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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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Meng Y, Su W, Ma Y, Liu L, Gu X, Wu D, Shu X, Lai Q, Tang Y, Wu L, Wang Y. Assessment of genetic diversity and variety identification based on developed retrotransposon-based insertion polymorphism (RBIP) markers in sweet potato (Ipomoea batatas (L.) Lam.). Sci Rep 2021; 11:17116. [PMID: 34429441 PMCID: PMC8385064 DOI: 10.1038/s41598-021-95876-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/28/2021] [Indexed: 11/15/2022] Open
Abstract
Sweet potato, a dicotyledonous and perennial plant, is the third tuber/root crop species behind potato and cassava in terms of production. Long terminal repeat (LTR) retrotransposons are highly abundant in sweet potato, contributing to genetic diversity. Retrotransposon-based insertion polymorphism (RBIP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there have been no transposon marker-based genetic diversity analyses of sweet potato. Here, we reported a structure-based analysis of the sweet potato genome, a total of 21555 LTR retrotransposons, which belonged to the main LTR-retrotransposon subfamilies Ty3-gypsy and Ty1-copia were identified. After searching and selecting using Hidden Markov Models (HMMs), 1616 LTR retrotransposon sequences containing at least two models were screened. A total of 48 RBIP primers were synthesized based on the high copy numbers of conserved LTR sequences. Fifty-six amplicons with an average polymorphism of 91.07% were generated in 105 sweet potato germplasm resources based on RBIP markers. A Unweighted Pair Group Method with Arithmatic Mean (UPGMA) dendrogram, a model-based genetic structure and principal component analysis divided the sweet potato germplasms into 3 groups containing 8, 53, and 44 germplasms. All the three analyses produced significant groupwise consensus. However, almost all the germplasms contained only one primary locus. The analysis of molecular variance (AMOVA) among the groups indicated higher intergroup genetic variation (53%) than intrapopulation genetic variation. In addition, long-term self-retention may cause some germplasm resources to exhibit variable segregation. These results suggest that these sweet potato germplasms are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the utility of RBIP markers for determining the intraspecies variability of sweet potato and have the potential to be used as core primer pairs for variety identification, genetic diversity assessment and linkage map construction. The results could provide a good theoretical reference and guidance for germplasm research and breeding.
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Affiliation(s)
- Yusha Meng
- Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.,Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, 310021, People's Republic of China
| | - Wenjin Su
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Yanping Ma
- Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.,Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, 310021, People's Republic of China
| | - Lei Liu
- Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.,Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, 310021, People's Republic of China
| | - Xingguo Gu
- Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.,Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, 310021, People's Republic of China
| | - Dianxing Wu
- State Key Laboratory of Rice Biology, Institute of Nuclear Agriculture Sciences, Zhejiang University, Hangzhou, 310029, People's Republic of China
| | - Xiaoli Shu
- State Key Laboratory of Rice Biology, Institute of Nuclear Agriculture Sciences, Zhejiang University, Hangzhou, 310029, People's Republic of China
| | - Qixian Lai
- Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.,Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, 310021, People's Republic of China
| | - Yong Tang
- Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.,Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, 310021, People's Republic of China
| | - Liehong Wu
- Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.
| | - Yin Wang
- Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China. .,Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, 310021, People's Republic of China.
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Jiang S, Wang X, Shi C, Luo J. Genome-Wide Identification and Analysis of High-Copy-Number LTR Retrotransposons in Asian Pears. Genes (Basel) 2019; 10:genes10020156. [PMID: 30781727 PMCID: PMC6409787 DOI: 10.3390/genes10020156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 11/16/2022] Open
Abstract
A large proportion of the genome of 'Suli' pear (Pyrus pyrifolia) contains long terminal repeat retrotransposons (LTR-RTs), which suggests that LTR-RTs have played important roles in the evolution of Pyrus. Further analysis of retrotransposons, particularly of high-copy-number LTR-RTs in different species, will provide new insights into the evolutionary history of Pyrus. A total of 4912 putative LTR-RTs classified into 198 subfamilies were identified in the 'Suli' pear genome. Six Asian pear accessions, including cultivars and wild species, were resequenced. The comparison of copy number for each LTR-RT subfamily was evaluated in Pyrus accessions, and data showed up to four-fold differences for some subfamilies. This contrast suggests different fates for retrotransposon families in the evolution of Pyrus. Fourteen high-copy-number subfamilies were identified in Asian pears, and more than 50% of the LTR-RTs in the genomes of all Pyrus accessions were from these 14 identified LTR-RT subfamilies. Their average insertion time was 3.42 million years ago, which suggests that these subfamilies were recently inserted into the genome. Many homologous and specific retrotransposon insertion sites were identified in oriental and occidental pears, suggesting that the duplication of retrotransposons has occurred throughout almost the entire origin and evolution of Pyrus species. The LTR-RTs show high heterogeneity, and their copy numbers vary in different Pyrus species. Thus, our findings suggest that LTR-RTs are an important source of genetic variation among Pyrus species.
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Affiliation(s)
- Shuang Jiang
- Forestry and Pomology Research Institute, Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Xiaoqing Wang
- Forestry and Pomology Research Institute, Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Chunhui Shi
- Forestry and Pomology Research Institute, Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Jun Luo
- Forestry and Pomology Research Institute, Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
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Xue H, Wang S, Yao JL, Deng CH, Wang L, Su Y, Zhang H, Zhou H, Sun M, Li X, Yang J. Chromosome level high-density integrated genetic maps improve the Pyrus bretschneideri 'DangshanSuli' v1.0 genome. BMC Genomics 2018; 19:833. [PMID: 30463521 PMCID: PMC6249763 DOI: 10.1186/s12864-018-5224-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 11/06/2018] [Indexed: 01/23/2023] Open
Abstract
Background Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the European (Pyrus communis) and Chinese (P. bretschneideri) pear genomes have not been published in public databases so far. Results To anchor the scaffolds of P. bretschneideri ‘DangshanSuli’ (DS) v1.0 genome into pseudo-chromosomes, two genetic maps (MH and YM maps) were constructed using half sibling populations of Chinese pear crosses, ‘Mantianhong’ (MTH) × ‘Hongxiangsu’ (HXS) and ‘Yuluxiang’ (YLX) × MTH, from 345 and 162 seedlings, respectively, which were prepared for SNP discovery using genotyping-by-sequencing (GBS) technology. The MH and YM maps, each with 17 linkage groups (LGs), were constructed from 2606 and 2489 SNP markers and spanned 1847 and 1668 cM, respectively, with average marker intervals of 0.7. The two maps were further merged with a previously published genetic map (BD) based on the cross ‘Bayuehong’ (BYH) × ‘Dangshansuli’ (DS) to build a new integrated MH-YM-BD map. By using 7757 markers located on the integrated MH-YM-BD map, 898 scaffolds (400.57 Mb) of the DS v1.0 assembly were successfully anchored into 17 pseudo-chromosomes, accounting for 78.8% of the assembled genome size. About 88.31% of them (793 scaffolds) were directionally anchored with two or more markers on the pseudo-chromosomes. Furthermore, the errors in each pseudo-chromosome (especially 1, 5, 7 and 11) were manually corrected and pseudo-chromosomes 1, 5 and 7 were extended by adding 19, 12 and 14 scaffolds respectively in the newly constructed DS v1.1 genome. Synteny analyses revealed that the DS v1.1 genome had high collinearity with the apple genome, and the homologous fragments between pseudo-chromosomes were similar to those found in previous studies. Moreover, the red-skin trait of Asian pear was mapped to an identical locus as identified previously. Conclusions The accuracy of DS v1.1 genome was improved by using larger mapping populations and merged genetic map. With more than 400 MB anchored to 17 pseudo-chromosomes, the new DS v1.1 genome provides a critical tool that is essential for studies of pear genetics, genomics and molecular breeding. Electronic supplementary material The online version of this article (10.1186/s12864-018-5224-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huabai Xue
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Suke Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Jia-Long Yao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China.,The New Zealand Institute for Plant and Food Research Limited, Auckland, 1025, New Zealand
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland, 1025, New Zealand
| | - Long Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Yanli Su
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Huirong Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Huangkai Zhou
- Guangzhou Gene Denovo Biotechnology Co., Ltd, Guangzhou, 510320, China
| | - Minshan Sun
- Guangzhou Gene Denovo Biotechnology Co., Ltd, Guangzhou, 510320, China
| | - Xiugen Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China.
| | - Jian Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China.
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Kalendar R, Amenov A, Daniyarov A. Use of retrotransposon-derived genetic markers to analyse genomic variability in plants. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 46:15-29. [PMID: 30939255 DOI: 10.1071/fp18098] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/23/2018] [Indexed: 06/09/2023]
Abstract
Transposable elements (TEs) are common mobile genetic elements comprising several classes and making up the majority of eukaryotic genomes. The movement and accumulation of TEs has been a major force shaping the genes and genomes of most organisms. Most eukaryotic genomes are dominated by retrotransposons and minimal DNA transposon accumulation. The 'copy and paste' lifecycle of replicative transposition produces new genome insertions without excising the original element. Horizontal TE transfer among lineages is rare. TEs represent a reservoir of potential genomic instability and RNA-level toxicity. Many TEs appear static and nonfunctional, but some are capable of replicating and mobilising to new positions, and somatic transposition events have been observed. The overall structure of retrotransposons and the domains responsible for the phases of their replication are highly conserved in all eukaryotes. TEs are important drivers of species diversity and exhibit great variety in their structure, size and transposition mechanisms, making them important putative actors in evolution. Because TEs are abundant in plant genomes, various applications have been developed to exploit polymorphisms in TE insertion patterns, including conventional or anchored PCR, and quantitative or digital PCR with primers for the 5' or 3' junction. Alternatively, the retrotransposon junction can be mapped using high-throughput next-generation sequencing and bioinformatics. With these applications, TE insertions can be rapidly, easily and accurately identified, or new TE insertions can be found. This review provides an overview of the TE-based applications developed for plant species and assesses the contributions of TEs to the analysis of plants' genetic diversity.
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Affiliation(s)
- Ruslan Kalendar
- Department of Agricultural Sciences, PO Box 27 (Latokartanonkaari 5), FI-00014 University of Helsinki, Helsinki, Finland
| | - Asset Amenov
- RSE 'National Center for Biotechnology', 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
| | - Asset Daniyarov
- RSE 'National Center for Biotechnology', 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
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Yue X, Zheng X, Zong Y, Jiang S, Hu C, Yu P, Liu G, Cao Y, Hu H, Teng Y. Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia. FRONTIERS IN PLANT SCIENCE 2018; 9:591. [PMID: 29868056 PMCID: PMC5949605 DOI: 10.3389/fpls.2018.00591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/16/2018] [Indexed: 05/03/2023]
Abstract
Asian pear plays an important role in the world pear industry, accounting for over 70% of world total production volume. Commercial Asian pear production relies on four major pear cultivar groups, Japanese pear (JP), Chinese white pear (CWP), Chinese sand pear (CSP), and Ussurian pear (UP), but their origins remain controversial. We estimated the genetic diversity levels and structures in a large sample of existing local cultivars to investigate the origins of Asian pears using twenty-five genome-covering nuclear microsatellite (simple sequence repeats, nSSR) markers and two non-coding chloroplast DNA (cpDNA) regions (trnL-trnF and accD-psaI). High levels of genetic diversity were detected for both nSSRs (HE = 0.744) and cpDNAs (Hd = 0.792). The major variation was found within geographic populations of cultivated pear groups, demonstrating a close relationship among cultivar groups. CSPs showed a greater genetic diversity than CWPs and JPs, and lowest levels of genetic differentiation were detected among them. Phylogeographical analyses indicated that the CSP, CWP, and JP were derived from the same progenitor of Pyrus pyrifolia in China. A dissemination route of cultivated P. pyrifolia estimated by approximate Bayesian computation suggested that cultivated P. pyrifolia from the Middle Yangtze River Valley area contributed the major genetic resources to the cultivars, excluding those of southwestern China. Three major genetic groups of cultivated Pyrus pyrifolia were revealed using nSSRs and a Bayesian statistical inference: (a) JPs; (b) cultivars from South-Central China northward to northeastern China, covering the main pear production area in China; (c) cultivars from southwestern China to southeastern China, including Yunnan, Guizhou, Guangdong, Guangxi, and Fujian Provinces. This reflected the synergistic effects of ecogeographical factors and human selection during cultivar spread and improvement. The analyses indicated that UP cultivars might be originated from the interspecific hybridization of wild Pyrus ussuriensis with cultivated Pyrus pyrifolia. The combination of uniparental DNA sequences and nuclear markers give us a better understanding of origins and genetic relationships for Asian pear groups and will be beneficial for the future improvement of Asian pear cultivars.
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Affiliation(s)
- Xiaoyan Yue
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Xiaoyan Zheng
- College of Ecology, Lishui University, Lishui, China
| | - Yu Zong
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Shuang Jiang
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Chunyun Hu
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Peiyuan Yu
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Guoqin Liu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yufen Cao
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
| | - Hongju Hu
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yuanwen Teng
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
- *Correspondence: Yuanwen Teng,
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Primitive Genepools of Asian Pears and Their Complex Hybrid Origins Inferred from Fluorescent Sequence-Specific Amplification Polymorphism (SSAP) Markers Based on LTR Retrotransposons. PLoS One 2016; 11:e0149192. [PMID: 26871452 PMCID: PMC4752223 DOI: 10.1371/journal.pone.0149192] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/28/2016] [Indexed: 12/25/2022] Open
Abstract
Recent evidence indicated that interspecific hybridization was the major mode of evolution in Pyrus. The genetic relationships and origins of the Asian pear are still unclear because of frequent hybrid events, fast radial evolution, and lack of informative data. Here, we developed fluorescent sequence-specific amplification polymorphism (SSAP) markers with lots of informative sites and high polymorphism to analyze the population structure among 93 pear accessions, including nearly all species native to Asia. Results of a population structure analysis indicated that nearly all Asian pear species experienced hybridization, and originated from five primitive genepools. Four genepools corresponded to four primary Asian species: P. betulaefolia, P. pashia, P. pyrifolia, and P. ussuriensis. However, cultivars of P. ussuriensis were not monophyletic and introgression occurred from P. pyrifolia. The specific genepool detected in putative hybrids between occidental and oriental pears might be from occidental pears. The remaining species, including P. calleryana, P. xerophila, P. sinkiangensis, P. phaeocarpa, P. hondoensis, and P. hopeiensis in Asia, were inferred to be of hybrid origins and their possible genepools were identified. This study will be of great help for understanding the origin and evolution of Asian pears.
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Jiang S, Cai D, Sun Y, Teng Y. Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome. Mob DNA 2016; 7:1. [PMID: 26779288 PMCID: PMC4715297 DOI: 10.1186/s13100-016-0058-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/05/2016] [Indexed: 01/28/2023] Open
Abstract
Background Long terminal repeat (LTR)-retrotransposons constitute 42.4 % of the genome of the ‘Suli’ pear (Pyrus pyrifolia white pear group), implying that retrotransposons have played important roles in Pyrus evolution. Therefore, further analysis of retrotransposons will enhance our understanding of the evolutionary history of Pyrus. Results We identified 1836 LTR-retrotransposons in the ‘Suli’ pear genome, of which 440 LTR-retrotransposons were predicted to contain at least two of three gene models (gag, integrase and reverse transcriptase). Because these were most likely to be functional transposons, we focused our analyses on this set of 440. Most of the LTR-retrotransposons were estimated to have inserted into the genome less than 2.5 million years ago. Sequence analysis showed that the reverse transcriptase component of the identified LTR-retrotransposons was highly heterogeneous. Analyses of transcripts assembled from RNA-Seq databases of two cultivars of Pyrus species showed that LTR-retrotransposons were expressed in the buds and fruit of Pyrus. A total of 734 coding sequences in the ‘Suli’ genome were disrupted by the identified LTR-retrotransposons. Five high-copy-number LTR-retrotransposon families were identified in Pyrus. These families were rarely found in the genomes of Malus and Prunus, but were distributed extensively in Pyrus and abundance varied between species. Conclusions We identified potentially functional, full-length LTR-retrotransposons with three gene models in the ‘Suli’ genome. The analysis of RNA-seq data demonstrated that these retrotransposons are expressed in the organs of pears. The differential copy number of LTR-retrotransposon families between Pyrus species suggests that the transposition of retrotransposons is an important evolutionary force driving the genetic divergence of species within the genus. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0058-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuang Jiang
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058 China ; Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 China
| | - Danying Cai
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021 China
| | - Yongwang Sun
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058 China ; The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, The Ministry of Agriculture of China, Hangzhou, Zhejiang 310058 China ; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, Zhejiang 310058 China
| | - Yuanwen Teng
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058 China ; The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, The Ministry of Agriculture of China, Hangzhou, Zhejiang 310058 China ; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, Zhejiang 310058 China
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