002/ece3.8075] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022] Open
Abstract
Why invasive species can rapidly adapt to novel environments is a puzzling question known as the genetic paradox of invasive species. This paradox is explainable in terms of transposable elements (TEs) activity, which are theorized to be powerful mutational forces to create genetic variation. Mikania micrantha, a noxious invasive weed, in this sense provides an excellent opportunity to test the explanation. The genetic and epigenetic variation of 21 invasive populations of M. micrantha in southern China have been examined by using transposon display (TD) and transposon methylation display (TMD) techniques to survey 12 TE superfamilies. Our results showed that M. micrantha populations maintained an almost equally high level of TE-based genetic and epigenetic variation and they have been differentiated into subpopulations genetically and epigenetically. A similar positive spatial genetic and epigenetic structure pattern was observed within 300 m. Six and seven TE superfamilies presented significant genetic and epigenetic isolation by distance (IBD) pattern. In total, 59 genetic and 86 epigenetic adaptive TE loci were identified. Of them, 51 genetic and 44 epigenetic loci were found to correlate with 25 environmental variables (including precipitation, temperature, vegetation coverage, and soil metals). Twenty-five transposon-inserted genes were sequenced and homology-based annotated, which are found to be involved in a variety of molecular and cellular functions. Our research consolidates the importance of TE-associated genetic and epigenetic variation in the rapid adaptation and invasion of M. micrantha.
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Affiliation(s)
- Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen UniversityShenzhenChina
| | - Qiqi Huang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ting Wang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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13
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Detecting Genetic Mobility Using a Transposon-Based Marker System in Gamma-Ray Irradiated Soybean Mutants. PLANTS 2021; 10:plants10020373. [PMID: 33671964 PMCID: PMC7919005 DOI: 10.3390/plants10020373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
Transposable elements (TEs)—major components of eukaryotic genomes—have the ability to change location within a genome. Because of their mobility, TEs are important for genome diversification and evolution. Here, a simple rapid method, using the consensus terminal inverted repeat sequences of PONG, miniature inverted-repeat transposable element (MITE)-Tourist (M-t) and MITE-Stowaway (M-s) as target region amplification polymorphism (TE-TRAP) markers, was employed to investigate the mobility of TEs in a gamma-irradiated soybean mutant pool. Among the different TE-TRAP primer combinations, the average polymorphism level and polymorphism information content value were 57.98% and 0.14, respectively. Only the PONG sequence separated the mutant population into three major groups. The inter-mutant population variance, determined using the PONG marker (3.151 and 29%) was greater than that of the M-t (2.209 and 20%) and M-s (2.766 and 18%) markers, whereas the reverse was true for the intra-mutant population variations, with M-t and M-s values, being 15.151 (82%) and 8.895 (80%), respectively, compared with the PONG marker (7.646 and 71%). Thus, the MITE markers revealed more dynamic and active mobility levels than the PONG marker in gamma-ray irradiated soybean mutant lines. The TE-TRAP technique associated with sensitive MITEs is useful for investigating genetic diversity and TE mobilization, providing tools for mutant selection in soybean mutation breeding.
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14
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Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding. Mol Biol Rep 2020; 47:3155-3167. [PMID: 32162128 DOI: 10.1007/s11033-020-05365-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/29/2020] [Indexed: 12/20/2022]
Abstract
Plant molecular breeding is expected to give significant gains in cultivar development through development and utilization of suitable molecular marker systems for genetic diversity analysis, rapid DNA fingerprinting, identification of true hybrids, trait mapping and marker-assisted selection. Transposable elements (TEs) are the most abundant component in a genome and being used as genetic markers in the plant molecular breeding. Here, we review on the high copious transposable element belonging to class-II DNA TEs called "miniature inverted-repeat transposable elements" (MITEs). MITEs are ubiquitous, short and non-autonomous DNA transposable elements which have a tendency to insert into genes and genic regions have paved a way for the development of functional DNA marker systems in plant genomes. This review summarises the characteristics of MITEs, principles and methodologies for development of MITEs based DNA markers, bioinformatics tools and resources for plant MITE discovery and their utilization in crop improvement.
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15
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Li Q, Ramasamy S, Singh P, Hagel JM, Dunemann SM, Chen X, Chen R, Yu L, Tucker JE, Facchini PJ, Yeaman S. Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy. Nat Commun 2020; 11:1190. [PMID: 32132540 PMCID: PMC7055283 DOI: 10.1038/s41467-020-15040-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/10/2020] [Indexed: 02/08/2023] Open
Abstract
Genes in plant secondary metabolic pathways enable biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression of BIA genes increases within clusters and identify candidates with unknown function based on clustering and covariation in expression and alkaloid production. Copy number variation in critical BIA genes correlates with stark differences in alkaloid production, linking noscapine production with an 11-gene deletion, and increased thebaine/decreased morphine production with deletion of a T6ODM cluster. Our results show that the opium poppy genome is still dynamically evolving in ways that contribute to medically and industrially important phenotypes.
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Affiliation(s)
- Qiushi Li
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sukanya Ramasamy
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Sonja M Dunemann
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Xue Chen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Rongji Chen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Lisa Yu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Joseph E Tucker
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
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16
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Ilyas M, Irfan M, Mahmood T, Hussain H, Latif-ur-Rehman, Naeem I, Khaliq-ur-Rahman. Analysis of Germin-like Protein Genes (OsGLPs) Family in Rice Using Various In silico Approaches. Curr Bioinform 2020. [DOI: 10.2174/1574893614666190722165130] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background:
Germin-like Proteins (GLPs) play an important role in various stresses.
Rice contains 43 GLPs, among which many remain functionally unexplored. The computational
analysis will provide significant insight into their function.
Objective:
To find various structural properties, functional importance, phylogeny and expression
pattern of all OsGLPs using various bioinformatics tools.
Methods:
Physiochemical properties, sub-cellular localization, domain composition, Nglycosylation
and Phosphorylation sites, and 3D structural models of the OsGLPs were predicted
using various bioinformatics tools. Functional analysis was carried out with the Search Tool for
the Retrieval of Interacting Genes/Proteins (STRING) and Blast2GO servers. The expression
profile of the OsGLPs was predicted by retrieving the data for expression values from tissuespecific
and hormonal stressed array libraries of RiceXPro. Their phylogenetic relationship was
computed using Molecular and Evolutionary Genetic Analysis (MEGA6) tool.
Results:
Most of the OsGLPs are stable in the cellular environment with a prominent expression in
the extracellular region (57%) and plasma membrane (33%). Besides, 3 basic cupin domains, 7
more were reported, among which NTTNKVGSNVTLINV, FLLAALLALASWQAI, and
MASSSF were common to 99% of the sequences, related to bacterial pathogenicity, peroxidase
activity, and peptide signal activity, respectively. Structurally, OsGLPs are similar but functionally
they are diverse with novel enzymatic activities of oxalate decarboxylase, lyase, peroxidase, and
oxidoreductase. Expression analysis revealed prominent activities in the root, endosperm, and
leaves. OsGLPs were strongly expressed by abscisic acid, auxin, gibberellin, cytokinin, and
brassinosteroid. Phylogenetically they showed polyphyletic origin with a narrow genetic
background of 0.05%. OsGLPs of chromosome 3, 8, and 12 are functionally more important due to
their defensive role against various stresses through co-expression strategy.
Conclusion:
The analysis will help to utilize OsGLPs in future food programs.
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Affiliation(s)
- Muhammad Ilyas
- Department of Botany, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Irfan
- Department of Botany, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Tariq Mahmood
- Department of Botany, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan
| | - Hazrat Hussain
- Department of Biotechnology, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Latif-ur-Rehman
- Department of Biotechnology, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Ijaz Naeem
- Department of Biotechnology, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Khaliq-ur-Rahman
- Department of Chemistry, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
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17
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Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O'Connor CH, Hirsch CD, Ross-Ibarra J, Hirsch CN, Springer NM. Transposable elements contribute to dynamic genome content in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1052-1065. [PMID: 31381222 DOI: 10.1111/tpj.14489] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/15/2019] [Accepted: 07/26/2019] [Indexed: 05/05/2023]
Abstract
Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH207) with uniform structural annotations of TEs. Among these genomes we identified approximately 400 000 TEs that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TEs include a combination of recent transposition events as well as deletions of older TEs. There are examples of polymorphic TEs within each of the superfamilies of TEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in annotated gene content among these genotypes. TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TEs in driving variation in genome organization and gene content. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://github.com/SNAnderson/maizeTE_variation; https://mcstitzer.github.io/maize_TEs.
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Affiliation(s)
- Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Michelle C Stitzer
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, CA, 95616, USA
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
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18
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Kojima KK. Structural and sequence diversity of eukaryotic transposable elements. Genes Genet Syst 2019; 94:233-252. [DOI: 10.1266/ggs.18-00024] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Kenji K. Kojima
- Genetic Information Research Institute
- Department of Life Sciences, National Cheng Kung University
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19
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Touati R, Oueslati AE, Messaoudi I, Lachiri Z. The Helitron family classification using SVM based on Fourier transform features applied on an unbalanced dataset. Med Biol Eng Comput 2019; 57:2289-2304. [PMID: 31422557 DOI: 10.1007/s11517-019-02027-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
Abstract
Helitrons are mobile sequences which belong to the class 2 of eukaryotic transposons. Their specificity resides in their mechanism of transposition: the rolling circle mechanism. They play an important role in remodeling proteomes due to their ability to modify existing genes and introducing new ones. A major difficulty in identifying and classifying Helitron families comes from the complex structure, the unspecified length, and the unbalanced appearance number of each Helitron type. The Helitron's recognition is still not solved in literature. The purpose of this paper is to characterize and classify Helitron types using spectral features and support vector machine (SVM) classification technique. Thus, the helitronic DNA is transformed into a numerical form using the FCGS2 coding technique. Then, a set of spectral features is extracted from the smoothed Fourier transform applied on the FCGS2 signals. Based on the spectral signature and the classification's confusion matrix, we demonstrated that some specific classes which do not show similarities, such as HelitronY2 and NDNAX3, are easily discriminated with important accuracy rates exceeding 90%. However, some Helitron types have great similarities such as the following: Helitron1, HelitronY1, HelitronY1A, and HelitronY4. Our system is also able to predict them with promising values reaching 70%. Graphical abstract The Helitron recognizer based on features extracted from smoothed Fourier transform.
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Affiliation(s)
- Rabeb Touati
- LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), University of Tunis El Manar, Tunis, Tunisia.
- SITI Laboratory, National School of Engineers of Tunis (ENIT), University Tunis El Manar, BP 37, le Belvédère, 1002, Tunis, Tunisia.
| | - Afef Elloumi Oueslati
- SITI Laboratory, National School of Engineers of Tunis (ENIT), University Tunis El Manar, BP 37, le Belvédère, 1002, Tunis, Tunisia
- Electrical Engineering Department, National School of Engineers of Carthage (ENICarthage), University of Carthage, Carthage, Tunisia
| | - Imen Messaoudi
- SITI Laboratory, National School of Engineers of Tunis (ENIT), University Tunis El Manar, BP 37, le Belvédère, 1002, Tunis, Tunisia
- Industrial Computing Department, Higher Institute of Information Technologies and Communications (ISTIC), University of Carthage, Carthage, Tunisia
| | - Zied Lachiri
- SITI Laboratory, National School of Engineers of Tunis (ENIT), University Tunis El Manar, BP 37, le Belvédère, 1002, Tunis, Tunisia
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20
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Krasileva KV. The role of transposable elements and DNA damage repair mechanisms in gene duplications and gene fusions in plant genomes. CURRENT OPINION IN PLANT BIOLOGY 2019; 48:18-25. [PMID: 30849712 DOI: 10.1016/j.pbi.2019.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 05/02/2023]
Abstract
Plant genomes are shaped by structural variation. Gene-size insertions and among most prominent events and can have significant effects on amplification of gene families as well as facilitate new gene fusions. Transposable elements as well as plant DNA repair machinery have overlapping contributions to these events, and often work in synergy. Activity of transposable elements is often lineage specific and can preferentially affect specific gene families, such as disease resistance genes. Once duplicated, genes themselves can serve templates for additional variation that can arise from non-allelic homologous recombination. Non-homologous DNA repair mechanisms contribute to additional variation and diversify the mechanisms of gene movement, such as through ligation of extra-chromosomal DNA fragments. Genomic processes that generate structural variation can be induced by stress and, therefore, can provide adaptive potential. This review describes mechanisms that contribute to gene-size structural variation in plants, result in gene duplication and generation of new plant genes through gene fusion.
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Affiliation(s)
- Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States.
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21
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Bayer PE, Golicz AA, Tirnaz S, Chan CK, Edwards D, Batley J. Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:789-800. [PMID: 30230187 PMCID: PMC6419861 DOI: 10.1111/pbi.13015] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/16/2018] [Accepted: 09/14/2018] [Indexed: 05/19/2023]
Abstract
Brassica oleracea is an important agricultural species encompassing many vegetable crops including cabbage, cauliflower, broccoli and kale; however, it can be susceptible to a variety of fungal diseases such as clubroot, blackleg, leaf spot and downy mildew. Resistance to these diseases is meditated by specific disease resistance genes analogs (RGAs) which are differently distributed across B. oleracea lines. The sequenced reference cultivar does not contain all B. oleracea genes due to gene presence/absence variation between individuals, which makes it necessary to search for RGA candidates in the B. oleracea pangenome. Here we present a comparative analysis of RGA candidates in the pangenome of B. oleracea. We show that the presence of RGA candidates differs between lines and suggests that in B. oleracea, SNPs and presence/absence variation drive RGA diversity using separate mechanisms. We identified 59 RGA candidates linked to Sclerotinia, clubroot, and Fusarium wilt resistance QTL, and these findings have implications for crop breeding in B. oleracea, which may also be applicable in other crops species.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVic.Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Chon‐Kit Kenneth Chan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
- Australian Genome Research FacilityMelbourneVic.Australia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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22
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Li S, Wang R, Jin H, Ding Y, Cai C. Molecular Characterization and Expression Profile Analysis of Heat Shock Transcription Factors in Mungbean. Front Genet 2019; 9:736. [PMID: 30687395 PMCID: PMC6336897 DOI: 10.3389/fgene.2018.00736] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/22/2018] [Indexed: 11/30/2022] Open
Abstract
Heat shock transcription factors (Hsfs) are essential elements in plant signal transduction pathways that mediate gene expression in response to various abiotic stresses. Mungbean (Vigna radiata) is an important crop worldwide. The emergence of a genome database now allows for functional analysis of mungbean genes. In this study, we dissect the mungbean Hsfs using genome-wide identification and expression profiles. We characterized a total of 24 VrHsf genes and classified them into three groups (A, B, and C) based on their phylogeny and conserved domain structures. All VrHsf genes exhibit highly conserved exon-intron organization, with two exons and one intron. In addition, all VrHsf proteins contain 16 distinct motifs. Chromosome location analysis revealed that VrHsf genes are located on 8 of the 11 mungbean chromosomes, and that seven duplicated gene pairs had formed among them. Moreover, transcription patterns of VrHsf genes varied in different tissues, indicating their different roles in plant growth and development. We identified multiple stress related cis-elements in VrHsf promoter regions 2 kb upstream of the translation initiation codons, and the expression of most VrHsf genes was altered under different stress conditions, suggesting their potential functions in stress resistance pathways. These molecular characterization and expression profile analyses of VrHsf genes provide essential information for further function investigation.
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Affiliation(s)
- Shuai Li
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Runhao Wang
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hanqi Jin
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yanhua Ding
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunmei Cai
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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Xiaodong X, Olukolu B, Yang Q, Balint-Kurti P. Identification of a locus in maize controlling response to a host-selective toxin derived from Cochliobolus heterostrophus, causal agent of southern leaf blight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2601-2612. [PMID: 30191251 DOI: 10.1007/s00122-018-3175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/25/2018] [Indexed: 06/08/2023]
Abstract
A host-selective, proteinaceous maize toxin was identified from the culture filtrate of the maize pathogen Cochliobolus heterostrophus. A dominant gene for toxin susceptibility was identified on maize chromosome 4. A toxic activity was identified from the culture filtrate (CF) of the fungus Cochliobolus heterostrophus, causal agent of the maize disease southern leaf blight (SLB) with differential toxicity on maize lines. Two independent mapping populations; a 113-line recombinant inbred line population and a 258-line association population, were used to map loci associated with sensitivity to the CF at the seedling stage. A major QTL on chromosome 4 was identified at the same locus using both populations. Mapping in the association population defined a 400 kb region that contained the sensitivity locus. By comparing CF-sensitivity of the parents of the RIL population with that of the F1 progeny, we determined that the sensitivity allele was dominant. No relationship was observed between CF-sensitivity in seedlings and SLB susceptibility in mature plants; however, a significant correlation (- 0.58) was observed between SLB susceptibility and CF-sensitivity in seedlings. The activity of the CF was light-dependent and was sensitive to pronase, indicating that the toxin was proteinaceous.
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Affiliation(s)
- Xie Xiaodong
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, 27695-7616, USA
| | - Bode Olukolu
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, 27695-7616, USA
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Qin Yang
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, 27695-7616, USA
- College of Agronomy and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, 27695-7616, USA.
- USDA-ARS Plant Science Research Unit, Raleigh, NC, 27695, USA.
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Shao GM, Li XY, Wang Y, Wang ZW, Li Z, Zhang XJ, Zhou L, Gui JF. Whole Genome Incorporation and Epigenetic Stability in a Newly Synthetic Allopolyploid of Gynogenetic Gibel Carp. Genome Biol Evol 2018; 10:2394-2407. [PMID: 30085110 PMCID: PMC6143163 DOI: 10.1093/gbe/evy165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/23/2022] Open
Abstract
Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid animals is scarce. In this study, the genome constitution and DNA methylation inheritance in a newly synthetic allopolyploid of gynogenetic gibel carp were analyzed. The incorporation of a whole genome of paternal common carp sperm in the allopolyploid was confirmed by genomic in situ hybridization, chromosome localization of 45S rDNAs, and sequence comparison. Pooled sample-based methylation sensitive amplified polymorphism (MSAP) revealed that an overwhelming majority (98.82%) of cytosine methylation patterns in the allopolyploid were inherited from its parents of hexaploid gibel carp clone D and common carp. Compared to its parents, 11 DNA fragments in the allopolyploid were proved to be caused by interindividual variation, recombination, deletion, and mutation through individual sample-based MSAP and sequencing. Contrast to the rapid and remarkable epigenetic changes in most of analyzed neopolyploids, no cytosine methylation variation was detected in the gynogenetic allopolyploid. Therefore, the newly synthetic allopolyploid of gynogenetic gibel carp combined genomes from its parents and maintained genetic and epigenetic stability after its formation and subsequently seven successive gynogenetic generations. Our current results provide a paradigm for recurrent polyploidy consequences in the gynogenetic allopolyploid animals.
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Affiliation(s)
- Guang-Ming Shao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet 2018; 50:1289-1295. [PMID: 30061735 DOI: 10.1038/s41588-018-0182-0] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 06/05/2018] [Indexed: 12/24/2022]
Abstract
Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.
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Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes. Mol Genet Genomics 2018; 293:1301-1316. [PMID: 29804262 DOI: 10.1007/s00438-018-1449-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 05/17/2018] [Indexed: 12/30/2022]
Abstract
This study focused on the construction of a database of transposable elements (TEs) from Rosaceae plants, the third most economically important plant family in temperate regions, and its transcriptomics applications. The evolutionary effects of TEs on gene regulation have been explored, and TE insertions can be the molecular bases of changes in gene structure and function. However, a specific Rosaceae plant TE database (RPTEdb) is lacking. The genomes of several Rosaceae plants have been sequenced, providing the opportunity to mine TE data at a whole-genome level. Therefore, we constructed the RPTEdb, a collective and comprehensive database of 19,596 annotated TEs in the genomes of Rosaceae plants using previously described identification and annotation methods and published genome sequences. The user-friendly web-based database provides access to research tools through hyperlinks, including Browse, TE tree, tools, JBrowse, and search sections, and through the inputting of sequences on the main webpage. Next, we performed one advanced application in which TEs near predicted long non-coding RNA (lncRNA) and mRNA domains within white and red petal-tissue transcriptomes of Prunus mume 'Fuban Tiaozhi' were identified, revealing 16 TEs that overlapped or were near 16 differentially expressed lncRNA domains, and 54 TEs that overlapped or were near 54 differentially expressed mRNA domains, and the TEs' possible functions were also discussed. We believe that the RPTEdb will contribute to the understanding of TE roles in the structural, functional and evolutionary dynamics of Rosaceae plant genomes.
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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Horns F, Petit E, Hood ME. Massive Expansion of Gypsy-Like Retrotransposons in Microbotryum Fungi. Genome Biol Evol 2018; 9:363-371. [PMID: 28164239 PMCID: PMC5381629 DOI: 10.1093/gbe/evx011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2017] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are selfish, autonomously replicating DNA sequences that constitute a major component of eukaryotic genomes and contribute to genome evolution through their movement and amplification. Many fungal genomes, including the anther-smut fungi in the basidiomycete genus Microbotryum, have genome defense mechanisms, such as repeat-induced point mutation (RIP), which hypermutate repetitive DNA and limit TE activity. Little is known about how hypermutation affects the tempo of TE activity and their sequence evolution. Here we report the identification of a massive burst-like expansion of Gypsy-like retrotransposons in a strain of Microbotryum. This TE expansion evidently occurred in the face of RIP-like hypermutation activity. By examining the fitness of individual TE insertion variants, we found that RIP-like mutations impair TE fitness and limit proliferation. Our results provide evidence for a punctuated pattern of TE expansion in a fungal genome, similar to that observed in animals and plants. While targeted hypermutation is often thought of as an effective protection against mobile element activity, our findings suggest that active TEs can persist and undergo selection while they proliferate in genomes that have RIP-like defenses.
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Affiliation(s)
- Felix Horns
- Department of Biology, Amherst College, Amherst, MA
| | - Elsa Petit
- Department of Biology, Amherst College, Amherst, MA
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29
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Nani TF, Schnable JC, Washburn JD, Albert P, Pereira WA, Sobrinho FS, Birchler JA, Techio VH. Location of low copy genes in chromosomes of Brachiaria spp. Mol Biol Rep 2018; 45:109-118. [PMID: 29330722 DOI: 10.1007/s11033-018-4144-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/27/2017] [Indexed: 01/09/2023]
Abstract
Repetitive DNA sequences have been widely used in cytogenetic analyses. The use of gene sequences with a low-copy-number, however, is little explored especially in plants. To date, the karyotype details in Brachiaria spp. are limited to the location of rDNA sites. The challenge lies in developing new probes based on incomplete sequencing data for the genus or complete sequencing of related species, since there are no model species with a sequenced genome in Brachiaria spp. The present study aimed at the physical location of conserved genes in chromosomes of Brachiaria ruziziensis, Brachiaria brizantha, and Brachiaria decumbens using RNAseq data, as well as sequences of Setaria italica and Sorghum bicolor through the fluorescent in situ hybridization technique. Five out of approximately 90 selected sequences generated clusters in the chromosomes of the species of Brachiaria studied. We identified genes in synteny with 5S and 45S rDNA sites, which contributed to the identification of chromosome pairs carrying these genes. In some cases, the species of Brachiaria evaluated had syntenic segments conserved across the chromosomes. The use of genomic sequencing data is essential for the enhancement of cytogenetic analyses.
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Affiliation(s)
- Thaís Furtado Nani
- Department of Biology, Federal University of Lavras, Lavras, Minas Gerais State, Brazil
| | | | - Jacob D Washburn
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Patrice Albert
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | | | - Fausto Souza Sobrinho
- Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Embrapa Gado de Leite (CNPGL), Juiz de Fora, Minas Gerais State, Brazil
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Vânia Helena Techio
- Department of Biology, Federal University of Lavras, Lavras, Minas Gerais State, Brazil.
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Markova DN, Mason-Gamer RJ. Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae. BMC Evol Biol 2017; 17:178. [PMID: 28774284 PMCID: PMC5543537 DOI: 10.1186/s12862-017-1028-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 07/26/2017] [Indexed: 11/10/2022] Open
Abstract
Background Transposable elements are major contributors to genome size and variability, accounting for approximately 70–80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated. In this work, we surveyed for PIF- and Pong-related transcriptional activity in 13 diploid Triticeae species, all of which have been previously shown to harbor extensive within-genome diversity of both groups of elements. Results The results revealed that PIF elements have considerable transcriptional activity in Triticeae, suggesting that they can escape the initial levels of plant cell control and are regulated at the post-transcriptional level. Phylogenetic analysis of 156 PIF cDNA transposase fragments along with 240 genomic partial transposase sequences showed that most, if not all, PIF clades are transcriptionally competent, and that multiple transposases coexisting within a single genome have the potential to act simultaneously. In contrast, we did not detect any transcriptional activity of Pong elements in any sample. Conclusions The lack of Pong element transcription shows that even closely related transposon families can exhibit wide variation in their transposase transcriptional activity within the same genome. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1028-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dragomira N Markova
- Department of Biological Sciences, University of Illinois at Chicago, M/C 067 840 West Taylor Street, Chicago, IL, 60607, USA. .,Present address: Department of Plant Sciences (mail stop 3), 151 Asmundson Hall, University of California, Davis, CA, 95616, USA.
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, M/C 067 840 West Taylor Street, Chicago, IL, 60607, USA
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de Moraes RLR, Bertollo LAC, Marinho MMF, Yano CF, Hatanaka T, Barby FF, Troy WP, Cioffi MDB. Evolutionary Relationships and Cytotaxonomy Considerations in the Genus Pyrrhulina (Characiformes, Lebiasinidae). Zebrafish 2017; 14:536-546. [PMID: 28767325 DOI: 10.1089/zeb.2017.1465] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although fishes exhibit the greatest biodiversity among the vertebrates, a large percentage of this fauna is still underexplored on evolutionary cytogenetic questions, particularly the miniature species. The Lebiasinidae family is a particular example for such case. This study is the first one presenting differential cytogenetic methods, such as C-banding, repetitive DNAs mapping, comparative genomic hybridization (CGH), and whole chromosome painting in lebiasinid species. Pyrrhulina australis and Pyrrhulina aff. australis were deeply investigated concerning their chromosomal patterns and evolutionary relationships. These species have a very similar morphology, but they can be distinguished by a longitudinal midlateral faintly dark stripe exclusive for Pyrrhulina aff. australis. Both species presented 2n = 40 chromosomes (4st +36a), without heteromorphic sex chromosomes. However, despite their morphological and karyotype resemblance, it was evidenced that both species have already gone through a significant genomic divergence, thus corresponding to distinct evolutionary units. Furthermore, to give additional support to some proposals on evolutionary relationship among Lebiasinidae with other fish families, a chromosomal comparative approach with Erythrinus erythrinus, a representative species of the Erythrinidae family, was also performed. In addition to have similar karyotype structure, mainly composed by acrocentric chromosomes, both species share uncommon genomic similarities, such as (i) syntenic location of 5S and 18S rDNA sequences; (ii) huge dispersion of multiple 5S rDNA sites in the karyotypes; and (iii) complex association between 5S rDNA and Rex3 elements. CGH experiments, despite reinforcing some shared genomic homologies, also highlighted that both Pyrrhulina and Erythrinus have a range of nonoverlapping species-specific signals. The overall chromosomal data proved to be effective markers for the cytotaxonomy and evolutionary process among Lebiasinidae fishes.
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Affiliation(s)
| | | | | | - Cassia Fernanda Yano
- 1 Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar) , São Carlos, Brazil
| | - Terumi Hatanaka
- 1 Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar) , São Carlos, Brazil
| | - Felipe Faix Barby
- 1 Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar) , São Carlos, Brazil
| | - Waldo Pinheiro Troy
- 3 Departamento de Ciências Biológicas, Universidade do Estado de Mato Grosso , Campus de Tangará da Serra, Tangará da Serra, Brazil
| | - Marcelo de Bello Cioffi
- 1 Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar) , São Carlos, Brazil
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Zeng F, Lian X, Zhang G, Yu X, Bradley CA, Ming R. A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts. GENOMICS DATA 2017; 13:54-63. [PMID: 28736701 PMCID: PMC5508496 DOI: 10.1016/j.gdata.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/17/2017] [Accepted: 07/07/2017] [Indexed: 11/08/2022]
Abstract
Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. Here, we report the genome sequence of C. sojina, and comparative genome analysis with plant pathogen members of the genus Mycosphaerella (Zymoseptoria. tritici (synonyms M. graminicola), M. pini, M. populorum and M. fijiensis - pathogens of wheat, pine, poplar and banana, respectively). Synteny or collinearity was limited between genomes of major Mycosphaerella pathogens. Comparative analysis with these related pathogen genomes indicated distinct genome-wide repeat organization features. It suggests repetitive elements might be responsible for considerable evolutionary genomic changes. These results reveal the background of genomic differences and similarities between Dothideomycete species. Wide diversity as well as conservation on genome features forms the potential genomic basis of the pathogen specialization, such as pathogenicity to woody vs. herbaceous hosts. Through comparative genome analysis among five Dothideomycete species, our results have shed light on the genome features of these related fungi species. It provides insight for understanding the genomic basis of fungal pathogenicity and disease resistance in the crop hosts.
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Affiliation(s)
- Fanchang Zeng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China.,Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
| | - Xin Lian
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Guirong Zhang
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
| | - Xiaoman Yu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA.,FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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Borgognone A, Castanera R, Muguerza E, Pisabarro AG, Ramírez L. Somatic transposition and meiotically driven elimination of an active helitron family in Pleurotus ostreatus. DNA Res 2017; 24:103-115. [PMID: 28431016 PMCID: PMC5397611 DOI: 10.1093/dnares/dsw060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/14/2016] [Indexed: 01/31/2023] Open
Abstract
Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny. Further investigation of HELPO2 flanking sites showed that gene conversion may contribute to the elimination of such repetitive elements in meiosis, favouring the presence of HELPO2 vacant loci. In addition, the analysis of HELPO2 content in a reconstructed pedigree of subclones maintained under different culture conditions revealed an event of helitron somatic transposition. Additional analyses of genome and transcriptome data indicated that P. ostreatus carries active RNAi machinery that could be involved in the control of transposable element proliferation. Our results provide the first evidence of helitron mobilization in the fungal kingdom and highlight the interaction between genome defence mechanisms and invasive DNA.
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Affiliation(s)
| | | | | | | | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
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36
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Chellapan BV, van Dam P, Rep M, Cornelissen BJC, Fokkens L. Non-canonical Helitrons in Fusarium oxysporum. Mob DNA 2016; 7:27. [PMID: 27990178 PMCID: PMC5148889 DOI: 10.1186/s13100-016-0083-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/03/2016] [Indexed: 01/18/2023] Open
Abstract
Background Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi. Results Here, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics. Conclusions FOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0083-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Biju Vadakkemukadiyil Chellapan
- Department of Computational Biology and Bioinformatics, University of Kerala, Karyavattom Campus, Karyavattom PO, Trivandrum, Kerala India ; Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
| | - Peter van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
| | - Ben J C Cornelissen
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
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37
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Xiong W, Dooner HK, Du C. Rolling-circle amplification of centromeric Helitrons in plant genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:1038-1045. [PMID: 27553634 DOI: 10.1111/tpj.13314] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
The unusual eukaryotic Helitron transposons can readily capture host sequences and are, thus, evolutionarily important. They are presumed to amplify by rolling-circle replication (RCR) because some elements encode predicted proteins homologous to RCR prokaryotic transposases. In support of this replication mechanism, it was recently shown that transposition of a bat Helitron generates covalently closed circular intermediates. Another strong prediction is that RCR should generate tandem Helitron concatemers, yet almost all Helitrons identified to date occur as solo elements in the genome. To investigate alternative modes of Helitron organization in present-day genomes, we have applied the novel computational tool HelitronScanner to 27 plant genomes and have uncovered numerous tandem arrays of partially decayed, truncated Helitrons in all of them. Strikingly, most of these Helitron tandem arrays are interspersed with other repeats in centromeres. Many of these arrays have multiple Helitron 5' ends, but a single 3' end. The number of repeats in any one array can range from a handful to several hundreds. We propose here an RCR model that conforms to the present Helitron landscape of plant genomes. Our study provides strong evidence that plant Helitrons amplify by RCR and that the tandemly arrayed replication products accumulate mostly in centromeres.
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Affiliation(s)
- Wenwei Xiong
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA
| | - Hugo K Dooner
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08801, USA
| | - Chunguang Du
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA
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Helitron-like transposons contributed to the mating system transition from out-crossing to self-fertilizing in polyploid Brassica napus L. Sci Rep 2016; 6:33785. [PMID: 27650318 PMCID: PMC5030654 DOI: 10.1038/srep33785] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/01/2016] [Indexed: 12/19/2022] Open
Abstract
The mating system transition in polyploid Brassica napus (AACC) from out-crossing to selfing is a typical trait to differentiate it from their diploid progenitors. Elucidating the mechanism of mating system transition has profound consequences for understanding the speciation and evolution in B. napus. Functional complementation experiment has shown that the insertion of 3.6 kb into the promoter of self-incompatibility male determining gene, BnSP11-1 leads to its loss of function in B. napus. The inserted fragment was found to be a non-autonomous Helitron transposon. Further analysis showed that the inserted 3.6 kb non-autonomous Helitron transposon was widely distributed in B. napus accessions which contain the S haplotype BnS-1. Through promoter deletion analysis, an enhancer and a putative cis-regulatory element (TTCTA) that were required for spatio-temporal specific expression of BnSP11-1 were identified, and both might be disrupted by the insertion of Helitron transposon. We suggested that the insertion of Helitron transposons in the promoter of BnSP11-1 gene had altered the mating system and might facilitated the speciation of B. napus. Our findings have profound consequences for understanding the self-compatibility in B. napus as well as for the trait variations during evolutionary process of plant polyploidization.
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Dong L, Huo N, Wang Y, Deal K, Wang D, Hu T, Dvorak J, Anderson OD, Luo MC, Gu YQ. Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:495-506. [PMID: 27228577 DOI: 10.1111/tpj.13214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 06/05/2023]
Abstract
Prolamin and resistance gene families are important in wheat food use and in defense against pathogen attacks, respectively. To better understand the evolution of these multi-gene families, the DNA sequence of a 2.8-Mb genomic region, representing an 8.8 cM genetic interval and harboring multiple prolamin and resistance-like gene families, was analyzed in the diploid grass Aegilops tauschii, the D-genome donor of bread wheat. Comparison with orthologous regions from rice, Brachypodium, and sorghum showed that the Ae. tauschii region has undergone dramatic changes; it has acquired more than 80 non-syntenic genes and only 13 ancestral genes are shared among these grass species. These non-syntenic genes, including prolamin and resistance-like genes, originated from various genomic regions and likely moved to their present locations via sequence evolution processes involving gene duplication and translocation. Local duplication of non-syntenic genes contributed significantly to the expansion of gene families. Our analysis indicates that the insertion of prolamin-related genes occurred prior to the separation of the Brachypodieae and Triticeae lineages. Unlike in Brachypodium, inserted prolamin genes have rapidly evolved and expanded to encode different classes of major seed storage proteins in Triticeae species. Phylogenetic analyses also showed that the multiple insertions of resistance-like genes and subsequent differential expansion of each R gene family. The high frequency of non-syntenic genes and rapid local gene evolution correlate with the high recombination rate in the 2.8-Mb region with nine-fold higher than the genome-wide average. Our results demonstrate complex evolutionary dynamics in this agronomically important region of Triticeae species.
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Affiliation(s)
- Lingli Dong
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Karin Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tiezhu Hu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Olin D Anderson
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA.
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Abstract
Helitrons, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of Helitrons called Helentrons, Proto-Helentron, and Helitron2. Helitrons and Helentrons make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in Drosophila and many other animal genomes. The purpose of this review is to summarize what we have learned about Helitrons in the decade since their discovery. First, we describe the history of autonomous Helitrons, and their variants. Second, we explain the common coding features and difference in structure of canonical Helitrons versus the endonuclease-encoding Helentrons. Third, we review how Helitrons and Helentrons are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate Helitrons is carried out and how to validate candidate Helitrons. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where Helitrons are found, including discussions of vertical versus horizontal transfer, the propensity of Helitrons and Helentrons to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.
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Haberer G, Mayer KF, Spannagl M. The big five of the monocot genomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:33-40. [PMID: 26866569 DOI: 10.1016/j.pbi.2016.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/14/2016] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
Monocots represent a monophyletic clade of the angiosperms that - based on fossil and molecular records - originated at around the Early Cretaceous from aquatic and wetland ancestors. Among their members are important crops including maize, wheat, rice, sorghum and barley, accounting for the major source for the daily calorie uptake by humans. Reflecting this importance, the partly large and complex genomes of these plants were major targets for ambitious and innovative sequencing projects, which will be discussed in this review article.
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Affiliation(s)
- Georg Haberer
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Klaus Fx Mayer
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
| | - Manuel Spannagl
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
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Bai Z, Chen J, Liao Y, Wang M, Liu R, Ge S, Wing RA, Chen M. The impact and origin of copy number variations in the Oryza species. BMC Genomics 2016; 17:261. [PMID: 27025496 PMCID: PMC4812662 DOI: 10.1186/s12864-016-2589-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 03/15/2016] [Indexed: 02/16/2023] Open
Abstract
Background Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice. Results Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome ‘Nipponbare’. Using Oryza glaberrima as the outgroup, 80 % of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including OsMADS56, BPH14, OsDCL2b and OsMADS30, implying that CNVs might have contributed to phenotypic variations in rice. Most CNV genes were found to be located in non-co-linear positions by comparison to O. glaberrima. One of the origins of these non-co-linear genes was genomic duplications caused by transposon activity or double-strand break repair. Comprehensive analysis of mutation mechanisms suggested an abundance of CNVs formed by non-homologous end-joining and mobile element insertion. Conclusions This study showed the impact and origin of copy number variations in rice on a genomic scale. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2589-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zetao Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Liao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meijiao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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Maneechot N, Yano CF, Bertollo LAC, Getlekha N, Molina WF, Ditcharoen S, Tengjaroenkul B, Supiwong W, Tanomtong A, de Bello Cioffi M. Genomic organization of repetitive DNAs highlights chromosomal evolution in the genus Clarias (Clariidae, Siluriformes). Mol Cytogenet 2016; 9:4. [PMID: 26793275 PMCID: PMC4719708 DOI: 10.1186/s13039-016-0215-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/07/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The genus Clarias (Clariidae, Siluriformes) contains at least 61 species naturally spread over vast regions of Asia, India and Africa. However, Clarias species have also been introduced in many different countries and represent the most widespread catfishes in the world. These fishes are also known as "walking catfishes" due to their ability to move over land. A large degree of chromosomal variation has been previously found in this family, mainly using conventional cytogenetic investigations, with diploid chromosome numbers ranging between 48 and 100. In this study, we analyzed the karyotype structure and distribution of four repetitive DNA sequences (5S and 18S rDNAs and (CA)15 and (GA)15 microsatellites) in three Clarias species (C. batrachus, C. gariepinus, C. macrocephalus), as well as in a probable natural hybrid of the two latter species from different Thailand river basins. RESULTS Clarias gariepinus and C. macrocephalus had 2n = 56 and 2n = 54, respectively, as well as karyotypes composed mainly by metacentric and submetacentric chromosomes. Their karyotypes differed in the number and location of 5S and 18S rDNA sites and in the degree of microsatellite accumulation. An intermediate chromosomal pattern incorporating those of the parental species was found in the probable hybrid, confirming its interspecific origin. Clarias batrachus had 2n = 104 chromosomes and its karyotype was dominated by mainly acrocentric elements, indicating that unusual multiple centric fissions were involved in its karyotype differentiation. The karyotype of this species presented an unexpected dispersion of ribosomal DNAs, possessing 54 and 12 sites of 5S and 18S rDNAs, respectively, as well as a high accumulation and differential distribution of both microsatellite repeats, representing 'hot spots' for chromosomal rearrangement. CONCLUSION Both conventional and molecular cytogenetic markers were useful tools for demonstrating remarkable evolutionary dynamism and highlighting multiple chromosomal rearrangements and hybridization events correlated with the notable karyotypic diversity of these walking catfishes.
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Affiliation(s)
- Nuntiya Maneechot
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Cassia Fernanda Yano
- />Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | | | - Nuntaporn Getlekha
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Wagner Franco Molina
- />Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN Brazil
| | - Sukhonthip Ditcharoen
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Bundit Tengjaroenkul
- />Department of Veterinary Clinical Medicine, Faculty of Veterinary Medicine, Muang, Khon Kaen 40002 Thailand
- />Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen 40002 Thailand
| | - Weerayuth Supiwong
- />Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000 Thailand
| | - Alongklod Tanomtong
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
- />Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen 40002 Thailand
| | - Marcelo de Bello Cioffi
- />Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
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Roffler S, Menardo F, Wicker T. The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants. Mob DNA 2015; 6:23. [PMID: 26688693 PMCID: PMC4683698 DOI: 10.1186/s13100-015-0054-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/04/2015] [Indexed: 11/29/2022] Open
Abstract
Background Helitrons are Class II transposons which are highly abundant in almost all eukaryotes. However, most Helitrons lack protein coding sequence. These non-autonomous elements are thought to hijack recombinase/helicase (RepHel) and possibly further enzymes from related, autonomous elements. Interestingly, many plant Helitrons contain an additional gene encoding a single-strand binding protein homologous to Replication Factor A (RPA), a highly conserved, single-copy gene found in all eukaryotes. Results Here, we describe the analysis of DHH_Mothra, a high-copy non-autonomous Helitron in the genome of rice (Oryza sativa). Mothra has a low GC-content and consists of two distinct blocs of tandem repeats. Based on homology between their termini, we identified a putative mother element which encodes an RPA-like protein but has no RepHel gene. Additionally, we found a putative autonomous sister-family with strong homology to the Mothra mother element in the RPA protein and terminal sequences, which we propose provides the RepHel domain for the Mothra family. Furthermore, we phylogenetically analyzed the evolutionary history of RPA-like proteins. Interestingly, plant Helitron RPAs (PHRPAs) are only found in monocotyledonous and dicotyledonous plants and they form a monophyletic group which branched off before the eukaryotic “core” RPAs. Conclusions Our data show how erosion of autonomous Helitrons can lead to different “levels” of autonomy within Helitron families and can create highly successful subfamilies of non-autonomous elements. Most importantly, our phylogenetic analysis showed that the PHRPA gene was most likely acquired via horizontal gene transfer from an unknown eukaryotic donor at least 145–300 million years ago in the common ancestor of monocotyledonous and dicotyledonous plants. This might have led to the evolution of a separate branch of the Helitron superfamily in plants. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0054-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Roffler
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Fabrizio Menardo
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Thomas Wicker
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
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Maurer-Alcalá XX, Katz LA. An epigenetic toolkit allows for diverse genome architectures in eukaryotes. Curr Opin Genet Dev 2015; 35:93-9. [PMID: 26649755 DOI: 10.1016/j.gde.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 02/04/2023]
Abstract
Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes are only possible due to the well-developed epigenetic toolkit, which probably existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic tree of life. Here we highlight how the changes in genome architecture in diverse eukaryotes are regulated by epigenetic processes, such as DNA elimination, genome rearrangements, and adaptive changes to genome architecture. The ability to epigenetically modify and regulate genomes has contributed greatly to the diversity of eukaryotes observed today.
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Affiliation(s)
- Xyrus X Maurer-Alcalá
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA.
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Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E. SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. Genome Biol Evol 2015; 7:3286-98. [PMID: 26560340 PMCID: PMC4700967 DOI: 10.1093/gbe/evv219] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The identification of conserved syntenic regions enables discovery of predicted
locations for orthologous and homeologous genes, even when no such gene is present.
This capability means that synteny-based methods are far more effective than sequence
similarity-based methods in identifying true-negatives, a necessity for studying gene
loss and gene transposition. However, the identification of syntenic regions requires
complex analyses which must be repeated for pairwise comparisons between any two
species. Therefore, as the number of published genomes increases, there is a growing
demand for scalable, simple-to-use applications to perform comparative genomic
analyses that cater to both gene family studies and genome-scale studies. We
implemented SynFind, a web-based tool that addresses this need. Given one query
genome, SynFind is capable of identifying conserved syntenic regions in any set of
target genomes. SynFind is capable of reporting per-gene information, useful for
researchers studying specific gene families, as well as genome-wide data sets of
syntenic gene and predicted gene locations, critical for researchers focused on
large-scale genomic analyses. Inference of syntenic homologs provides the basis for
correlation of functional changes around genes of interests between related
organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic
data from over 15,000 organisms from all domains of life as well as supporting
multiple releases of the same organism. SynFind makes use of a powerful job execution
framework that promises scalability and reproducibility. SynFind can be accessed at
http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind
using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.
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Affiliation(s)
- Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Matthew D Bomhoff
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Evan Briones
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona
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Xiong W, Du C. Mining hidden polymorphic sequence motifs from divergent plant helitrons. Mob Genet Elements 2015; 4:1-5. [PMID: 26442169 PMCID: PMC4588551 DOI: 10.4161/21592543.2014.971635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 09/24/2014] [Accepted: 09/29/2014] [Indexed: 12/02/2022] Open
Abstract
As a major driving force of genome evolution, transposons have been deviating from their original connotation as “junk” DNA ever since their important roles were revealed. The recently discovered Helitron transposons have been investigated in diverse eukaryotic genomes because of their remarkable gene-capture ability and other features that are crucial to our current understanding of genome dynamics. Helitrons are not canonical transposons in that they do not end in inverted repeats or create target site duplications, which makes them difficult to identify. Previous methods mainly rely on sequence alignment of conserved Helitron termini or manual curation. The abundance of Helitrons in genomes is still underestimated. We developed an automated and generalized tool, HelitronScanner, that identified a plethora of divergent Helitrons in many plant genomes. A local combinational variable approach as the key component of HelitronScanner offers a more granular representation of conserved nucleotide combinations and therefore is more sensitive in finding divergent Helitrons. This commentary provides an in-depth view of the local combinational variable approach and its association with Helitron sequence patterns. Analysis of Helitron terminal sequences shows that the local combinational variable approach is an efficacious representation of nucleotide patterns imperceptible at a full-sequence level.
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Affiliation(s)
- Wenwei Xiong
- Department of Biology and Molecular Biology; Montclair State University ; Montclair, NJ USA
| | - Chunguang Du
- Department of Biology and Molecular Biology; Montclair State University ; Montclair, NJ USA
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Nani TF, Cenzi G, Pereira DL, Davide LC, Techio VH. Ribosomal DNA in diploid and polyploid Setaria (Poaceae) species: number and distribution. COMPARATIVE CYTOGENETICS 2015; 9:645-660. [PMID: 26753080 PMCID: PMC4698577 DOI: 10.3897/compcytogen.v9i4.5456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/18/2015] [Indexed: 06/05/2023]
Abstract
Setaria Beauvois, 1812 is a genus of economically important forage species, including Setaria italica (Linnaeus, 1753) Beauvois, 1812 and Setaria viridis (Linnaeus, 1753) Beauvois, 1812, closely related species and considered as model systems for studies of C4 plants. However, complications and uncertainties related to taxonomy of other species of the genus are frequent due to the existence of numerous synonyms for the same species or multiple species with the same name, and overlapping of morphological characteristics. Cytogenetic studies in Setaria can be useful for taxonomic and evolutionary studies as well as for applications in breeding. Thus, this study is aimed at locating 45S and 5S rDNA sites through fluorescent in situ hybridization (FISH) in Setaria italica, Setaria viridis and Setaria sphacelata (Schumacher, 1827) Stapf, Hubbard, Moss, 1929 cultivars (cvs.) Narok and Nandi. Setaria italica and Setaria viridis have 18 chromosomes with karyotype formulas 6m + 3sm and 9m, respectively. The location of 45S and 5S rDNA for these species was in different chromosome pairs among the evaluated species. Setaria viridis presented a more symmetrical karyotype, strengthening the ancestral relationship with Setaria italica. Setaria sphacelata cvs. Narok and Nandi have 36 chromosomes, and karyotype formulas 11m+7sm and 16m+2sm, respectively. The 45S rDNA signals for both cultivars were also observed in distinct chromosome pairs; however chromosomes bearing 5S rDNA are conserved. Karyotypic variations found among the studied species are evidence of chromosomal rearrangements.
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Affiliation(s)
- Thaís Furtado Nani
- Federal University of Lavras, Department of Biology, Zip Code 37.200-000, Lavras, Minas Gerais State, Brazil
| | - Gisele Cenzi
- Federal University of Lavras, Department of Biology, Zip Code 37.200-000, Lavras, Minas Gerais State, Brazil
| | - Daniele Lais Pereira
- Federal University of Lavras, Department of Biology, Zip Code 37.200-000, Lavras, Minas Gerais State, Brazil
| | - Lisete Chamma Davide
- Federal University of Lavras, Department of Biology, Zip Code 37.200-000, Lavras, Minas Gerais State, Brazil
| | - Vânia Helena Techio
- Federal University of Lavras, Department of Biology, Zip Code 37.200-000, Lavras, Minas Gerais State, Brazil
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49
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Luo MC, You FM, Li P, Wang JR, Zhu T, Dandekar AM, Leslie CA, Aradhya M, McGuire PE, Dvorak J. Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genomics 2015; 16:707. [PMID: 26383694 PMCID: PMC4574618 DOI: 10.1186/s12864-015-1906-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 09/09/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Mutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis. RESULTS We first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number. CONCLUSION Slow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials.
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Affiliation(s)
- Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, Canada.
| | - Pingchuan Li
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, Canada.
| | - Ji-Rui Wang
- Department of Plant Sciences, University of California, Davis, CA, USA. .,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China.
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Mallikarjuna Aradhya
- United States Department of Agriculture-Agricultural Research Service Clonal Repository, Davis, CA, USA.
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, USA.
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50
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Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B. Genome Biol 2015; 16:188. [PMID: 26353816 PMCID: PMC4563886 DOI: 10.1186/s13059-015-0754-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/13/2015] [Indexed: 02/06/2023] Open
Abstract
Background Bread wheat is not only an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. Recently, we produced a high quality reference sequence of wheat chromosome 3B (774 Mb), which provides an excellent opportunity to study the evolutionary dynamics of a large and polyploid genome, specifically the impact of single gene duplications. Results We find that 27 % of the 3B predicted genes are non-syntenic with the orthologous chromosomes of Brachypodium distachyon, Oryza sativa, and Sorghum bicolor, whereas, by applying the same criteria, non-syntenic genes represent on average only 10 % of the predicted genes in these three model grasses. These non-syntenic genes on 3B have high sequence similarity to at least one other gene in the wheat genome, indicating that hexaploid wheat has undergone massive small-scale interchromosomal gene duplications compared to other grasses. Insertions of non-syntenic genes occurred at a similar rate along the chromosome, but these genes tend to be retained at a higher frequency in the distal, recombinogenic regions. The ratio of non-synonymous to synonymous substitution rates showed a more relaxed selection pressure for non-syntenic genes compared to syntenic genes, and gene ontology analysis indicated that non-syntenic genes may be enriched in functions involved in disease resistance. Conclusion Our results highlight the major impact of single gene duplications on the wheat gene complement and confirm the accelerated evolution of the Triticeae lineage among grasses. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0754-6) contains supplementary material, which is available to authorized users.
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