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Jin Y, Jia J, Yang Y, Zhu X, Yan H, Mao C, Najeeb A, Luo J, Sun M, Xie Z, Wang X, Huang L. DNAJ protein gene expansion mechanism in Panicoideae and PgDNAJ functional identification in pearl millet. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:149. [PMID: 38836874 DOI: 10.1007/s00122-024-04656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/21/2024] [Indexed: 06/06/2024]
Abstract
KEY MESSAGE Analyze the evolutionary pattern of DNAJ protein genes in the Panicoideae, including pearl millet, to identify and characterize the biological function of PgDNAJ genes in pearl millet. Global warming has become a major factor threatening food security and human development. It is urgent to analyze the heat-tolerant mechanism of plants and cultivate crops that are adapted to high temperature conditions. The Panicoideae are the second largest subfamily of the Poaceae, widely distributed in warm temperate and tropical regions. Many of these species have been reported to have strong adaptability to high temperature stress, such as pearl millet, foxtail millet and sorghum. The evolutionary differences in DNAJ protein genes among 12 Panicoideae species and 10 other species were identified and analyzed. Among them, 79% of Panicoideae DNAJ protein genes were associated with retrotransposon insertion. Analysis of the DNAJ protein pan-gene family in six pearl millet accessions revealed that the non-core genes contained significantly more TEs than the core genes. By identifying and analyzing the distribution and types of TEs near the DNAJ protein genes, it was found that the insertion of Copia and Gypsy retrotransposons provided the source of expansion for the DNAJ protein genes in the Panicoideae. Based on the analysis of the evolutionary pattern of DNAJ protein genes in Panicoideae, the PgDNAJ was obtained from pearl millet through identification. PgDNAJ reduces the accumulation of reactive oxygen species caused by high temperature by activating ascorbate peroxidase (APX), thereby improving the heat resistance of plants. In summary, these data provide new ideas for mining potential heat-tolerant genes in Panicoideae, and help to improve the heat tolerance of other crops.
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Affiliation(s)
- Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiyuan Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuchen Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xin Zhu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunli Mao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Atiqa Najeeb
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinchan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zheni Xie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Cao RB, Chen R, Liao KX, Li H, Xu GB, Jiang XL. Karyotype and LTR-RTs analysis provide insights into oak genomic evolution. BMC Genomics 2024; 25:328. [PMID: 38566015 PMCID: PMC10988972 DOI: 10.1186/s12864-024-10177-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests. RESULTS Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes. CONCLUSION Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.
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Affiliation(s)
- Rui-Bin Cao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Ran Chen
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Ke-Xin Liao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - He Li
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Gang-Biao Xu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Xiao-Long Jiang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China.
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Ning Y, Li Y, Lin HY, Kang EZ, Zhao YX, Dong SB, Li Y, Xia XF, Wang YF, Li CY. Chromosome-Scale Genome Assembly for Clubrush (Bolboschoenus planiculmis) Indicates a Karyotype with High Chromosome Number and Heterogeneous Centromere Distribution. Genome Biol Evol 2024; 16:evae039. [PMID: 38447062 PMCID: PMC10959549 DOI: 10.1093/gbe/evae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024] Open
Abstract
Bolboschoenus planiculmis (F.Schmidt) T.V.Egorova is a typical wetland plant in the species-rich Cyperaceae family. This species contributes prominently to carbon dynamics and trophic integration in wetland ecosystems. Previous studies have reported that the chromosomes of B. planiculmis are holocentric; i.e. they have kinetic activity along their entire length and carry multiple centromeres. This feature was suggested to lead to a rapid genome evolution through chromosomal fissions and fusions and participate to the diversification and ecological success of the Bolboschoenus genus. However, the specific mechanism remains uncertain, partly due to the scarcity of genetic information on Bolboschoenus. We present here the first chromosome-level genome assembly for B. planiculmis. Through the integration of high-quality long-read and short-read data, together with chromatin conformation using Hi-C technology, the ultimate genome assembly was 238.01 Mb with a contig N50 value of 3.61 Mb. Repetitive elements constituted 37.04% of the genome, and 18,760 protein-coding genes were predicted. The low proportion of long terminal repeat retrotransposons (∼9.62%) was similar to that reported for other Cyperaceae species. The Ks (synonymous substitutions per synonymous site) distribution suggested no recent large-scale genome duplication in this genome. The haploid assembly contained a large number of 54 pseudochromosomes with a small mean size of 4.10 Mb, covering most of the karyotype. The results of centromere detection support that not all the chromosomes in B. planiculmis have multiple centromeres, indicating more efforts are needed to fully reveal the specific style of holocentricity in cyperids and its evolutionary significance.
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Affiliation(s)
- Yu Ning
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, China
| | - Yang Li
- Huzhou University, Huzhou, China
| | - Hai Yan Lin
- Institute of Information Technology, Chongqing Academy of Forestry Sciences, Chongqing, China
| | - En Ze Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, China
| | - Yu Xin Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shu Bin Dong
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, China
| | - Xiao Fei Xia
- National Natural History Museum of China, Beijing, China
| | - Yi Fei Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, China
| | - Chun Yi Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
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Lan L, Leng L, Liu W, Ren Y, Reeve W, Fu X, Wu Z, Zhang X. The haplotype-resolved telomere-to-telomere carnation ( Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression. HORTICULTURE RESEARCH 2024; 11:uhad244. [PMID: 38225981 PMCID: PMC10788775 DOI: 10.1093/hr/uhad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/12/2023] [Indexed: 01/17/2024]
Abstract
Carnation (Dianthus caryophyllus) is one of the most valuable commercial flowers, due to its richness of color and form, and its excellent storage and vase life. The diverse demands of the market require faster breeding in carnations. A full understanding of carnations is therefore required to guide the direction of breeding. Hence, we assembled the haplotype-resolved gap-free carnation genome of the variety 'Baltico', which is the most common white standard variety worldwide. Based on high-depth HiFi, ultra-long nanopore, and Hi-C sequencing data, we assembled the telomere-to-telomere (T2T) genome to be 564 479 117 and 568 266 215 bp for the two haplotypes Hap1 and Hap2, respectively. This T2T genome exhibited great improvement in genome assembly and annotation results compared with the former version. The improvements were seen when different approaches to evaluation were used. Our T2T genome first informs the analysis of the telomere and centromere region, enabling us to speculate about specific centromere characteristics that cannot be identified by high-order repeats in carnations. We analyzed allele-specific expression in three tissues and the relationship between genome architecture and gene expression in the haplotypes. This demonstrated that the length of the genes, coding sequences, and introns, the exon numbers and the transposable element insertions correlate with gene expression ratios and levels. The insertions of transposable elements repress expression in gene regulatory networks in carnation. This gap-free finished T2T carnation genome provides a valuable resource to illustrate the genome characteristics and for functional genomics analysis in further studies and molecular breeding.
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Affiliation(s)
- Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch 6150, Western Australia, Australia
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Luhong Leng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weichao Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yonglin Ren
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch 6150, Western Australia, Australia
| | - Wayne Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch 6150, Western Australia, Australia
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoni Zhang
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Su Y, Zeeshan Ul Haq M, Liu X, Li Y, Yu J, Yang D, Wu Y, Liu Y. A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles. PLANTS (BASEL, SWITZERLAND) 2023; 12:3901. [PMID: 38005798 PMCID: PMC10675793 DOI: 10.3390/plants12223901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Casparian strip membrane domain protein-like (CASPL) genes are key genes for the formation and regulation of the Casparian strip and play an important role in plant abiotic stress. However, little research has focused on the members, characteristics, and biological functions of the patchouli PatCASPL gene family. In this study, 156 PatCASPL genes were identified at the whole-genome level. Subcellular localization predicted that 75.6% of PatCASPL proteins reside on the cell membrane. A phylogenetic analysis categorized PatCASPL genes into five subclusters alongside Arabidopsis CASPL genes. In a cis-acting element analysis, a total of 16 different cis-elements were identified, among which the photo-responsive element was the most common in the CASPL gene family. A transcriptome analysis showed that p-hydroxybenzoic acid, an allelopathic autotoxic substance, affected the expression pattern of PatCASPLs, including a total of 27 upregulated genes and 30 down-regulated genes, suggesting that these PatCASPLs may play an important role in the regulation of patchouli continuous cropping obstacles by affecting the formation and integrity of Casparian strip bands. These results provided a theoretical basis for exploring and verifying the function of the patchouli PatCASPL gene family and its role in continuous cropping obstacles.
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Affiliation(s)
- Yating Su
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Muhammad Zeeshan Ul Haq
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Xiaofeng Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Yang Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Jing Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Dongmei Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Yougen Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Ya Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
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Liu B, Zhao M. How transposable elements are recognized and epigenetically silenced in plants? CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102428. [PMID: 37481986 DOI: 10.1016/j.pbi.2023.102428] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023]
Abstract
Plant genomes are littered with transposable elements (TEs). Because TEs are potentially highly mutagenic, host organisms have evolved a set of defense mechanisms to recognize and epigenetically silence them. Although the maintenance of TE silencing is well studied, our understanding of the initiation of TE silencing is limited, but it clearly involves small RNAs and DNA methylation. Once TEs are silent, the silent state can be maintained to subsequent generations. However, under some circumstances, such inheritance is unstable, leading to the escape of TEs to the silencing machinery, resulting in the transcriptional activation of TEs. Epigenetic control of TEs has been found to be closely linked to many other epigenetic phenomena, such as genomic imprinting, and is known to contribute to regulation of genes, especially those near TEs. Here we review and discuss the current models of TE silencing, its unstable inheritance after hybridization, and the effects of epigenetic regulation of TEs on genomic imprinting.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
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7
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Chen Y, Fang T, Su H, Duan S, Ma R, Wang P, Wu L, Sun W, Hu Q, Zhao M, Sun L, Dong X. A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots. PLANT COMMUNICATIONS 2023; 4:100469. [PMID: 36307985 PMCID: PMC10030368 DOI: 10.1016/j.xplc.2022.100469] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/18/2022] [Accepted: 10/23/2022] [Indexed: 05/04/2023]
Abstract
Astragalus membranaceus var. mongholicus (AMM), a member of the Leguminosae, is one of the most important medicinal plants worldwide. The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine. Here, we report the first chromosome-level reference genome of AMM, comprising nine pseudochromosomes with a total size of 1.47 Gb and 27 868 protein-encoding genes. Comparative genomic analysis reveals that AMM has not experienced an independent whole-genome duplication (WGD) event after the WGD event shared by the Papilionoideae species. Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago, which may explain the large size of the AMM genome. Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded, and our data indicate that tandem duplication has been the main driver for expansion of these families. Among the expanded families, the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM, suggesting their roles in the biosynthesis of phenylpropanoid compounds. The functional versatility of 2,3-oxidosqualene cyclase genes in cluster III may play a critical role in the diversification of triterpenoids in AMM. Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.
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Affiliation(s)
- Yi Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ting Fang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - He Su
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou 510120, China
| | - Sifei Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ruirui Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ping Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lin Wu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Wenbin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qichen Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Lianjun Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Xuehui Dong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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Pei MS, Liu HN, Wei TL, Yu YH, Guo DL. Large-scale discovery of non-conventional peptides in grape ( Vitis vinifera L.) through peptidogenomics. HORTICULTURE RESEARCH 2022; 9:uhac023. [PMID: 35531313 PMCID: PMC9070638 DOI: 10.1093/hr/uhac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Non-conventional peptides (NCPs), which are peptides derived from previously unannotated coding sequences, play important biological roles in plants. In this study, we used peptidogenomic methods that integrated mass spectrometry (MS) peptidomics and a six-frame translation database to extensively identify NCPs in grape. In total, 188 and 2021 non-redundant peptides from the Arabidopsis thaliana and Vitis vinifera L. protein database at Ensembl/URGI and an individualized peptidogenomic database were identified. Unlike conventional peptides, these NCPs derived mainly from intergenic, intronic, upstream ORF, 5'UTR, 3'UTR, and downstream ORF regions. These results show that unannotated regions are translated more broadly than we thought. We also found that most NCPs were derived from regions related to phenotypic variations, LTR retrotransposons, and domestication selection, indicating that the NCPs have an important function in complex biological processes. We also found that the NCPs were developmentally specific and had transient and specific functions in grape berry development. In summary, our study is the first to extensively identify NCPs in grape. It demonstrated that there was a large amount of translation in the genome. These results lay a foundation for studying the functions of NCPs and also provide a reference for the discovery of new functional genes in grape.
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Affiliation(s)
- Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Tong-Lu Wei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
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Wang N, Chen S, Xie L, Wang L, Feng Y, Lv T, Fang Y, Ding H. The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses. Ecol Evol 2022; 12:e8637. [PMID: 35222983 PMCID: PMC8848467 DOI: 10.1002/ece3.8637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/07/2022] Open
Abstract
Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.‐Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single‐copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single‐copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132–133 genes, including 85–87 protein‐coding genes, 37–38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37–43 long repeats and 175–178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.
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Affiliation(s)
- NingJie Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - ShuiFei Chen
- Research Center for Nature Conservation and Biodiversity State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains State Environmental Protection Key Laboratory on Biosafety Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment Nanjing China
| | - Lei Xie
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - YueYao Feng
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Ting Lv
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - YanMing Fang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Hui Ding
- Research Center for Nature Conservation and Biodiversity State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains State Environmental Protection Key Laboratory on Biosafety Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment Nanjing China
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10
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Yang Y, Liu X, Shi X, Ma J, Zeng X, Zhu Z, Li F, Zhou M, Guo X, Liu X. A High-Quality, Chromosome-Level Genome Provides Insights Into Determinate Flowering Time and Color of Cotton Rose ( Hibiscus mutabilis). FRONTIERS IN PLANT SCIENCE 2022; 13:818206. [PMID: 35251086 PMCID: PMC8896357 DOI: 10.3389/fpls.2022.818206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Hibiscus mutabilis (cotton rose) is a deciduous shrub or small tree of the Malvaceae family. Here, we report a chromosome-scale assembly of the H. mutabilis genome based on a combination of single-molecule sequencing and Hi-C technology. We obtained an optimized assembly of 2.68 Gb with a scaffold N50 length of 54.7 Mb. An integrated strategy of homology-based, de novo, and transcriptome-based gene predictions identified 118,222 protein-coding genes. Repetitive DNA sequences made up 58.55% of the genome, and LTR retrotransposons were the most common repetitive sequence type, accounting for 53.15% of the genome. Through the use of Hi-C data, we constructed a chromosome-scale assembly in which Nanopore scaffolds were assembled into 46 pseudomolecule sequences. We identified important genes involved in anthocyanin biosynthesis and documented copy number variation in floral regulators. Phylogenetic analysis indicated that H. mutabilis was closely related to H. syriacus, from which it diverged approximately 15.3 million years ago. The availability of cotton rose genome data increases our understanding of the species' genetic evolution and will support further biological research and breeding in cotton rose, as well as other Malvaceae species.
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Affiliation(s)
| | | | | | - Jiao Ma
- Chengdu Botanical Garden, Chengdu, China
| | | | | | - Fangwen Li
- Chengdu Botanical Garden, Chengdu, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Xiaodan Guo
- Novogene Bioinformatics Institute, Beijing, China
| | - Xiaoli Liu
- Chengdu Botanical Garden, Chengdu, China
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11
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Gao Q, Yan D, Song S, Fan Y, Wang S, Liu Y, Huang Y, Rong C, Guo Y, Zhao S, Qin W, Xu J. Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. J Fungi (Basel) 2022; 8:jof8020167. [PMID: 35205921 PMCID: PMC8877449 DOI: 10.3390/jof8020167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 01/02/2023] Open
Abstract
Lentinula edodes is a tetrapolar basidiomycete with two haploid nuclei in each cell during most of their life cycle. Understanding the two haploid nuclei genome structures and their interactions on growth and fruiting body development has significant practical implications, especially for commercial cultivars. In this study, we isolated and assembled the two haploid genomes from a commercial strain of L. edodes using Illumina, HiFi, and Hi-C technologies. The total genome lengths were 50.93 Mb and 49.80 Mb for the two monokaryons SP3 and SP30, respectively, with each assembled into 10 chromosomes with 99.63% and 98.91% anchoring rates, respectively, for contigs more than 100 Kb. Genome comparisons suggest that two haploid nuclei likely derived from distinct genetic ancestries, with ~30% of their genomes being unique or non-syntenic. Consistent with a tetrapolar mating system, the two mating-type loci A (matA) and B (matB) of L. edodes were found located on two different chromosomes. However, we identified a new but incomplete homeodomain (HD) sublocus at ~2.8 Mb from matA in both monokaryons. Our study provides a solid foundation for investigating the relationships among cultivars and between cultivars and wild strains and for studying how two genetically divergent nuclei coordinate to regulate fruiting body formation in L. edodes.
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Affiliation(s)
- Qi Gao
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Dong Yan
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- Correspondence: (D.Y.); (J.X.)
| | - Shuang Song
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yangyang Fan
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Shouxian Wang
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yu Liu
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yu Huang
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- College of Agriculture and Food Engineering, Baise University, 21 Zhongshan Second Street, Youjiang District, Baise 533000, China
| | - Chengbo Rong
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yuan Guo
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Shuang Zhao
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Wentao Qin
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
- Correspondence: (D.Y.); (J.X.)
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12
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Long Terminal Repeat Retrotransposon Afut4 Promotes Azole Resistance of Aspergillus fumigatus by Enhancing the Expression of sac1 Gene. Antimicrob Agents Chemother 2021; 65:e0029121. [PMID: 34516252 DOI: 10.1128/aac.00291-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspergillus fumigatus causes a series of invasive diseases, including the high-mortality invasive aspergillosis, and has been a serious global health threat because of its increased resistance to the first-line clinical triazoles. We analyzed the whole-genome sequence of 15 A. fumigatus strains from China and found that long terminal repeat retrotransposons (LTR-RTs), including Afut1, Afut2, Afut3, and Afut4, are most common and have the largest total nucleotide length among all transposable elements in A. fumigatus. Deleting one of the most enriched Afut4977-sac1 in azole-resistant strains decreased azole resistance and downregulated its nearby gene, sac1, but it did not significantly affect the expression of genes of the ergosterol synthesis pathway. We then discovered that 5'LTR of Afut4977-sac1 had promoter activity and enhanced the adjacent sac1 gene expression. We found that sac1 is important to A. fumigatus, and the upregulated sac1 caused elevated resistance of A. fumigatus to azoles. Finally, we showed that Afut4977-sac1 has an evolution pattern similar to that of the whole genome of azole-resistant strains due to azoles; phylogenetic analysis of both the whole genome and Afut4977-sac1 suggests that the insertion of Afut4977-sac1 might have preceded the emergence of azole-resistant strains. Taking these data together, we found that the Afut4977-sac1 LTR-RT might be involved in the regulation of azole resistance of A. fumigatus by upregulating its nearby sac1 gene.
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13
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Boutanaev AM. Components of Intrageneric Genome Size Dynamics in Plants and Animals. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421080032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Yang Y, Huang L, Xu C, Qi L, Wu Z, Li J, Chen H, Wu Y, Fu T, Zhu H, Saand MA, Li J, Liu L, Fan H, Zhou H, Qin W. Chromosome-scale genome assembly of areca palm (Areca catechu). Mol Ecol Resour 2021; 21:2504-2519. [PMID: 34133844 DOI: 10.1111/1755-0998.13446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
Areca palm (Areca catechu L.; family Arecaceae) is an important tropical medicinal crop and is also used for masticatory and religious purposes in Asia. Improvements to areca properties made by traditional breeding tools have been very slow, and further advances in its cultivation and practical use require genomic information, which is still unavailable. Here, we present a chromosome-scale reference genome assembly for areca by combining Illumina and PacBio data with Hi-C mapping technologies, covering the predicted A. catechu genome length (2.59 Gb, variety "Reyan#1") to an estimated 240× read depth. The assembly was 2.51 Gb in length with a scaffold N50 of 1.7Mb. The scaffolds were then further assembled into 16 pseudochromosomes, with an N50 of 172 Mb. Transposable elements comprised 80.37% of the areca genome, and 68.68% of them were long-terminal repeat retrotransposon elements. The areca palm genome was predicted to harbour 31,571 protein-coding genes and overall, 92.92% of genes were functionally annotated, including enriched and expanded families of genes responsible for biosynthesis of flavonoid, anthocyanin, monoterpenoid and their derivatives. Comparative analyses indicated that A. catechu probably diverged from its close relatives Elaeis guineensis and Cocos nucifera approximately 50.3 million years ago (Ma). Two whole genome duplication events in areca palm were found to be shared by palms and monocots, respectively. This genome assembly and associated resources represents an important addition to the palm genomics community and will be a valuable resource that will facilitate areca palm breeding and improve our understanding of areca palm biology and evolution.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Chunyan Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lan Qi
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Jia Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Tao Fu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hui Zhu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Liyun Liu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Haikou Fan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Huanqi Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Weiquan Qin
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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15
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Yañez-Santos AM, Paz RC, Paz-Sepúlveda PB, Urdampilleta JD. Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences. Chromosome Res 2021; 29:261-284. [PMID: 34086192 DOI: 10.1007/s10577-021-09663-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/01/2023]
Abstract
Capsicum annuum is a species that has undergone an expansion of the size of its genome caused mainly by the amplification of repetitive DNA sequences, including mobile genetic elements. Based on information obtained from sequencing the genome of pepper, the estimated fraction of retroelements is approximately 81%, and previous results revealed an important contribution of lineages derived from Gypsy superfamily. However, the dynamics of the retroelements in the C. annuum genome is poorly understood. In this way, the present work seeks to investigate the phylogenetic diversity and genomic abundance of the families of autonomous (complete and intact) LTR retroelements from C. annuum and inspect their distribution along its chromosomes. In total, we identified 1151 structurally full-length retroelements (340 Copia; 811 Gypsy) grouped in 124 phylogenetic families in the base of their retrotranscriptase. All the evolutive lineages of LTR retroelements identified in plants were present in pepper; however, three of them comprise 83% of the entire LTR retroelements population, the lineages Athila, Del/Tekay, and Ale/Retrofit. From them, only three families represent 70.8% of the total number of the identified retroelements. A massive family-specific wave of amplification of two of them occurred in the last 0.5 Mya (GypsyCa_16; CopiaCa_01), whereas the third is more ancient and occurred 3.0 Mya (GypsyCa_13). Fluorescent in situ hybridization performed with family and lineage-specific probes revealed contrasting patterns of chromosomal affinity. Our results provide a database of the populations LTR retroelements specific to C. annuum genome. The most abundant families were analyzed according to chromosome insertional preferences, suppling useful tools to the design of retroelement-based markers specific to the species.
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Affiliation(s)
- Anahí Mara Yañez-Santos
- CIGEOBIO (FCEFyN, UNSJ/CONICET), Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia, San Juan, Argentina.,Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
| | - Rosalía Cristina Paz
- CIGEOBIO (FCEFyN, UNSJ/CONICET), Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia, San Juan, Argentina.
| | - Paula Beatriz Paz-Sepúlveda
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET) - Comisión de Investigaciones Científicas (CIC) - Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Juan Domingo Urdampilleta
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
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16
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Yang Y, Bocs S, Fan H, Armero A, Baudouin L, Xu P, Xu J, This D, Hamelin C, Iqbal A, Qadri R, Zhou L, Li J, Wu Y, Ma Z, Issali AE, Rivallan R, Liu N, Xia W, Peng M, Xiao Y. Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance. Commun Biol 2021; 4:105. [PMID: 33483627 PMCID: PMC7822834 DOI: 10.1038/s42003-020-01593-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 12/09/2020] [Indexed: 01/30/2023] Open
Abstract
Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n = 32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398, Montpellier, France
| | - Haikuo Fan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Alix Armero
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Luc Baudouin
- CIRAD, UMR AGAP, F-34398, Montpellier, France.
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.
| | - Pengwei Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Junyang Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Dominique This
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Chantal Hamelin
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398, Montpellier, France
| | - Amjad Iqbal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Rashad Qadri
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Lixia Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Zilong Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, P. R. China
| | - Auguste Emmanuel Issali
- Station Cocotier Marc Delorme, Centre National De Recherche Agronomique (CNRA)07 B.P. 13, Port Bouet, Côte d'Ivoire
| | - Ronan Rivallan
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Na Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Wei Xia
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, P. R. China.
| | - Yong Xiao
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
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17
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Liu B, Iwata-Otsubo A, Yang D, Baker RL, Liang C, Jackson SA, Liu S, Ma J, Zhao M. Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:34-48. [PMID: 33098166 DOI: 10.1111/tpj.15037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/19/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
In comparison with retrotransposons, DNA transposons make up a smaller proportion of most plant genomes. However, these elements are often proximal to genes to affect gene expression depending on the activity of the transposons, which is largely reflected by the activity of the transposase genes. Here, we show that three AT-rich introns were retained in the TNP2-like transposase genes of the Bot1 (Brassica oleracea transposon 1) CACTA transposable elements in Brassica oleracea, but were lost in the majority of the Bot1 elements in Brassica rapa. A recent burst of transposition of Bot1 was observed in B. oleracea, but not in B. rapa. This burst of transposition is likely related to the activity of the TNP2-like transposase genes as the expression values of the transposase genes were higher in B. oleracea than in B. rapa. In addition, distinct populations of small RNAs (21, 22 and 24 nt) were detected from the Bot1 elements in B. oleracea, but the vast majority of the small RNAs from the Bot1 elements in B. rapa are 24 nt in length. We hypothesize that the different activity of the TNP2-like transposase genes is likely associated with the three introns, and intron loss is likely reverse transcriptase mediated. Furthermore, we propose that the Bot1 family is currently undergoing silencing in B. oleracea, but has already been silenced in B. rapa. Taken together, our data provide new insights into the differentiation of transposons and their role in the asymmetric evolution of these two closely related Brassica species.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Aiko Iwata-Otsubo
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602,, USA
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Robert L Baker
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602,, USA
| | - Shengyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, OH, 45056, USA
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18
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Zhang SJ, Liu L, Yang R, Wang X. Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:321-332. [PMID: 33137519 PMCID: PMC7801240 DOI: 10.1016/j.gpb.2018.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/31/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022]
Abstract
The dynamic activity of transposable elements (TEs) contributes to the vast diversity of genome size and architecture among plants. Here, we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons (LTR-RTs) in Arabidopsis thaliana (Ath) and three of its relatives, Arabidopsis lyrata (Aly), Eutrema salsugineum (Esa), and Schrenkiella parvula (Spa), in Brassicaceae. Our analyses revealed the distinct evolutionary dynamics of Gypsyretrotransposons, which reflects the different patterns of genome size changes of the four species over the past million years. The rate of Gypsy transposition in Aly is approximately five times more rapid than that of Ath and Esa, suggesting an expanding Aly genome. Gypsy insertions in Esa are strictly confined to pericentromeric heterochromatin and associated with dramatic centromere expansion. In contrast, Gypsy insertions in Spa have been largely suppressed over the last million years, likely as a result of a combination of an inherent molecular mechanism of preferential DNA removal and purifying selection at Gypsy elements. Additionally, species-specific clades of Gypsy elements shaped the distinct genome architectures of Aly and Esa.
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Affiliation(s)
- Shi-Jian Zhang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Lei Liu
- Beijing Key Laboratory of Plant Resources Research and Development, School of Sciences, Beijing Technology and Business University, Beijing 100048, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China.
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19
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Zhang Z, Qu C, Zhang K, He Y, Zhao X, Yang L, Zheng Z, Ma X, Wang X, Wang W, Wang K, Li D, Zhang L, Zhang X, Su D, Chang X, Zhou M, Gao D, Jiang W, Leliaert F, Bhattacharya D, De Clerck O, Zhong B, Miao J. Adaptation to Extreme Antarctic Environments Revealed by the Genome of a Sea Ice Green Alga. Curr Biol 2020; 30:3330-3341.e7. [PMID: 32619486 DOI: 10.1016/j.cub.2020.06.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 01/21/2023]
Abstract
The unicellular green alga Chlamydomonas sp. ICE-L thrives in polar sea ice, where it tolerates extreme low temperatures, high salinity, and broad seasonal fluctuations in light conditions. Despite the high interest in biotechnological uses of this species, little is known about the adaptations that allow it to thrive in this harsh and complex environment. Here, we assembled a high-quality genome sequence of ∼542 Mb and found that retrotransposon proliferation contributed to the relatively large genome size of ICE-L when compared to other chlorophytes. Genomic features that may support the extremophilic lifestyle of this sea ice alga include massively expanded gene families involved in unsaturated fatty acid biosynthesis, DNA repair, photoprotection, ionic homeostasis, osmotic homeostasis, and reactive oxygen species detoxification. The acquisition of multiple ice binding proteins through putative horizontal gene transfer likely contributed to the origin of the psychrophilic lifestyle in ICE-L. Additional innovations include the significant upregulation under abiotic stress of several expanded ICE-L gene families, likely reflecting adaptive changes among diverse metabolic processes. Our analyses of the genome, transcriptome, and functional assays advance general understanding of the Antarctic green algae and offer potential explanations for how green plants adapt to extreme environments.
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Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Changfeng Qu
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Kaijian Zhang
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Yingying He
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Zhou Zheng
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Xixi Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Wenyu Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Kai Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Dan Li
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Liping Zhang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xin Zhang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Danyan Su
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Xin Chang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Dan Gao
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Frederik Leliaert
- Biology Department, Ghent University, 9000 Ghent, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China.
| | - Jinlai Miao
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China.
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20
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Boutanaev AM, Nemchinov LG. Genome Size Dynamics within Multiple Genera of Diploid Seed Plants. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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da Costa ZP, Cauz-Santos LA, Ragagnin GT, Van Sluys MA, Dornelas MC, Berges H, de Mello Varani A, Vieira MLC. Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis. Mol Biol Rep 2019; 46:6117-6133. [DOI: 10.1007/s11033-019-05047-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/28/2019] [Indexed: 12/23/2022]
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22
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Lantican DV, Strickler SR, Canama AO, Gardoce RR, Mueller LA, Galvez HF. De Novo Genome Sequence Assembly of Dwarf Coconut ( Cocos nucifera L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species. G3 (BETHESDA, MD.) 2019; 9:2377-2393. [PMID: 31167834 PMCID: PMC6686914 DOI: 10.1534/g3.119.400215] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/31/2019] [Indexed: 11/23/2022]
Abstract
We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. The draft genome was improved through Chicago sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality.
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Affiliation(s)
- Darlon V Lantican
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | | | - Alma O Canama
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | - Roanne R Gardoce
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | | | - Hayde F Galvez
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
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23
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Orozco-Arias S, Isaza G, Guyot R. Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. Int J Mol Sci 2019; 20:E3837. [PMID: 31390781 PMCID: PMC6696364 DOI: 10.3390/ijms20153837] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales 170001, Colombia
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Romain Guyot
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales 170001, Colombia.
- Institut de Recherche pour le Développement, CIRAD, University Montpellier, 34000 Montpellier, France.
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24
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Bayless AM, Zapotocny RW, Han S, Grunwald DJ, Amundson KK, Bent AF. The rhg1-a ( Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene. PLANT DIRECT 2019; 3:e00164. [PMID: 31468029 PMCID: PMC6712407 DOI: 10.1002/pld3.164] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/13/2019] [Accepted: 08/02/2019] [Indexed: 05/14/2023]
Abstract
Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a ("Peking-type," low-copy number, three or fewer Rhg1 repeats) and rhg1-b ("PI 88788-type," high-copy number, four or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode α-SNAP (alpha-Soluble NSF Attachment Protein) variants α-SNAP Rhg1 LC and α-SNAP Rhg1 HC, respectively, with differing atypical C-terminal domains, that contribute to SCN resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (α-SNAP-encoding) gene. We termed this retrotransposon "RAC," for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1WT (single-copy) soybeans. RAC is an intact element residing within intron 1, anti-sense to the rhg1-a α-SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic α-SNAP Rhg1 LC mRNA and protein abundance were not detected. From the native rhg1-a RAC+ genomic context, elevated α-SNAP Rhg1 LC protein abundance was observed in syncytium cells, as was previously observed for α-SNAP Rhg1 HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just ~42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded α-SNAPRhg1LC, and thus, they are not rhg1-a. rhg1-a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1-a haplotypes.
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Affiliation(s)
- Adam M. Bayless
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Ryan W. Zapotocny
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Shaojie Han
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | | | - Kaela K. Amundson
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Andrew F. Bent
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
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25
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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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26
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Munhoz CF, Costa ZP, Cauz-Santos LA, Reátegui ACE, Rodde N, Cauet S, Dornelas MC, Leroy P, Varani ADM, Bergès H, Vieira MLC. A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species. Sci Rep 2018; 8:13024. [PMID: 30158558 PMCID: PMC6115403 DOI: 10.1038/s41598-018-31330-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022] Open
Abstract
Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes.
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Affiliation(s)
- Carla Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Zirlane Portugal Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Luiz Augusto Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Alina Carmen Egoávil Reátegui
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Nathalie Rodde
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Stéphane Cauet
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Marcelo Carnier Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brazil
| | - Philippe Leroy
- INRA, UCA, UMR 1095, GDEC, 63000, Clermont-Ferrand, France
| | - Alessandro de Mello Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, 14884-900, Jaboticabal, Brazil
| | - Hélène Bergès
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
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27
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Lyu H, He Z, Wu CI, Shi S. Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes. THE NEW PHYTOLOGIST 2018; 217:428-438. [PMID: 28960318 DOI: 10.1111/nph.14784] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/10/2017] [Indexed: 05/18/2023]
Abstract
Several clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing. To study this molecular convergence, we sequenced multiple mangrove genomes. In this study, we focused on the evolution of transposable elements (TEs) in relation to the genome size evolution. TEs, generally considered genomic parasites, are the most common components of woody plant genomes. Analyzing the long terminal repeat-retrotransposon (LTR-RT) type of TE, we estimated their death rates by counting solo-LTRs and truncated elements. We found that all lineages of mangroves massively and convergently reduce TE loads in comparison to their nonmangrove relatives; as a consequence, genome size reduction happens independently in all six mangrove lineages; TE load reduction in mangroves can be attributed to the paucity of young elements; the rarity of young LTR-RTs is a consequence of fewer births rather than access death. In conclusion, mangrove genomes employ a convergent strategy of TE load reduction by suppressing element origination in their independent adaptation to a new environment.
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Affiliation(s)
- Haomin Lyu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
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28
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Xu Z, Liu J, Ni W, Peng Z, Guo Y, Ye W, Huang F, Zhang X, Xu P, Guo Q, Shen X, Du J. GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3084694. [PMID: 28365739 PMCID: PMC5467567 DOI: 10.1093/database/bax013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/13/2017] [Indexed: 11/21/2022]
Abstract
Although several diploid and tetroploid Gossypium species genomes have been sequenced, the well annotated web-based transposable elements (TEs) database is lacking. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the cotton genome, a comprehensive, specific, and user-friendly web-based database, Gossypium raimondii transposable elements database (GrTEdb), was constructed. A total of 14 332 TEs were structurally annotated and clearly categorized in G. raimondii genome, and these elements have been classified into seven distinct superfamilies based on the order of protein-coding domains, structures and/or sequence similarity, including 2929 Copia-like elements, 10 368 Gypsy-like elements, 299 L1, 12 Mutators, 435 PIF-Harbingers, 275 CACTAs and 14 Helitrons. Meanwhile, the web-based sequence browsing, searching, downloading and blast tool were implemented to help users easily and effectively to annotate the TEs or TE fragments in genomic sequences from G. raimondii and other closely related Gossypium species. GrTEdb provides resources and information related with TEs in G. raimondii, and will facilitate gene and genome analyses within or across Gossypium species, evaluating the impact of TEs on their host genomes, and investigating the potential interaction between TEs and protein-coding genes in Gossypium species. Database URL: http://www.grtedb.org/
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Affiliation(s)
- Zhenzhen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Liu
- Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wanchao Ni
- Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhen Peng
- Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yue Guo
- Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology, The Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fang Huang
- Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xianggui Zhang
- Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Peng Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Qi Guo
- Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jianchang Du
- Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Yin H, Wu X, Shi D, Chen Y, Qi K, Ma Z, Zhang S. TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species. Mob DNA 2017; 8:14. [PMID: 29093758 PMCID: PMC5659011 DOI: 10.1186/s13100-017-0098-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/18/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5'-'TG'-'CA'-3' motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures and evolutionary history. RESULTS Here, we report two new LTR-RT subfamilies (TGTT and AACA) with atypical dinucleotide ends of 5'-'TG'-'TT'-3', and 5'-'AA'-'CA'-3' in pear, apple, peach and mei. In total, 91 intact LTR-RTs were identified and classified into four TGTT and four AACA families. A structural annotation analysis showed that the four TGTT families, together with AACA1 and AACA2, belong to the Copia-like superfamily, whereas AACA3 and AACA4 appeared to be TRIM elements. The average amplification time frames for the eight families ranged from 0.05 to 2.32 million years. Phylogenetics coupled with sequence analyses revealed that the TGTT1 elements of peach were horizontally transferred from apple. In addition, 32 elements from two TGTT and three AACA families had detectable transcriptional activation, and a qRT-PCR analysis indicated that their expression levels varied dramatically in different species, organs and stress treatments. CONCLUSIONS Two novel LTR-RT subfamilies that terminated with non-palindromic dinucleotides at the ends of their LTRs were identified in four Rosaceae species, and a deep analysis showed their recent activity, horizontal transfer and varied transcriptional levels in different species, organs and stress treatments. This work enhances our understanding of the structural variation and evolutionary history of LTR-RTs in plants and also provides a valuable resource for future investigations of LTR-RTs having specific structures in other species.
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Affiliation(s)
- Hao Yin
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiao Wu
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Dongqing Shi
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yangyang Chen
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kaijie Qi
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Zhengqiang Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Li Q, Zhang Y, Zhang Z, Li X, Yao D, Wang Y, Ouyang X, Li Y, Song W, Xiao Y. A D-genome-originated Ty1/Copia-type retrotransposon family expanded significantly in tetraploid cottons. Mol Genet Genomics 2017; 293:33-43. [PMID: 28849273 DOI: 10.1007/s00438-017-1359-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
Retrotransposons comprise of a major fraction of higher plant genomes, and their proliferation and elimination have profound effects on genome evolution and gene functions as well. Previously we found a D-genome-originated Ty1/Copia-type LTR (DOCL) retrotransposon in the chromosome A08 of upland cotton. To further characterize the DOCL retrotransposon family, a total of 342 DOCL retrotransposons were identified in the sequenced cotton genomes, including 73, 157, and 112 from Gossypium raimondii, G. hirsutum, and G. barbadense, respectively. According to phylogenetic analysis, the DOCL family was divided into nine groups (G1-G9), among which five groups (G1-G4 and G9, including 292 members) were proliferated after the formation of tetraploid cottons. It was found that the majority of DOCL retrotransposons (especially those in G2, G3 and G9) inserted in non-allelic loci in G. hirsutum and G. barbadense, suggesting that their proliferations were relatively independent in different tetraploid cottons. Furthermore, DOCL retrotransposons inserted in coding regions largely eliminated expression of the targeted genes in G. hirsutum or G. barbadense. Our data suggested that recent proliferation of retrotransposon families like DOCL was one of important evolutionary forces driving diversification and evolution of tetraploid cottons.
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Affiliation(s)
- Qian Li
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Yue Zhang
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Zhengsheng Zhang
- College of Agronomy and Biological Science and Technology, Southwest University, Beibei, Chongqing, China
| | - Xianbi Li
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Dan Yao
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Yi Wang
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Xufen Ouyang
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Yaohua Li
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Wu Song
- Institute of Xinjiang Naturally-Colored Cotton, China Colored Cotton (Group) Company, Urumchi, Xinjiang Uygur Autonomous Region, China
| | - Yuehua Xiao
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China.
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High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism. Genetics 2017; 206:1373-1388. [PMID: 28533438 DOI: 10.1534/genetics.116.196014] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 05/12/2017] [Indexed: 11/18/2022] Open
Abstract
During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry ∼60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (<26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals.
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Rey-Baños R, Sáenz de Miera LE, García P, Pérez de la Vega M. Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.). PLoS One 2017; 12:e0176728. [PMID: 28448614 PMCID: PMC5407846 DOI: 10.1371/journal.pone.0176728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/14/2017] [Indexed: 12/02/2022] Open
Abstract
Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type) none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry out further genetic analyses.
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Affiliation(s)
- Rita Rey-Baños
- Área de Genética, Dpto. de Biología Molecular, Universidad de León, León, Spain
| | - Luis E. Sáenz de Miera
- Área de Genética, Dpto. de Biología Molecular, Universidad de León, León, Spain
- * E-mail:
| | - Pedro García
- Área de Genética, Dpto. de Biología Molecular, Universidad de León, León, Spain
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Galván-Gordillo SV, Concepción Martínez-Navarro A, Xoconostle-Cázares B, Ruiz-Medrano R. Bioinformatic analysis of Arabidopsis reverse transcriptases with a zinc-finger domain. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Si Z, Du B, Huo J, He S, Liu Q, Zhai H. A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition. BMC Genomics 2016; 17:945. [PMID: 27871234 PMCID: PMC5117676 DOI: 10.1186/s12864-016-3302-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 11/15/2016] [Indexed: 11/14/2022] Open
Abstract
Background Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species. Results The BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93–10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana. Conclusions The first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3302-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zengzhi Si
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Bing Du
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Jinxi Huo
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Shaozhen He
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China.
| | - Hong Zhai
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China.
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Qiu GH. Genome defense against exogenous nucleic acids in eukaryotes by non-coding DNA occurs through CRISPR-like mechanisms in the cytosol and the bodyguard protection in the nucleus. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 767:31-41. [DOI: 10.1016/j.mrrev.2016.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 10/22/2015] [Accepted: 01/03/2016] [Indexed: 02/07/2023]
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Marcon HS, Domingues DS, Silva JC, Borges RJ, Matioli FF, Fontes MRDM, Marino CL. Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic. BMC PLANT BIOLOGY 2015; 15:198. [PMID: 26268941 PMCID: PMC4535378 DOI: 10.1186/s12870-015-0550-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/12/2015] [Indexed: 06/01/2023]
Abstract
BACKGROUND In Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome. RESULTS We characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one Copia family, RLC_egBianca_1. Protein theoretical models suggest different properties between Copia and Gypsy domains. IRAP and REMAP markers suggested genomic polymorphisms among Eucalyptus species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values. CONCLUSION Our strategy was successful in isolating transcriptionally active retrotransposons in Eucalyptus, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among Eucalyptus species.
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Affiliation(s)
- Helena Sanches Marcon
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
| | - Douglas Silva Domingues
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil.
| | - Juliana Costa Silva
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná - IAPAR, Londrina, Brazil.
| | - Rafael Junqueira Borges
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil.
| | - Fábio Filippi Matioli
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil.
| | - Marcos Roberto de Mattos Fontes
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil.
| | - Celso Luis Marino
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Instituto de Biotecnologia da UNESP - IBTEC, Botucatu, Brazil.
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Santos AA, Penha HA, Bellec A, Munhoz CDF, Pedrosa-Harand A, Bergès H, Vieira MLC. Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome. BMC Genomics 2014; 15:816. [PMID: 25260959 PMCID: PMC4189760 DOI: 10.1186/1471-2164-15-816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/22/2014] [Indexed: 12/16/2022] Open
Abstract
Background The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. Results The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n = 9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). Conclusions We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-816) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", P,O, Box 83, 13400-970 Piracicaba, Brazil.
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Yin H, Du J, Li L, Jin C, Fan L, Li M, Wu J, Zhang S. Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.). Genome Biol Evol 2014; 6:1423-36. [PMID: 24899073 PMCID: PMC4079214 DOI: 10.1093/gbe/evu114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants.
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Affiliation(s)
- Hao Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China
| | - Jianchang Du
- Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Leiting Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China
| | - Cong Jin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China
| | - Lian Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China
| | - Meng Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China
| | - Jun Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China
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