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Navaratna TA, Alansari N, Eisenberg AR, O'Malley MA. Anaerobic fungi contain abundant, diverse, and transcriptionally active Long Terminal Repeat retrotransposons. Fungal Genet Biol 2024; 172:103897. [PMID: 38750926 DOI: 10.1016/j.fgb.2024.103897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/14/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Long Terminal Repeat (LTR) retrotransposons are a class of repetitive elements that are widespread in the genomes of plants and many fungi. LTR retrotransposons have been associated with rapidly evolving gene clusters in plants and virulence factor transfer in fungal-plant parasite-host interactions. We report here the abundance and transcriptional activity of LTR retrotransposons across several species of the early-branching Neocallimastigomycota, otherwise known as the anaerobic gut fungi (AGF). The ubiquity of LTR retrotransposons in these genomes suggests key evolutionary roles in these rumen-dwelling biomass degraders, whose genomes also contain many enzymes that are horizontally transferred from other rumen-dwelling prokaryotes. Up to 10% of anaerobic fungal genomes consist of LTR retrotransposons, and the mapping of sequences from LTR retrotransposons to transcriptomes shows that the majority of clusters are transcribed, with some exhibiting expression greater than 104 reads per kilobase million mapped reads (rpkm). Many LTR retrotransposons are strongly differentially expressed upon heat stress during fungal cultivation, with several exhibiting a nearly three-log10 fold increase in expression, whereas growth substrate variation modulated transcription to a lesser extent. We show that some LTR retrotransposons contain carbohydrate-active enzymes (CAZymes), and the expansion of CAZymes within genomes and among anaerobic fungal species may be linked to retrotransposon activity. We further discuss how these widespread sequences may be a source of promoters and other parts towards the bioengineering of anaerobic fungi.
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Affiliation(s)
- Tejas A Navaratna
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States
| | - Nabil Alansari
- Department of Chemical Engineering, UC Santa Barbara, United States
| | - Amy R Eisenberg
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States
| | - Michelle A O'Malley
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States; Department of Bioengineering, UC Santa Barbara, United States.
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Papolu PK, Ramakrishnan M, Mullasseri S, Kalendar R, Wei Q, Zou L, Ahmad Z, Vinod KK, Yang P, Zhou M. Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1064847. [PMID: 36570931 PMCID: PMC9780303 DOI: 10.3389/fpls.2022.1064847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/21/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR retrotransposons) are the most abundant group of mobile genetic elements in eukaryotic genomes and are essential in organizing genomic architecture and phenotypic variations. The diverse families of retrotransposons are related to retroviruses. As retrotransposable elements are dispersed and ubiquitous, their "copy-out and paste-in" life cycle of replicative transposition leads to new genome insertions without the excision of the original element. The overall structure of retrotransposons and the domains responsible for the various phases of their replication is highly conserved in all eukaryotes. The two major superfamilies of LTR retrotransposons, Ty1/Copia and Ty3/Gypsy, are distinguished and dispersed across the chromosomes of higher plants. Members of these superfamilies can increase in copy number and are often activated by various biotic and abiotic stresses due to retrotransposition bursts. LTR retrotransposons are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. Additionally, LTR retrotransposons influence the gene expression patterns of adjacent genes by modulating potential small interfering RNA (siRNA) and RNA-directed DNA methylation (RdDM) pathways. Furthermore, comparative and evolutionary analysis of the most important crop genome sequences and advanced technologies have elucidated the epigenetics and structural and functional modifications driven by LTR retrotransposon during speciation. However, mechanistic insights into LTR retrotransposons remain obscure in plant development due to a lack of advancement in high throughput technologies. In this review, we focus on the key role of LTR retrotransposons response in plants during heat stress, the role of centromeric LTR retrotransposons, and the role of LTR retrotransposon markers in genome expression and evolution.
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Affiliation(s)
- Pradeep K. Papolu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi, Kerala, India
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Long−Hai Zou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | | | - Ping Yang
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
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Miyao A, Yamanouchi U. Transposable element finder (TEF): finding active transposable elements from next generation sequencing data. BMC Bioinformatics 2022; 23:500. [PMID: 36418944 PMCID: PMC9682801 DOI: 10.1186/s12859-022-05011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Detection of newly transposed events by transposable elements (TEs) from next generation sequence (NGS) data is difficult, due to their multiple distribution sites over the genome containing older TEs. The previously reported Transposon Insertion Finder (TIF) detects TE transpositions on the reference genome from NGS short reads using end sequences of target TE. TIF requires the sequence of target TE and is not able to detect transpositions for TEs with an unknown sequence. RESULT The new algorithm Transposable Element Finder (TEF) enables the detection of TE transpositions, even for TEs with an unknown sequence. TEF is a finding tool of transposed TEs, in contrast to TIF as a detection tool of transposed sites for TEs with a known sequence. The transposition event is often accompanied with a target site duplication (TSD). Focusing on TSD, two algorithms to detect both ends of TE, TSDs and target sites are reported here. One is based on the grouping with TSDs and direct comparison of k-mers from NGS without similarity search. The other is based on the junction mapping of TE end sequence candidates. Both methods succeed to detect both ends and TSDs of known active TEs in several tests with rice, Arabidopsis and Drosophila data and discover several new TEs in new locations. PCR confirmed the detected transpositions of TEs in several test cases in rice. CONCLUSIONS TEF detects transposed TEs with TSDs as a result of TE transposition, sequences of both ends and their inserted positions of transposed TEs by direct comparison of NGS data between two samples. Genotypes of transpositions are verified by counting of junctions of head and tail, and non-insertion sequences in NGS reads. TEF is easy to run and independent of any TE library, which makes it useful to detect insertions from unknown TEs bypassed by common TE annotation pipelines.
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Affiliation(s)
- Akio Miyao
- grid.416835.d0000 0001 2222 0432Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8518 Japan
| | - Utako Yamanouchi
- grid.416835.d0000 0001 2222 0432Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8518 Japan
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Yan Z, Sang L, Ma Y, He Y, Sun J, Ma L, Li S, Miao F, Zhang Z, Huang J, Wang Z, Yang G. A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis. BMC PLANT BIOLOGY 2022; 22:332. [PMID: 35820796 PMCID: PMC9277957 DOI: 10.1186/s12870-022-03707-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/20/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. RESULTS The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism. CONCLUSIONS We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.
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Affiliation(s)
- Zhenfei Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lijun Sang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yue Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yong He
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Juan Sun
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Shuo Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Fuhong Miao
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Zixin Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | | | - Zengyu Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
| | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
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Koo H, Kim S, Park HS, Lee SJ, Paek NC, Cho J, Yang TJ. Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin. Mob DNA 2022; 13:18. [PMID: 35698176 PMCID: PMC9190103 DOI: 10.1186/s13100-022-00274-2] [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: 01/25/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022] Open
Abstract
Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, amplification LTRs of eclDNAs followed by sequencing (ALE-seq) uncover the current transpositional potential of the LTR-RTs. The ALE-seq protocol was validated by identification of Tos17 in callus of Nipponbare cultivar. Here, we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in rice cultivar Dongjin callus based on the ALE-seq technology. Each Oryco family member has paired LTRs with identical sequences and internal domain regions. Comparison of the two LTR-RTs revealed 97% sequence identity in their internal domains and 65% sequence identity in their LTRs. These two putatively active Oryco LTR-RT family members could be used to expand our knowledge of retrotransposition mechanisms and the effects of LTR-RTs on the rice genome.
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Affiliation(s)
- Hyunjin Koo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Soomin Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Sang-Ji Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Jungnam Cho
- CAS-JIC Centre of Excellence for Plant and Microbial Science, 200032, Shanghai, China
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea.
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Wang K, Xiang D, Xia K, Sun B, Khurshid H, Esh AMH, Zhang H. Characterization of Repetitive DNA in Saccharum officinarum and Saccharum spontaneum by Genome Sequencing and Cytological Assays. FRONTIERS IN PLANT SCIENCE 2022; 13:814620. [PMID: 35273624 PMCID: PMC8902033 DOI: 10.3389/fpls.2022.814620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
In most plant species, DNA repeated elements such as satellites and retrotransposons are composing the majority of their genomes. Saccharum officinarum (2n = 8x = 80) and S. spontaneum (2n = 40-128) are the two fundamental donors of modern sugarcane cultivars. These two species are polyploids with large genome sizes and are enriched in repetitive elements. In this work, we adopted a de novo strategy to isolate highly repetitive and abundant sequences in S. officinarum LA Purple and S. spontaneum SES208. The findings obtained from alignment to the genome assemblies revealed that the vast majority of the repeats (97.9% in LA Purple and 96.5% in SES208) were dispersed in the respective genomes. Fluorescence in situ hybridization assays were performed on 27 representative repeats to investigate their distributions and abundances. The results showed that the copies of some highly repeated sequences, including rDNA and centromeric or telomeric repeats, were underestimated in current genome assemblies. The analysis of the raw read mapping strategy showed more copy numbers for all studied repeats, suggesting that copy number underestimation is common for highly repeated sequences in current genome assemblies of LA Purple and SES208. In addition, the data showed that the centromeric retrotransposons in all SES208 centromeres were absent in certain S. spontaneum clones with different ploidies. This rapid turnover of centromeric DNA in sugarcane provides new clues regarding the pattern of centromeric retrotransposon formation and accumulation.
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Affiliation(s)
- Kai Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Dong Xiang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Xia
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bo Sun
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haris Khurshid
- Oilseeds Research Program, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ayman M. H. Esh
- Sugar Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong, China
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Dai SF, Zhu XG, Hutang GR, Li JY, Tian JQ, Jiang XH, Zhang D, Gao LZ. Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza. FRONTIERS IN PLANT SCIENCE 2022; 13:921937. [PMID: 35874017 PMCID: PMC9301470 DOI: 10.3389/fpls.2022.921937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/16/2022] [Indexed: 05/08/2023]
Abstract
Genome size variation and evolutionary forces behind have been long pursued in flowering plants. The genus Oryza, consisting of approximately 25 wild species and two cultivated rice, harbors eleven extant genome types, six of which are diploid (AA, BB, CC, EE, FF, and GG) and five of which are tetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL). To obtain the most comprehensive knowledge of genome size variation in the genus Oryza, we performed flow cytometry experiments and estimated genome sizes of 166 accessions belonging to 16 non-AA genome Oryza species. k-mer analyses were followed to verify the experimental results of the two accessions for each species. Our results showed that genome sizes largely varied fourfold in the genus Oryza, ranging from 279 Mb in Oryza brachyantha (FF) to 1,203 Mb in Oryza ridleyi (HHJJ). There was a 2-fold variation (ranging from 570 to 1,203 Mb) in genome size among the tetraploid species, while the diploid species had 3-fold variation, ranging from 279 Mb in Oryza brachyantha (FF) to 905 Mb in Oryza australiensis (EE). The genome sizes of the tetraploid species were not always two times larger than those of the diploid species, and some diploid species even had larger genome sizes than those of tetraploids. Nevertheless, we found that genome sizes of newly formed allotetraploids (BBCC-) were almost equal to totaling genome sizes of their parental progenitors. Our results showed that the species belonging to the same genome types had similar genome sizes, while genome sizes exhibited a gradually decreased trend during the evolutionary process in the clade with AA, BB, CC, and EE genome types. Comparative genomic analyses further showed that the species with different rice genome types may had experienced dissimilar amplification histories of retrotransposons, resulting in remarkably different genome sizes. On the other hand, the closely related rice species may have experienced similar amplification history. We observed that the contents of transposable elements, long terminal repeats (LTR) retrotransposons, and particularly LTR/Gypsy retrotransposons varied largely but were significantly correlated with genome sizes. Therefore, this study demonstrated that LTR retrotransposons act as an active driver of genome size variation in the genus Oryza.
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Affiliation(s)
- Shuang-feng Dai
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Xun-ge Zhu
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ge-rang Hutang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-yue Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Jia-qi Tian
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Xian-hui Jiang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Dan Zhang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Li-zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Li-zhi Gao,
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Nicolau M, Picault N, Moissiard G. The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. Cells 2021; 10:cells10112952. [PMID: 34831175 PMCID: PMC8616336 DOI: 10.3390/cells10112952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.
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Affiliation(s)
- Melody Nicolau
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Correspondence:
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Sheeja TE, Kumar IPV, Giridhari A, Minoo D, Rajesh MK, Babu KN. Amplified Fragment Length Polymorphism: Applications and Recent Developments. Methods Mol Biol 2021; 2222:187-218. [PMID: 33301096 DOI: 10.1007/978-1-0716-0997-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.
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Affiliation(s)
- Thotten Elampilay Sheeja
- Indian Institute of Spices Research, Kozhikode, Kerala, India.
- Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India.
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Ahmed S, Rashid MAR, Zafar SA, Azhar MT, Waqas M, Uzair M, Rana IA, Azeem F, Chung G, Ali Z, Atif RM. Genome-wide investigation and expression analysis of APETALA-2 transcription factor subfamily reveals its evolution, expansion and regulatory role in abiotic stress responses in Indica Rice (Oryza sativa L. ssp. indica). Genomics 2020; 113:1029-1043. [PMID: 33157261 DOI: 10.1016/j.ygeno.2020.10.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/08/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
Rice is an important cereal crop that serves as staple food for more than half of the world population. Abiotic stresses resulting from changing climatic conditions are continuously threating its yield and production. Genes in APETALA-2 (AP2) family encode transcriptional regulators implicated during regulation of developmental processes and abiotic stress responses but their identification and characterization in indica rice was still missing. In this context, twenty-six genes distributed among eleven chromosomes in Indica rice encoding AP2 transcription-factor subfamily were identified and their diverse haplotypes were studied. Phylogenetic analysis of OsAP2 TF family-members grouped them into three clades indicating conservation of clades among cereals. Segmental duplications were observed to be principal route of evolution, supporting the higher positive selection-pressure, which were estimated to be originated about 10.57 to 56.72 million years ago (MYA). Conserved domain analysis and intron-exon distribution pattern of identified OsAP2s revealed their exclusive distribution among the specific clades of the phylogenetic tree. Moreover, the members of osa-miR172 family were also identified potentially targeting four OsAP2 genes. The real-time quantitative expression profiling of OsAP2s under heat stress conditions in contrasting indica rice genotypes revealed the differential expression pattern of OsAP2s (6 genes up-regulated and 4 genes down-regulated) in stress- and genotype-dependent manner. These findings unveiled the evolutionary pathways of AP2-TF in rice, and can help the functional characterization under developmental and stress responses.
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Affiliation(s)
- Sohaib Ahmed
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Abdul Rehman Rashid
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming 650500, China; Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan.
| | - Syed Adeel Zafar
- National key facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; School of Agriculture Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Muhammad Waqas
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Uzair
- National key facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Iqrar Ahmad Rana
- Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Republic of Korea.
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan 66000, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad-38040 Pakistan.
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11
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Li W, Li K, Zhang QJ, Zhu T, Zhang Y, Shi C, Liu YL, Xia EH, Jiang JJ, Shi C, Zhang LP, Huang H, Tong Y, Liu Y, Zhang D, Zhao Y, Jiang WK, Zhao YJ, Mao SY, Jiao JY, Xu PZ, Yang LL, Yin GY, Gao LZ. Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata, from Illumina and PacBio sequencing reads. THE PLANT GENOME 2020; 13:e20001. [PMID: 33016624 DOI: 10.1002/tpg2.20001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 11/17/2019] [Indexed: 05/24/2023]
Abstract
African wild rice Oryza longistaminata, one of the eight AA- genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high-quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating Illumina and PacBio sequencing datasets. The final genome assembly comprised only 107 scaffolds and was approximately ∼363.5 Mb, representing ∼92.7% of the estimated African wild rice genome (∼392 Mb). The N50 lengths of the assembled contigs and scaffolds were ∼46.49 Kb and ∼6.83 Mb, indicating ∼3.72-fold and ∼18.8-fold improvement in length compared to the earlier released assembly (∼12.5 Kb and 364 Kb, respectively). Aided with Hi-C data and syntenic relationship with O. sativa, these assembled scaffolds were anchored into 12 pseudo-chromosomes. Genome annotation and comparative genomic analysis reveal that lineage-specific expansion of gene families that respond to biotic- and abiotic stresses are of great potential for mining novel alleles to overcome major diseases and abiotic adaptation in rice breeding programs. This reference genome of African wild rice will greatly enlarge the existing database of rice genome resources and unquestionably form a solid base to understand genomic basis underlying highly valued phenotypic traits and search for novel gene sources in O. longistaminata for the future rice breeding programs.
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Affiliation(s)
- Wei Li
- Inst. of Genomics and Bioinformatics, South China Agricultural Univ., Guangzhou, 510642, China
| | - Kui Li
- Inst. of Genomics and Bioinformatics, South China Agricultural Univ., Guangzhou, 510642, China
| | - Qun-Jie Zhang
- Inst. of Genomics and Bioinformatics, South China Agricultural Univ., Guangzhou, 510642, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Ting Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
- College of Life Science, Liaoning Normal Univ., Dalian, 116081, China
| | - Yun Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Cong Shi
- Inst. of Genomics and Bioinformatics, South China Agricultural Univ., Guangzhou, 510642, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Jian-Jun Jiang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Chao Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
- Univ. of the Chinese Acad. of Sciences, Beijing, 100039, China
| | - Li-Ping Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Yuan Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Dan Zhang
- Inst. of Genomics and Bioinformatics, South China Agricultural Univ., Guangzhou, 510642, China
| | - Yuan Zhao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Wen-Kai Jiang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - You-Jie Zhao
- Yunnan Agricultural University, Kunming, 650201, China
| | - Shu-Yan Mao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Jun-Ying Jiao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Ping-Zhen Xu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Li-Li Yang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
| | - Guo-Ying Yin
- Inst. of Genomics and Bioinformatics, South China Agricultural Univ., Guangzhou, 510642, China
| | - Li-Zhi Gao
- Inst. of Genomics and Bioinformatics, South China Agricultural Univ., Guangzhou, 510642, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Inst. of Botany, Chinese Acad. of Sciences, Kunming, 650204, China
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12
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Suguiyama VF, Vasconcelos LAB, Rossi MM, Biondo C, de Setta N. The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages. PLoS One 2019; 14:e0214542. [PMID: 31107873 PMCID: PMC6527191 DOI: 10.1371/journal.pone.0214542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022] Open
Abstract
Long terminal repeat retrotransposons (LTR-RTs) in plant genomes differ in abundance, structure and genomic distribution, reflecting the large number of evolutionary lineages. Elements within lineages can be considered populations, in which each element is an individual in its genomic environment. In this way, it would be reasonable to apply microevolutionary analyses to understand transposable element (TE) evolution, such as those used to study the genetic structure of natural populations. Here, we applied a Bayesian method to infer genetic structure of populations together with classical phylogenetic and dating tools to analyze LTR-RT evolution using the monocot Setaria italica as a model species. In contrast to a phylogeny, the Bayesian clusterization method identifies populations by assigning individuals to one or more clusters according to the most probabilistic scenario of admixture, based on genetic diversity patterns. In this work, each LTR-RT insertion was considered to be one individual and each LTR-RT lineage was considered to be a single species. Nine evolutionary lineages of LTR-RTs were identified in the S. italica genome that had different genetic structures with variable numbers of clusters and levels of admixture. Comprehensive analysis of the phylogenetic, clusterization and time of insertion data allowed us to hypothesize that admixed elements represent sequences that harbor ancestral polymorphic sequence signatures. In conclusion, application of microevolutionary concepts in genome evolution studies is suitable as a complementary approach to phylogenetic analyses to address the evolutionary history and functional features of TEs.
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Affiliation(s)
- Vanessa Fuentes Suguiyama
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | | | - Maria Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cibele Biondo
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Nathalia de Setta
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
- * E-mail:
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13
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Liu Y, El-Kassaby YA. Novel Insights into Plant Genome Evolution and Adaptation as Revealed through Transposable Elements and Non-Coding RNAs in Conifers. Genes (Basel) 2019; 10:genes10030228. [PMID: 30889931 PMCID: PMC6470726 DOI: 10.3390/genes10030228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/03/2023] Open
Abstract
Plant genomes are punctuated by repeated bouts of proliferation of transposable elements (TEs), and these mobile bursts are followed by silencing and decay of most of the newly inserted elements. As such, plant genomes reflect TE-related genome expansion and shrinkage. In general, these genome activities involve two mechanisms: small RNA-mediated epigenetic repression and long-term mutational decay and deletion, that is, genome-purging. Furthermore, the spatial relationships between TE insertions and genes are an important force in shaping gene regulatory networks, their downstream metabolic and physiological outputs, and thus their phenotypes. Such cascading regulations finally set up a fitness differential among individuals. This brief review demonstrates factual evidence that unifies most updated conceptual frameworks covering genome size, architecture, epigenetic reprogramming, and gene expression. It aims to give an overview of the impact that TEs may have on genome and adaptive evolution and to provide novel insights into addressing possible causes and consequences of intimidating genome sizes (20⁻30 Gb) in a taxonomic group, conifers.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
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14
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Choi JY, Purugganan MD. Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice. Mol Biol Evol 2019; 35:365-382. [PMID: 29126199 PMCID: PMC5850837 DOI: 10.1093/molbev/msx284] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on five factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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15
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Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species. G3-GENES GENOMES GENETICS 2017; 7:1875-1885. [PMID: 28413161 PMCID: PMC5473765 DOI: 10.1534/g3.116.037572] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid evolution of LTR retrotransposons not only divergently shaped the architecture of rice genomes but also contributed to the process of speciation and diversification of rice.
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16
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Xia EH, Zhang HB, Sheng J, Li K, Zhang QJ, Kim C, Zhang Y, Liu Y, Zhu T, Li W, Huang H, Tong Y, Nan H, Shi C, Shi C, Jiang JJ, Mao SY, Jiao JY, Zhang D, Zhao Y, Zhao YJ, Zhang LP, Liu YL, Liu BY, Yu Y, Shao SF, Ni DJ, Eichler EE, Gao LZ. The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis. MOLECULAR PLANT 2017; 10:866-877. [PMID: 28473262 DOI: 10.1016/j.molp.2017.04.002] [Citation(s) in RCA: 351] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 05/18/2023]
Abstract
Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.
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Affiliation(s)
- En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Jun Sheng
- Yunnan Agricultural University, Kunming 650204, China
| | - Kui Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Qun-Jie Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Agrobiological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | | | - Yun Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yuan Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Ting Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; College of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Wei Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong Nan
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Cong Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Chao Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Jun Jiang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Shu-Yan Mao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jun-Ying Jiao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Dan Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Yuan Zhao
- Yunnan Agricultural University, Kunming 650204, China
| | - You-Jie Zhao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Li-Ping Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ben-Ying Liu
- National Tea Tree Germplasm Bank, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - Yue Yu
- Macrogene Inc., Seoul 08511, South Korea
| | - Sheng-Fu Shao
- Jinhua International Camellia Germplasm Bank, Jinhua 321000, China
| | - De-Jiang Ni
- Department of Tea Science, Key Lab for Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070 China
| | - Evan E Eichler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
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17
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Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet 2017; 13:e1006630. [PMID: 28212378 PMCID: PMC5338827 DOI: 10.1371/journal.pgen.1006630] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/06/2017] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.
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Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza). PLoS One 2015. [PMID: 26208215 PMCID: PMC4514751 DOI: 10.1371/journal.pone.0132911] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica) and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown. Methodology/Principal Findings We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of Oryza by genomic in situ hybridization (GISH) and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs) and methylation stability of their flanking regions were also assessed. We made the following principle findings: (i) all three triploid hybrids are stable in both chromosome number and gross structure; (ii) stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (iii) alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (iv) transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner. Conclusions/Significance Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus Oryza are chromosomally stable but show immediate and highly stochastic genetic and epigenetic instabilities at the molecular level. These novel hybrids might provide a rich resource of genetic and epigenetic diversities for potential utilization in rice genetic improvements.
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Dhadi SR, Xu Z, Shaik R, Driscoll K, Ramakrishna W. Differential regulation of genes by retrotransposons in rice promoters. PLANT MOLECULAR BIOLOGY 2015; 87:603-13. [PMID: 25697955 DOI: 10.1007/s11103-015-0300-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 02/16/2015] [Indexed: 05/06/2023]
Abstract
Rice genome harbors genes and promoters with retrotransposon insertions. There is very little information about their function. The effect of retrotransposon insertions in four rice promoter regions on gene regulation, was investigated using promoter-reporter gene constructs with and without retrotransposons. Differences in expression levels of gus and egfp reporter genes in forward orientation and rfp in reverse orientation were evaluated in rice plants with transient expression employing quantitative RT-PCR analysis, histochemical GUS staining, and eGFP and RFP fluorescent microscopy. The presence of SINE in the promoter 1 (P1) resulted in higher expression levels of the reporter genes, whereas the presence of LINE in P2 or gypsy LTR retrotransposon in P3 reduced expression of the reporter genes. Furthermore, the SINE in P1 acts as an enhancer in contrast with the LINE in P2 and the gypsy LTR retrotransposon in P3 which act as silencers. CTAA and CGG motifs in these retrotransposons are the likely candidates for the downregulation compared to TCTT motif (SINE) which is a candidate for the upregulation of gene expression. The effect of retrotransposons on gene regulation correlated with the earlier investigation of conservation patterns of these four retrotransposon insertions in several rice accessions implying their evolutionary significance.
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Affiliation(s)
- Surendar Reddy Dhadi
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
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21
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Yadav CB, Bonthala VS, Muthamilarasan M, Pandey G, Khan Y, Prasad M. Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Res 2014; 22:79-90. [PMID: 25428892 PMCID: PMC4379977 DOI: 10.1093/dnares/dsu039] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations. Several TEs are highly polymorphic for insert location in the genome and this facilitates development of TE-based markers for various genotyping purposes. Considering this, a genome-wide analysis was performed in the model plant foxtail millet. A total of 30,706 TEs were identified and classified as DNA transposons (24,386), full-length Copia type (1,038), partial or solo Copia type (10,118), full-length Gypsy type (1,570), partial or solo Gypsy type (23,293) and Long- and Short-Interspersed Nuclear Elements (3,659 and 53, respectively). Further, 20,278 TE-based markers were developed, namely Retrotransposon-Based Insertion Polymorphisms (4,801, ∼24%), Inter-Retrotransposon Amplified Polymorphisms (3,239, ∼16%), Repeat Junction Markers (4,451, ∼22%), Repeat Junction-Junction Markers (329, ∼2%), Insertion-Site-Based Polymorphisms (7,401, ∼36%) and Retrotransposon-Microsatellite Amplified Polymorphisms (57, 0.2%). A total of 134 Repeat Junction Markers were screened in 96 accessions of Setaria italica and 3 wild Setaria accessions of which 30 showed polymorphism. Moreover, an open access database for these developed resources was constructed (Foxtail millet Transposable Elements-based Marker Database; http://59.163.192.83/ltrdb/index.html). Taken together, this study would serve as a valuable resource for large-scale genotyping applications in foxtail millet and related grass species.
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Affiliation(s)
- Chandra Bhan Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Venkata Suresh Bonthala
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | | | - Garima Pandey
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Yusuf Khan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
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Alzohairy AM, Gyulai GB, Ramadan MF, Edris S, Sabir JSM, Jansen RK, Eissa HF, Bahieldin A. Retrotransposon-based molecular markers for assessment of genomic diversity. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:781-789. [PMID: 32481032 DOI: 10.1071/fp13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/19/2014] [Indexed: 06/11/2023]
Abstract
Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in 'repeat seas' or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).
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Affiliation(s)
- Ahmed M Alzohairy
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - G Bor Gyulai
- Institute of Genetics and Biotechnology, St. István University, Gödöll?, H-2103, Hungary
| | - Mohamed F Ramadan
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Sherif Edris
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Jamal S M Sabir
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Robert K Jansen
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Hala F Eissa
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
| | - Ahmed Bahieldin
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
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Li SF, Gao WJ, Zhao XP, Dong TY, Deng CL, Lu LD. Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data. PLoS One 2014; 9:e97189. [PMID: 24810432 PMCID: PMC4014616 DOI: 10.1371/journal.pone.0097189] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/16/2014] [Indexed: 11/19/2022] Open
Abstract
Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory for Microorganisms and Functional Molecules, University of Henan Province, Xinxiang, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory for Microorganisms and Functional Molecules, University of Henan Province, Xinxiang, China
- * E-mail:
| | - Xin-Peng Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, China
| | - Tian-Yu Dong
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory for Microorganisms and Functional Molecules, University of Henan Province, Xinxiang, China
| | - Long-Dou Lu
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory for Microorganisms and Functional Molecules, University of Henan Province, Xinxiang, China
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Zhu T, Xu PZ, Liu JP, Peng S, Mo XC, Gao LZ. Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions. Mol Phylogenet Evol 2013; 70:348-61. [PMID: 24148990 DOI: 10.1016/j.ympev.2013.10.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 08/17/2013] [Accepted: 10/09/2013] [Indexed: 12/17/2022]
Abstract
Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding when and how they diversified have long been an issue of extensive interest but remain a mystery. Here, a data set comprising >60 kb of 53 singleton fragments and 16 intergenic regions is used to perform phylogenomic analyses of all eight AA- genome species plus four diploid Oryza species with BB-, CC-, EE- and GG- genomes. We fully reconstruct phylogenetic relationships of AA- genome species with confidence. Oryza meridionalis, native to Australia, is found to be the earliest divergent lineage around 2.93 mya, whereas O. punctata, a BB- genome species, serves as the best outgroup to distinguish their phylogenetic relationships. They separated from O. punctata approximately 9.11 mya during the Miocene epoch, and subsequently radiated to generate the entire AA- genome lineage diversity. The success in resolving the phylogeny of AA- genome species highlights the potential of phylogenomics to determine their divergence and evolutionary histories.
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Affiliation(s)
- Ting Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming 650204, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
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25
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Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y. The draft genome of sweet orange (Citrus sinensis). Nat Genet 2012. [PMID: 23179022 DOI: 10.1038/ng.2472] [Citation(s) in RCA: 497] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Gao D, Jimenez-Lopez JC, Iwata A, Gill N, Jackson SA. Functional and structural divergence of an unusual LTR retrotransposon family in plants. PLoS One 2012; 7:e48595. [PMID: 23119066 PMCID: PMC3485330 DOI: 10.1371/journal.pone.0048595] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 09/28/2012] [Indexed: 12/24/2022] Open
Abstract
Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and in silico approaches were used to determine the origin of Retrosat2 and putative function of ORF0. Our data show that not only is Retrosat2 highly abundant in the Oryza genus, it may yet be active in rice. Homologs of Retrosat2 were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the Retrosat2 family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of Retrosat2. Unlike the ORF1, the ORF0 sequences from Retrosat2 and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, Retrosat2 and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of Retrosat2 homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species.
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Affiliation(s)
- Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
| | - Jose C. Jimenez-Lopez
- Department of Biochemistry, Cell & Molecular Biology of Plants, Estacion Experimental del Zaidin, High Council for Scientific Research, Granada, Spain
| | - Aiko Iwata
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
| | - Navdeep Gill
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
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Vonholdt BM, Takuno S, Gaut BS. Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol 2012; 29:3193-203. [PMID: 22593226 DOI: 10.1093/molbev/mss129] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In plants, the genome of the host responds to the amplification of transposable elements (TEs) with DNA methylation. However, neither the factors involved in TE methylation nor the dynamics of the host-TE interaction are well resolved. Here, we identify 5,522 long terminal repeat retrotransposons (LTR-RT) in the genome of Oryza sativa ssp. japonica and then assess methylation for individual elements. Our analyses uncover three strong trends: long LTR-RTs are more highly methylated, the insertion times of LTR-RTs are negatively correlated with methylation, and young LTR-RTs tend to be closer to genes than older insertions. Additionally, a phylogenetic examination of the gypsy-like LTR-RT superfamily revealed that methylation is phylogenetically correlated. Given these observations, we present a model suggesting that the phylogenetic correlation among related LTR-RTs is a primary mechanism driving methylation. In this model, bursts of transposition produce new elements with high sequence similarity. The host machinery identifies proliferating elements as well as closely related LTR-RTs through cross-homology. In addition, our data are consistent with previous hypotheses that methylated LTR-RT elements are removed preferentially from regions near genes, explaining some of the observed age distribution.
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Affiliation(s)
- Bridgett M Vonholdt
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
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28
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Di Filippo M, Traini A, D'Agostino N, Frusciante L, Chiusano ML. Euchromatic and heterochromatic compositional properties emerging from the analysis of Solanum lycopersicum BAC sequences. Gene 2012; 499:176-81. [PMID: 22391094 DOI: 10.1016/j.gene.2012.02.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 02/20/2012] [Indexed: 11/15/2022]
Abstract
The consortium responsible for the sequencing of the tomato (Solanum lycopersicum) genome initially focused on the sequencing of the euchromatic regions using a BAC-by-BAC strategy. We analyzed the compositional features of the whole collection of BAC sequences publically available. This analysis highlights specific peculiarities of heterochromatic and euchromatic BACs, in particular: the whole BAC collection has i) a large variability in repeat and gene content, ii) a positive and significant correlation of LTR retrotransposons of the Gypsy class with the repeat content and iii) the preferential location of the SINEs (short interspersed nuclear elements) in BAC sequences showing a low repeat content. Our results point out a typical design of the tomato chromosomes and pave the way for further investigations on the relationship between DNA primary structure and chromatin organization in Solanaceae genomes.
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Affiliation(s)
- Miriam Di Filippo
- University of Naples Federico II, Dept. of Soil, Plant, Environmental and Animal Production Sciences, Via Università 100, 80055 Portici, Italy.
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Abstract
Plant genomes are unique in an intriguing feature: the range of their size variation is unprecedented among living organisms. Although polyploidization contributes to this variability, transposable elements (TEs) seem to play the pivotal role. TEs, often considered intragenomic parasites, not only affect the genome size of the host, but also interact with other genes, disrupting and creating new functions and regulatory networks. Coevolution of plant genomes and TEs has led to tight regulation of TE activity, and growing evidence suggests their relationship became mutualistic. Although the expansions of TEs represent certain costs for the host genomes, they may also bring profits for populations, helping to overcome challenging environmental (biotic/abiotic stress) or genomic (hybridization and allopolyploidization) conditions. In this paper, we discuss the possibility that the possession of inducible TEs may provide a selective advantage for various plant populations.
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30
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Gao LL, Hane JK, Kamphuis LG, Foley R, Shi BJ, Atkins CA, Singh KB. Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing. BMC Genomics 2011; 12:521. [PMID: 22014081 PMCID: PMC3206524 DOI: 10.1186/1471-2164-12-521] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/21/2011] [Indexed: 11/26/2022] Open
Abstract
Background Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. Recent interest is being directed at NLL to improve grain production, disease and pest management and health benefits of the grain. However, studies have been hindered by a lack of extensive genomic resources for the species. Results A NLL BAC library was constructed consisting of 111,360 clones with an average insert size of 99.7 Kbp from cv Tanjil. The library has approximately 12 × genome coverage. Both ends of 9600 randomly selected BAC clones were sequenced to generate 13985 BAC end-sequences (BESs), covering approximately 1% of the NLL genome. These BESs permitted a preliminary characterisation of the NLL genome such as organisation and composition, with the BESs having approximately 39% G:C content, 16.6% repetitive DNA and 5.4% putative gene-encoding regions. From the BESs 9966 simple sequence repeat (SSR) motifs were identified and some of these are shown to be potential markers. Conclusions The NLL BAC library and BAC-end sequences are powerful resources for genetic and genomic research on lupin. These resources will provide a robust platform for future high-resolution mapping, map-based cloning, comparative genomics and assembly of whole-genome sequencing data for the species.
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Affiliation(s)
- Ling-Ling Gao
- Plant Industry, Commonwealth Scientific and Industrial Research Organisation, Private Bag No, 5, Wembley WA 6913, Australia
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Xu Z, Rafi S, Ramakrishna W. Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters. Genome 2011; 54:629-38. [DOI: 10.1139/g11-030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retrotransposons are ubiquitous in higher plant genomes. The presence or absence of retrotransposons in whole genome and high throughput genomic sequence (HTGS) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. Approximately half of the Oryza sativa subsp. japonica ‘Nipponbare’ promoters with retrotransposons conserved in Oryza sativa subsp. indica ‘93-11’ and four wild rice species showed higher sequence conservation in retrotransposon than nonretrotransposon regions. We further investigated, in detail, the evolutionary dynamics of five retrotransposons in the promoter regions of 95 rice genotypes. Our data suggest that four of five insertions (Rp2–Rp5) occurred in the ancestor of AA genome, while the other insertion (Rp1) predates the ancestral divergence of Oryza officinalis (CC genome). Four retrotransposons (Rp2–Rp5) were present in 52% (Rp2), 29% (Rp3), 53% (Rp4), and 43% (Rp5) of the rice genotypes with AA genome type, and the fifth retrotransposon (Rp1) was present in 95% of the rice genotypes with AA, BBCC, or CC genome types. Furthermore, most of these retrotransposons were found to evolve slower than flanking promoter regions, suggesting a role in promoter function for regulating downstream genes.
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Affiliation(s)
- Z. Xu
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - S. Rafi
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - W. Ramakrishna
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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Spliceosomal intron size expansion in domesticated grapevine (Vitis vinifera). BMC Res Notes 2011; 4:52. [PMID: 21385391 PMCID: PMC3058033 DOI: 10.1186/1756-0500-4-52] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 03/08/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spliceosomal introns are important components of eukaryotic genes as their structure, sizes and contents reflect the architecture of gene and genomes. Intron size, determined by both neutral evolution, repetitive elements activities and potential functional constraints, varies significantly in eukaryotes, suggesting unique dynamics and evolution in different lineages of eukaryotic organisms. However, the evolution of intron size, is rarely studied. To investigate intron size dynamics in flowering plants, in particular domesticated grapevines, a survey of intron size and content in wine grape (Vitis vinifera Pinot Noir) genes was conducted by assembling and mapping the transcriptome of V. vinifera genes from ESTs to characterize and analyze spliceosomal introns. RESULTS Uncommonly large size of spliceosomal intron was observed in V. vinifera genome, otherwise inconsistent with overall genome size dynamics when comparing Arabidopsis, Populus and Vitis. In domesticated grapevine, intron size is generally not related to gene function. The composition of enlarged introns in grapevines indicated extensive transposable element (TE) activity within intronic regions. TEs comprise about 80% of the expanded intron space and in particular, recent LTR retrotransposon insertions are enriched in these intronic regions, suggesting an intron size expansion in the lineage leading to domesticated grapevine, instead of size contractions in Arabidopsis and Populus. Comparative analysis of selected intronic regions in V. vinifera cultivars and wild grapevine species revealed that accelerated TE activity was associated with grapevine domestication, and in some cases with the development of specific cultivars. CONCLUSIONS In this study, we showed intron size expansion driven by TE activities in domesticated grapevines, likely a result of long-term vegetative propagation and intensive human care, which simultaneously promote TE proliferation and repress TE removal mechanisms such as recombination. The intron size expansion observed in domesticated grapevines provided an example of rapid plant genome evolution in response to artificial selection and propagation, and may shed light on the important genomic changes during domestication. In addition, the transcriptome approach used to gather intron size data significantly improved annotations of the V. vinifera genome.
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Lin J, Kudrna D, Wing RA. Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis). J Biomed Biotechnol 2010; 2011:476723. [PMID: 21234344 PMCID: PMC3017946 DOI: 10.1155/2011/476723] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/28/2010] [Indexed: 12/17/2022] Open
Abstract
We describe the construction and characterization of a publicly available BAC library for the tea plant, Camellia sinensis. Using modified methods, the library was constructed with the aim of developing public molecular resources to advance tea plant genomics research. The library consists of a total of 401,280 clones with an average insert size of 135 kb, providing an approximate coverage of 13.5 haploid genome equivalents. No empty vector clones were observed in a random sampling of 576 BAC clones. Further analysis of 182 BAC-end sequences from randomly selected clones revealed a GC content of 40.35% and low chloroplast and mitochondrial contamination. Repetitive sequence analyses indicated that LTR retrotransposons were the most predominant sequence class (86.93%-87.24%), followed by DNA retrotransposons (11.16%-11.69%). Additionally, we found 25 simple sequence repeats (SSRs) that could potentially be used as genetic markers.
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Affiliation(s)
- Jinke Lin
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
- Department of Tea Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dave Kudrna
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
| | - Rod A. Wing
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson AZ 85721, USA
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34
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Wang HY, Tian Q, Ma YQ, Wu Y, Miao GJ, Ma Y, Cao DH, Wang XL, Lin C, Pang J, Liu B. Transpositional reactivation of two LTR retrotransposons in rice-Zizania recombinant inbred lines (RILs). Hereditas 2010; 147:264-77. [PMID: 21166796 DOI: 10.1111/j.1601-5223.2010.02181.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hybridization is prevalent in plants, which plays important roles in genome evolution. Apart from direct transfer and recombinatory generation of genetic variations by hybridization, de novo genetic instabilities can be induced by the process per se. One mechanism by which such de novo genetic variability can be generated by interspecific hybridization is transpositional reactivation of quiescent parental transposable elements (TEs) in the nascent hybrids. We have reported previously that introgressive hybridization between rice (Oryza sativa L.) and Zizania latifolia Griseb had induced rampant mobilization of three TEs, a copia-like LTR retrotransposon Tos17, a MITE mPing and a class II TE belonging to the hAT superfamily, Dart/nDart. In this study, we further found that two additional LTR retrotransposons, a gypsy-like (named RIRE2) and a copia-like (named Copia076), were also transpositionally reactivated in three recombinant inbred lines (RILs) derived from introgressive hybridization between rice and Z. latifolia. Novel bands of these two retroelements appeared in the RILs relative to their rice parental line (cv. Matsumae) in Southern blot, suggestive of retrotransposition, which was substantiated by transposon display (TD) and locus-specific PCR amplification for insertion sites. Both elements were found to be transcribed but at variable levels in the leaf tissue of the parental line and the RILs, suggesting that transcriptional control was probably not a mechanism for their transpositional activity in the RILs. Expression analysis of four genes adjacent to de novo insertions by Copia076 revealed marked difference in the transcript abundance for each of the genes between the RILs and their rice parental line, but the alterations in expression appeared unrelated with the retroelement insertions.
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Affiliation(s)
- Hong-Yan Wang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, PR China
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Long L, Ou X, Liu J, Lin X, Sheng L, Liu B. The spaceflight environment can induce transpositional activation of multiple endogenous transposable elements in a genotype-dependent manner in rice. JOURNAL OF PLANT PHYSIOLOGY 2009; 166:2035-45. [PMID: 19628300 DOI: 10.1016/j.jplph.2009.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2009] [Revised: 06/21/2009] [Accepted: 06/21/2009] [Indexed: 05/08/2023]
Abstract
Spaceflight represents a unique environmental condition whereby dysregulated gene expression and genomic instability can be provoked. However, detailed molecular characterization of the nature of genetic changes induced by spaceflight is yet to be documented in a higher eukaryote. Transposable elements (TEs) are ubiquitous and have played a significant role in genome evolution. Mounting evidence indicates that TEs constitute the genomic fraction that is susceptible and responsive to environmental perturbations, and hence, most likely manifesting genetic instabilities in times of stress. A predominant means for TEs to cause genetic instability is via their transpositional activation. Here we show that spaceflight has induced transposition of several endogenous TEs in rice, which belong to distinct classes including the miniature inverted terminal repeat TEs (MITEs) and long-terminal repeat (LTR) retrotransposons. Of three rice lines studied, transposition of TEs were detected in the plants germinated from space-flown dry seeds of two lines (RZ1 and RZ35), which are genetically homogeneous and stabilized recombinant inbred lines (RILs) derived from a pure-line rice cultivar, Matsumae. In contrast, the TEs remained immobile in plants derived from space-flown seeds of Matsumae itself, indicating a genotype-dependent manner of TE transposition under the spaceflight environment. Further examination showed that at least in some cases transposition of TEs was associated with cytosine demethylation within the elements. Moreover, the spaceflight-induced TE activity was heritable to organismal progenies. Thus, our results implicate that the spaceflight environment represents a potent mutagenic environment that can cause genetic instabilities by eliciting transposition of otherwise totally quiescent endogenous TEs in a higher eukaryote.
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Affiliation(s)
- Likun Long
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
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Petit J, Bourgeois E, Stenger W, Bès M, Droc G, Meynard D, Courtois B, Ghesquière A, Sabot F, Panaud O, Guiderdoni E. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus. Mol Genet Genomics 2009; 282:633-52. [PMID: 19856189 DOI: 10.1007/s00438-009-0493-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/06/2009] [Indexed: 11/27/2022]
Abstract
Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O. longistaminata. The presence of Tos17 at three insertion sites was confirmed by retrotransposon-based insertion polymorphism (RBIP) in a sample of O. sativa accessions. The first insertion, located on chromosome 3 was only found in two japonica accessions from the Bhutan region while the second insertion, located on chromosome 10 was specific to the varietal groups 1, 2, and 5. The third insertion located on chromosome 7 corresponds to the only insertion shown active in rice so far, notably in cv. Nipponbare, where it has been extensively used for insertion mutagenesis. This copy was only found in a few varieties of the japonica group 6 and in one group 5 accession. Taken together, these results confirm that Tos17 was probably present in the ancestor of A-genome species and that some copies of the element remained active in some Oryza lineages--notably in O. rufipogon and O. longistaminata--as well as in the indica and japonica O. sativa L. lineages.
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Affiliation(s)
- Julie Petit
- CIRAD, UMR DAP, TAA96/03, 2477 Avenue Agropolis, 34398, Montpellier Cedex 5, France
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Wang H, Chai Y, Chu X, Zhao Y, Wu Y, Zhao J, Ngezahayo F, Xu C, Liu B. Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability. BMC PLANT BIOLOGY 2009; 9:63. [PMID: 19476655 PMCID: PMC2696445 DOI: 10.1186/1471-2229-9-63] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 05/29/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Inter-specific hybridization occurs frequently in plants, which may induce genetic and epigenetic instabilities in the resultant hybrids, allopolyploids and introgressants. It remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression, whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked. RESULTS We report here the identification of a rice mutator-phenotype from a set of rice plants derived from a crossing experiment involving two remote and apparently incompatible species, Oryza sativa L. and Oenothera biennis L. The mutator-phenotype (named Tong211-LP) showed distinct alteration in several traits, with the most striking being substantially enlarged panicles. Expectably, gel-blotting by total genomic DNA of the pollen-donor showed no evidence for introgression. Characterization of Tong211-LP (S0) and its selfed progenies (S1) ruled out contamination (via seed or pollen) or polyploidy as a cause for its dramatic phenotypic changes, but revealed transgenerational mobilization of several previously characterized transposable elements (TEs), including a MITE (mPing), and three LTR retrotransposons (Osr7, Osr23 and Tos17). AFLP and MSAP fingerprinting revealed extensive, transgenerational alterations in cytosine methylation and to a less extent also genetic variation in Tong211-LP and its immediate progenies. mPing mobility was found to correlate with cytosine methylation alteration detected by MSAP but not with genetic variation detected by AFLP. Assay by q-RT-PCR of the steady-state transcript abundance of a set of genes encoding for the various putative DNA methyltransferases, 5-methylcytosine DNA glycosylases, and small interference RNA (siRNA) pathway-related proteins showed that, relative to the rice parental line, heritable perturbation in expression of 12 out of the 13 genes occurred in the mutator-phenotype and its sefled progenies. CONCLUSION Transgenerational epigenetic instability in the form of altered cytosine methylation and its associated TE activity occurred in a rice mutator-phenotype produced by pollinating the rice stigma with pollens of O. biennis. Heritably perturbed homeostatic expression-state of genes involved in maintenance of chromatin structure is likely an underlying cause for the alien pollination-induced transgenerational epigenetic/genetic instability, and which occurred apparently without entailing genome merger or genetic introgression.
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Affiliation(s)
- Hongyan Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Yang Chai
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Xiucheng Chu
- Tonghua Academy of Agricultural Sciences, Hailong 135007, Jilin Province, PR China
| | - Yunyang Zhao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Jihong Zhao
- Tonghua Academy of Agricultural Sciences, Hailong 135007, Jilin Province, PR China
| | - Frédéric Ngezahayo
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
- Key Laboratory of Applied Statistics of MOE, Northeast Normal University, Changchun 130024, PR China
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Iruela M, Pistón F, Cubero JI, Millán T, Barro F, Gil J. The marker SCK13(603) associated with resistance to ascochyta blight in chickpea is located in a region of a putative retrotransposon. PLANT CELL REPORTS 2009; 28:53-60. [PMID: 18815788 DOI: 10.1007/s00299-008-0609-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 09/04/2008] [Accepted: 09/07/2008] [Indexed: 05/08/2023]
Abstract
The sequence characterized amplified region (SCAR) marker SCK13(603), associated with ascochyta blight resistance in a chickpea recombinant inbred line (RIL) population, was used as anchored sequence for genome walking. The PCRs performed in the walking steps to walk in the same direction produced eight bands in 5' direction and five bands in 3' direction with a length ranking from 530 to 2,871 bp. The assembly of the bands sequences along with the sequence of SCK13(603) resulted in 7,815 bp contig. Blastn analyses showed stretches of DNA sequence mainly distributed from the nucleotides 1,500 to 4,500 significantly similar to Medicago truncatula genomic DNA. Three open reading frames (ORFs) were identified and blastp analysis of predicted amino acids sequences revealed that ORF1, ORF2 and ORF3 had significant similarity to a CCHC zinc finger protein, to an integrase, and to a precursor of the glucoamylase s1/s2, respectively, from M. truncatula. The high homology of the putative proteins derived from ORF1 and ORF2 with retrotransposon proteins and the prediction of the existence of conserved domains usually present in retrotransposon proteins indicate that the marker SCK13(603) is located in a region of a putative retrotransposon. The information generated in this study has contributed to increase the knowledge of this important region for blight resistance in chickpea.
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Affiliation(s)
- Marta Iruela
- Dpto. Mejora Genética Vegetal, IAS-CSIC, Córdoba, 14080, Córdoba, Spain
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Wawrzynski A, Ashfield T, Chen NWG, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E, Chacko B, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Howell S, Ilut D, Lai H, Del Campo SM, Metcalf M, O'Bleness M, Pfeil BE, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Tucker DM, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MAS, Young ND, Innes RW. Replication of nonautonomous retroelements in soybean appears to be both recent and common. PLANT PHYSIOLOGY 2008; 148:1760-71. [PMID: 18952860 PMCID: PMC2593652 DOI: 10.1104/pp.108.127910] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Accepted: 10/22/2008] [Indexed: 05/19/2023]
Abstract
Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.
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Affiliation(s)
- Adam Wawrzynski
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res 2008; 19:243-54. [PMID: 19029538 DOI: 10.1101/gr.083360.108] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Although the proliferation of LTR retrotransposons can cause major genomic modification and reorganization, the evolutionary dynamics that affect their frequency in host genomes are poorly understood. We analyzed patterns of genetic variation among LTR retrotransposons from Oryza sativa to investigate the type of selective forces that potentially limit their amplification and subsequent population of a nuclear genome. We performed both intra- and interfamily analyses of patterns of molecular sequence variation across multiple LTR retrotransposon genes. This analysis involved more than 1000 LTR retrotransposon sequences from 14 separate families that varied in both their insertion dates and full-length copy numbers. We uncovered evidence of strong purifying selection across all gene regions, but also indications that rare episodes of positive selection and adaptation to the host genome occur. Furthermore, our results indicate that LTR retrotransposons exhibit different but predictable patterns of sequence variation depending on their date of transposition, suggesting that LTR retrotransposons, regardless of superfamily and family classifications, show similar "life-histories."
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Affiliation(s)
- Regina S Baucom
- Department of Genetics, University of Georgia, Athens, Georgia 30602-7223, USA.
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Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics 2008; 180:1071-86. [PMID: 18780739 DOI: 10.1534/genetics.108.092304] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces.
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Hawkins JS, Hu G, Rapp RA, Grafenberg JL, Wendel JF. Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium. Genome 2008; 51:11-8. [PMID: 18356935 DOI: 10.1139/g07-099] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transposable elements contribute significantly to plant genome evolution in myriad ways, ranging from local insertional mutations to global effects exerted on genome size through accumulation. Differential accumulation and deletion of transposable elements may profoundly affect genome size, even among members of the same genus. One example is that of Gossypium (cotton), where much of the 3-fold genome size variation is due to differential accumulation of one gypsy-like LTR retrotransposon, Gorge3. Copia and non-LTR LINE retrotransposons are also major components of the Gossypium genome, but unlike Gorge3, their extant copy numbers do not correlate with genome size. In the present study, we describe the nature and timing of transposition for copia and LINE retrotransposons in Gossypium. Our findings indicate that copia retrotransposons have been active in each lineage since divergence from a common ancestor, and that they have proliferated in a punctuated manner. However, the evolutionary history of LINEs contrasts markedly with that of the copia retrotransposons. Although LINEs have also been active in each lineage, they have accumulated in a stochastically regular manner, and phylogenetic analysis suggests that extant LINE populations in Gossypium are dominated by ancient insertions. Interestingly, the magnitude of transpositional bursts in each lineage corresponds directly with extant estimated copy number.
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Affiliation(s)
- Jennifer S Hawkins
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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Le QH, Melayah D, Bonnivard E, Petit M, Grandbastien MA. Distribution dynamics of the Tnt1 retrotransposon in tobacco. Mol Genet Genomics 2007; 278:639-51. [PMID: 17786479 DOI: 10.1007/s00438-007-0281-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 07/26/2007] [Accepted: 07/31/2007] [Indexed: 11/29/2022]
Abstract
Retrotransposons contribute significantly to the size, organization and genetic diversity of plant genomes. Although many retrotransposon families have been reported in plants, to this day, the tobacco Tnt1 retrotransposon remains one of the few elements for which active transposition has been shown. Demonstration that Tnt1 activation can be induced by stress has lent support to the hypothesis that, under adverse conditions, transposition can be an important source of genetic variability. Here, we compared the insertion site preference of a collection of newly transposed and pre-existing Tnt1 copies identified in plants regenerated from protoplasts or tissue culture. We find that newly transposed Tnt1 copies are targeted within or close to host gene coding sequences and that the distribution of pre-existing insertions does not vary significantly from this trend. Therefore, in spite of their potential to disrupt neighboring genes, insertions within or near CDS are not preferentially removed with age. Elimination of Tnt1 insertions within or near coding sequences may be relaxed due to the polyploid nature of the tobacco genome. Tnt1 insertions within or near CDS are thus better tolerated and can putatively contribute to the diversification of tobacco gene function.
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Affiliation(s)
- Quang Hien Le
- Biomove, UMR 6547 CNRS Université Blaise Pascal-Clermont-Ferrand II, 24 Ave. des Landais, Aubière cedex, France
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Macas J, Neumann P, Navrátilová A. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics 2007; 8:427. [PMID: 18031571 PMCID: PMC2206039 DOI: 10.1186/1471-2164-8-427] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 11/21/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum). RESULTS Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. CONCLUSION We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35-48% of the genome. These data provide a starting point for further investigations of legume plant genomes based on their global comparative analysis and for the development of more sophisticated approaches for data mining.
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Affiliation(s)
- Jiří Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Pavel Neumann
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Alice Navrátilová
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
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Macas J, Neumann P, Navrátilová A. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics 2007. [PMID: 18031571 DOI: 10.1186/1471‐2164‐8‐427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum). RESULTS Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. CONCLUSION We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35-48% of the genome. These data provide a starting point for further investigations of legume plant genomes based on their global comparative analysis and for the development of more sophisticated approaches for data mining.
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Affiliation(s)
- Jirí Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovská 31, Ceské Budejovice, CZ-37005, Czech Republic.
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Ahsan N, Lee SH, Lee DG, Lee H, Lee SW, Bahk JD, Lee BH. Physiological and protein profiles alternation of germinating rice seedlings exposed to acute cadmium toxicity. C R Biol 2007; 330:735-46. [PMID: 17905393 DOI: 10.1016/j.crvi.2007.08.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 05/25/2007] [Accepted: 08/02/2007] [Indexed: 11/16/2022]
Abstract
Seed germination is a complex physiological process in plants that can be affected severely by heavy metals. The interference of germination by cadmium stress has not been well documented at the proteomic level. In the present study, in order to investigate the protein profile alternations during the germination stage following exposure to cadmium, a proteomic approach has been adopted in combination with morphological and physiological parameters. Seeds were exposed with a wide range of cadmium between 0.2 and 1.0 mM. Increases of cadmium concentration in the medium resulted in increased cadmium accumulation in seeds and TBARS content, whereas germination rate, shoot elongation, biomass, and water content were decreased significantly. Temporal changes of the total proteins were investigated by two-dimensional electrophoresis (2-DE). Twenty-one proteins were identified using MALDI-TOF mass spectrometry, which were upregulated at least 1.5-fold in response to cadmium stress. The identified proteins are involved in several processes, including defense and detoxification, antioxidant, protein biosynthesis, and germination processes. The identification of these proteins in the cadmium stress response provides new insight that can lead to a better understanding of the molecular basis of heavy metal responses of seeds at the germination stage.
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Affiliation(s)
- Nagib Ahsan
- Division of Applied Life Sciences (BK21 & EB-NCRC), Gyeongsang National University, Jinju 660-701, Republic of Korea
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Vitte C, Panaud O, Quesneville H. LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 2007; 8:218. [PMID: 17617907 PMCID: PMC1940013 DOI: 10.1186/1471-2164-8-218] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 07/06/2007] [Indexed: 12/02/2022] Open
Abstract
Background LTR retrotransposons are one of the main causes for plant genome size and structure evolution, along with polyploidy. The characterization of their amplification and subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we performed a detailed analysis of 41 LTR retrotransposon families in rice. Results Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal. Conclusion Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome.
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Affiliation(s)
- Clémentine Vitte
- Laboratoire Ecologie, Systématique et Evolution, Université Paris Sud, Orsay, France
- Laboratoire Bioinformatique et Génomique, Institut Jacques Monod, Paris, France
- Bennetzen laboratory, University of Georgia, Athens, GA, USA
| | - Olivier Panaud
- Laboratoire Génétique et Développement des Plantes, Université de Perpignan, Perpignan, France
| | - Hadi Quesneville
- Laboratoire Bioinformatique et Génomique, Institut Jacques Monod, Paris, France
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Wicker T, Keller B. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res 2007; 17:1072-81. [PMID: 17556529 PMCID: PMC1899118 DOI: 10.1101/gr.6214107] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Although copia retrotransposons are major components of all plant genomes, the evolutionary relationships between individual copia families and between elements from different plant species are only poorly studied. We used 20 copia families from the large-genome plants barley and wheat to identify 46 families of homologous copia elements from rice and 22 from Arabidopsis, two plant species with much smaller genomes. In total, 599 copia elements were analyzed. Phylogenetic analysis showed that copia elements from the four species can be classified into six ancient lineages that existed before the divergence of monocots and dicots. The six lineages show a surprising degree of conservation in sequence organization and other characteristics across species. Additionally, the phylogenetic data suggest at least one case of horizontal gene transfer between the Arabidopsis and rice lineages. Insertion time estimates for 522 high-copy elements showed that retrotransposons from rice were active at different times in waves of activity lasting 0.5-2 million years, depending on the family, whereas elements from wheat and barley had longer periods of activity. We estimated that half of the rice copia elements are truncated or otherwise rearranged after approximately 790,000 yr, which is almost twice the half-life of Arabidopsis elements. In contrast, wheat and barley copia elements appear to have a massively longer half-life, beyond our ability to estimate from the available data. These findings suggest that genome size can be explained by the specific rate of DNA removal from the genome and the length of active periods of retrotransposon families.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University of Zürich, Zürich, Switzerland.
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Lamb JC, Meyer JM, Corcoran B, Kato A, Han F, Birchler JA. Distinct chromosomal distributions of highly repetitive sequences in maize. Chromosome Res 2007; 15:33-49. [PMID: 17295125 DOI: 10.1007/s10577-006-1102-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The majority of genomic DNA in most plant species is made up of repetitive elements including satellites and retrotransposons. The maize genome is intermediate in size and abundance of repetitive elements between small genomes such as Arabidopsis and rice and larger genomes such as wheat. Although repetitive elements are present throughout the maize genome, individual families are non-randomly distributed along chromosomes. In this work we use fluorescence in-situ hybridization (FISH) to examine the distribution of abundant LTR retroelement families and satellites contained in heterochromatic blocks called knobs. Different retroelement families have distinct patterns of hybridization. Prem1 and Tekay, two very closely related elements, both hybridize along the length of all chromosomes but do so with greater intensity near the centromeres, although subtle differences are detectable between the hybridization patterns. Opie, Prem2/Ji, and Huck are enriched away from the centromeres and Grande is distributed uniformly along the chromosomes. Double labeling with proximally and distally enriched elements on pachytene chromosomes produces alternating blocks of element enrichment. The maize elements hybridized in the same general patterns to chromosomes of maize relatives including Zea diploperennis and Tripsacum dactyloides. Additionally, abundant Tripsacum LTR retroelements are enriched in similar chromosomal regions among the different species. The 180 bp knob satellite is present in large blocks at interstitial locations on chromosome arms. With long exposures, smaller sites of hybridization are detected at the ends of chromosomes, adjacent to the telomere tract. This distal position for knob satellites is conserved among Zea and Tripsacum species.
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Affiliation(s)
- Jonathan C Lamb
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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Tam SM, Causse M, Garchery C, Burck H, Mhiri C, Grandbastien MA. The distribution of copia-type retrotransposons and the evolutionary history of tomato and related wild species. J Evol Biol 2007; 20:1056-72. [PMID: 17465916 DOI: 10.1111/j.1420-9101.2007.01293.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Retrotransposons are mobile genetic elements that amplify throughout the genome and may be important contributors of genetic diversity. Their distribution is influenced by element behaviour and host-driven controls. We analysed the distribution of three copia-type retrotransposons, ToRTL1, T135 and Tnt1 using sequence-specific amplification polymorphism in self-compatible (SC) and incompatible (SI) species of Solanum subsection Lycopersicon, and genetically mapped polymorphic insertions in S. lycopersicum (tomato). The majority of polymorphic insertions (61%) are located in centromeric regions of the tomato genome. A significant positive relationship was detected between insertion polymorphisms and mating system, independent of selection as most insertions were found to be neutral. As insertion patterns successfully inferred interspecific relationships of Solanum subsection Lycopersicon, our results suggest that the distribution of ToRTL1, T135 and Tnt1 may essentially be determined by selection removing strongly deleterious insertions, with genetic drift and mating system, but not recombination rate, playing important roles.
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Affiliation(s)
- S M Tam
- Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, INRA, Centre de Versailles, F-78026 Versailles cedex, France
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