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Wei B, Liu H, Liu X, Xiao Q, Wang Y, Zhang J, Hu Y, Liu Y, Yu G, Huang Y. Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. BMC Genomics 2016; 17:536. [PMID: 27485608 PMCID: PMC4971691 DOI: 10.1186/s12864-016-2847-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 06/20/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Transposons (transposable elements or TEs) are DNA sequences that can change their position within the genome. A large number of TEs have been identified in reference genome of each crop(named accumulated TEs), which are the important part of genome. However, whether there existed TEs with different insert positions in resequenced crop accession genomes from those of reference genome (named non-reference transposable elements, non-ref TEs), and what the characteristics (such as the number, type and distribution) are. To identify and characterize crop non-ref TEs, we analyzed non-ref TEs in more than 125 accessions from rice (Oryza sativa), maize (Zea mays) and sorghum (Sorghum bicolor) using resequenced data with paired-end mapping methods. RESULTS We identified 13,066, 23,866 and 35,679 non-ref TEs in rice, maize and sorghum, respectively. Genome-wide characterization analysis shows that most of non-ref TEs were unique and non-ref TE classes shows different among rice, maize and sorghum. We found that non-ref TEs have a strong positive correlation with gene number and have a bias toward insertion near genes, but with a preference for avoiding coding regions in maize and sorghum. The genes affected by non-ref TE insertion were functionally enriched for stress response mechanisms in all three crops. CONCLUSIONS These observations suggest that transposon insertion is not a random event and it makes genomic diversity, which may affect the intraspecific adaption and evolution of crops.
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Affiliation(s)
- Bin Wei
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xin Liu
- Beijing Genome Institute and the Key Laboratory of Genomics of the Minister of Agriculture, Shenzhen, 518083, China
| | - Qianlin Xiao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongbin Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yubi Huang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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Liu YH, Zhang M, Wu C, Huang JJ, Zhang HB. DNA is structured as a linear "jigsaw puzzle" in the genomes of Arabidopsis, rice, and budding yeast. Genome 2014; 57:9-19. [PMID: 24564211 DOI: 10.1139/gen-2013-0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Knowledge of how a genome is structured and organized from its constituent elements is crucial to understanding its biology and evolution. Here, we report the genome structuring and organization pattern as revealed by systems analysis of the sequences of three model species, Arabidopsis, rice and yeast, at the whole-genome and chromosome levels. We found that all fundamental function elements (FFE) constituting the genomes, including genes (GEN), DNA transposable elements (DTE), retrotransposable elements (RTE), simple sequence repeats (SSR), and (or) low complexity repeats (LCR), are structured in a nonrandom and correlative manner, thus leading to a hypothesis that the DNA of the species is structured as a linear "jigsaw puzzle". Furthermore, we showed that different FFE differ in their importance in the formation and evolution of the DNA jigsaw puzzle structure between species. DTE and RTE play more important roles than GEN, LCR, and SSR in Arabidopsis, whereas GEN and RTE play more important roles than LCR, SSR, and DTE in rice. The genes having multiple recognized functions play more important roles than those having single functions. These results provide useful knowledge necessary for better understanding genome biology and evolution of the species and for effective molecular breeding of rice.
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Affiliation(s)
- Yun-Hua Liu
- a Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843-2474, USA
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Chang YL, Chuang HW, Meksem K, Wu FC, Chang CY, Zhang M, Zhang HB. Characterization of a plant-transformation-ready large-insert BIBAC library of Arabidopsis and bombardment transformation of a large-insert BIBAC of the library into tobacco. Genome 2011; 54:437-47. [PMID: 21585277 DOI: 10.1139/g11-011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plant-transformation-ready, large-insert binary bacterial artificial chromosome (BIBAC) libraries are of significance for functional and network analysis of large genomic regions, gene clusters, large-spanning genes, and complex loci in the post-genome era. Here, we report the characterization of a plant-transformation-ready BIBAC library of the sequenced Arabidopsis genome for which such a library is not available to the public, the transformation of a large-insert BIBAC of the library into tobacco by biolistic bombardment, and the expression analysis of its containing genes in transgenic plants. The BIBAC library was constructed from nuclear DNA partially digested with BamHI in the BIBAC vector pCLD04541. It contains 6144 clones and has a mean insert size of 108 kb, representing 5.2× equivalents of the Arabidopsis genome or a probability of greater than 99% of obtaining at least one positive clone from the library using a single-copy sequence as a probe. The transformation of the large-insert BIBAC and analyses of the transgenic plants showed that not only did transgenic plants have intact BIBAC DNA, but also could the BIBAC be transmitted stably into progenies and its containing genes be expressed actively. These results suggest that the large-insert BIBAC library, combined with the biolistic bombardment transformation method, could provide a useful tool for large-scale functional analysis of the Arabidopsis genome sequence and applications in plant-molecular breeding.
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Affiliation(s)
- Yueh-Long Chang
- Institute of Agricultural Biotechnology, National Chiayi University, Chiayi 600, Taiwan.
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Zhang XD. A method for effectively comparing gene effects in multiple conditions in RNAi and expression-profiling research. Pharmacogenomics 2010; 10:345-58. [PMID: 20397965 DOI: 10.2217/14622416.10.3.345] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To develop a new analytical method to address the issues of traditional contrast analysis for comparing gene effects in RNAi and expression-profiling research. METHODS & RESULTS I propose a new method consisting of contrast variable, standardized mean of contrast (SMC) and c(+)-probability analysis for comparing gene effects in multiple conditions. Compared with traditional contrast analysis, this new method has the following major advantages: it directly addresses the primary question of interest, namely the assessment of the strength of comparison; SMC and c(+)-probability capture data variability and are robust to sample size. The simulation and application studies show that traditional contrast analysis produces misleading results and erroneous conclusions whereas the new method produces reasonable results and sensible conclusions. CONCLUSIONS The new method may have a broad utility in comparing gene effects in multiple conditions including selecting hits in RNAi research and identifying differential expression in microarray experiments.
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Zhang M, Wu YH, Lee MK, Liu YH, Rong Y, Santos TS, Wu C, Xie F, Nelson RL, Zhang HB. Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors. Nucleic Acids Res 2010; 38:6513-25. [PMID: 20542917 PMCID: PMC2965241 DOI: 10.1093/nar/gkq524] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)-encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their ‘surplus’ genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms’ phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism’s morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.
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Affiliation(s)
- Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA
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Li Y, Uhm T, Ren C, Wu C, Santos TS, Lee MK, Yan B, Santos F, Zhang A, Scheuring C, Sanchez A, Millena AC, Nguyen HT, Kou H, Liu D, Zhang HB. A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence. Genome 2007; 50:278-88. [PMID: 17502901 DOI: 10.1139/g07-006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequencing of the rice genome has provided a platform for functional genomics research of rice and other cereal species. However, multiple approaches are needed to determine the functions of its genes and sequences and to use the genome sequencing results for genetic improvement of cereal crops. Here, we report a plant-transformation-competent, binary bacterial artificial chromosome (BIBAC) and bacterial artificial chromosome (BAC) based map of rice to facilitate these studies. The map was constructed from 20 835 BIBAC and BAC clones, and consisted of 579 overlapping BIBAC/BAC contigs. To facilitate functional analysis of chromosome 8 genomic sequence and cloning of the genes and QTLs mapped to the chromosome, we anchored the chromosomal contigs to the existing rice genetic maps. The chromosomal map consists of 11 contigs, 59 genetic markers, and 36 sequence tagged sites, spanning a total of ca. 38 Mb in physical length. Comparative analysis between the genetic and physical maps of chromosome 8 showed that there are 3 "hot" and 2 "cold" spots of genetic recombination along the chromosomal arms in addition to the "cold spot" in the centromeric region, suggesting that the sequence component contents of a chromosome may affect its local genetic recombination frequencies. Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding.
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Affiliation(s)
- Yaning Li
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA
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