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Du S, Hu X, Yang X, Yu W, Wang Z. Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China. Ecol Evol 2022; 12:e9101. [PMID: 35898427 PMCID: PMC9309028 DOI: 10.1002/ece3.9101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/04/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single-copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long-distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction-expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high-latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.
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Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern China Shanxi Agricultural University Taigu Jinzhong China
| | - Xiaoyan Hu
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern China Shanxi Agricultural University Taigu Jinzhong China
| | - Xiuyun Yang
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern China Shanxi Agricultural University Taigu Jinzhong China
| | - Wendong Yu
- College of Horticulture and Plant Protection Yangzhou University Yangzhou China
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry Chinese Academy of Forestry Beijing China
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Wang G, Zhou H, Gong H, He J, Luo Y, Hickford JGH, Hu J, Wang J, Liu X, Li S. Variation in the Lipin 1 Gene Is Associated with Birth Weight and Selected Carcass Traits in New Zealand Romney Sheep. Animals (Basel) 2020; 10:ani10020237. [PMID: 32028610 PMCID: PMC7071029 DOI: 10.3390/ani10020237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 11/16/2022] Open
Abstract
Lipin 1 plays an important role in lipid metabolism. In this study; we searched for variation in the ovine lipin 1 gene (LPIN1) in three gene regions (a 5' non-coding region; a region containing an alternatively spliced exon in intron 4; and a region containing coding exon 6) using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. The greatest amount of alleles was found in coding exon 6; with five sequences being detected. The effect of variation in this exon was investigated in 242 New Zealand Romney lambs derived from 12 sire-lines. The presence of variant E3 was associated with a decrease in birth weight (p = 0.005) and the proportion of leg yield (p = 0.045), but with an increase in hot carcass weight (p = 0.032) and the proportion of loin yield (p = 0.014). The presence of variant B3 was associated with an increased pre-weaning growth rate (p = 0.041), whereas the presence of variant C3 was associated with an increase in shoulder yield (p < 0.001). These results suggest that ovine LPIN1 variation may have value as a genetic marker for improving meat production and carcass traits.
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Affiliation(s)
- Guan Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Hua Gong
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jianning He
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Jon G H Hickford
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
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Kodori M, Douraghi M, Yaseri M, Rahbar M. The impact of primer sets on detection of the gene encoding biofilm-associated protein (Bap) in Acinetobacter baumannii: in silico and in vitro analysis. Lett Appl Microbiol 2017; 64:304-308. [PMID: 28099994 DOI: 10.1111/lam.12717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/05/2017] [Accepted: 01/11/2017] [Indexed: 11/29/2022]
Abstract
The Acinetobacter baumannii virulence protein Bap is encoded by a large gene and contains both variable sequence and repetitive modules. To date, four primer sets targeting different regions of bap have been designed, but no study has evaluated all these primers simultaneously for detection of bap. Here, we assessed the effect of primer sets Bap I-IV, on detection of bap both in silico and in vitro. Using the primer set Bap II, all 143 tested strains yielded an amplicon corresponding to the bap gene. This primer set showed the highest sensitivity (100, 95% CI: 97·9-100%) compared to the other primer sets. This study demonstrates that primer set Bap II performs with optimal efficiency for detection of the bap gene among different strains. SIGNIFICANCE AND IMPACT OF THE STUDY This study investigated the effect of nucleotide variation on PCR detection of the bap gene in various Acinetobacter baumannii strains. Since bap is the target gene for many detection assays, this variation can affect the detection efficiency. Here we present a primer set Bap II with optimal detection efficiency amongst 143 different strains, as shown by in silico and in vitro evidence.
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Affiliation(s)
- M Kodori
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - M Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - M Yaseri
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - M Rahbar
- Department of Microbiology, Reference Health Laboratories, Ministry of Health, Tehran, Iran
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Liu MS, Kuo TCY, Ko CY, Wu DC, Li KY, Lin WJ, Lin CP, Wang YW, Schafleitner R, Lo HF, Chen CY, Chen LFO. Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek). BMC Plant Biol 2016; 16:46. [PMID: 26887961 PMCID: PMC4756517 DOI: 10.1186/s12870-016-0736-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/09/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Mungbean (Vigna radiata [L.] R. Wilczek) is an important legume crop with high nutritional value in South and Southeast Asia. The crop plant is susceptible to a storage pest caused by bruchids (Callosobruchus spp.). Some wild and cultivated mungbean accessions show resistance to bruchids. Genomic and transcriptomic comparison of bruchid-resistant and -susceptible mungbean could reveal bruchid-resistant genes (Br) for this pest and give insights into the bruchid resistance of mungbean. RESULTS Flow cytometry showed that the genome size varied by 61 Mb (mega base pairs) among the tested mungbean accessions. Next generation sequencing followed by de novo assembly of the genome of the bruchid-resistant recombinant inbred line 59 (RIL59) revealed more than 42,000 genes. Transcriptomic comparison of bruchid-resistant and -susceptible parental lines and their offspring identified 91 differentially expressed genes (DEGs) classified into 17 major and 74 minor bruchid-resistance-associated genes. We found 408 nucleotide variations (NVs) between bruchid-resistant and -susceptible lines in regions spanning 2 kb (kilo base pairs) of the promoters of 68 DEGs. Furthermore, 282 NVs were identified on exons of 148 sequence-changed-protein genes (SCPs). DEGs and SCPs comprised genes involved in resistant-related, transposable elements (TEs) and conserved metabolic pathways. A large number of these genes were mapped to a region on chromosome 5. Molecular markers designed for variants of putative bruchid-resistance-associated genes were highly diagnostic for the bruchid-resistant genotype. CONCLUSIONS In addition to identifying bruchid-resistance-associated genes, we found that conserved metabolism and TEs may be modifier factors for bruchid resistance of mungbean. The genome sequence of a bruchid-resistant inbred line, candidate genes and sequence variations in promoter regions and exons putatively conditioning resistance as well as markers detecting these variants could be used for development of bruchid-resistant mungbean varieties.
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Affiliation(s)
- Mao-Sen Liu
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
| | - Tony Chien-Yen Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan.
| | - Chia-Yun Ko
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
| | - Dung-Chi Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan.
| | - Kuan-Yi Li
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan.
| | - Wu-Jui Lin
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan.
| | - Ching-Ping Lin
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
| | - Yen-Wei Wang
- AVRDC-the World Vegetable Center, 60 Yi-min Liao, Shanhua, Tainan, 74151, Taiwan.
| | - Roland Schafleitner
- AVRDC-the World Vegetable Center, 60 Yi-min Liao, Shanhua, Tainan, 74151, Taiwan.
| | - Hsiao-Feng Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan.
| | - Chien-Yu Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan.
| | - Long-Fang O Chen
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
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Abstract
Micro-RNA (miRNA) genes encode abundant small regulatory RNAs that play key roles during development and in homeostasis by fine tuning and buffering gene expression. This layer of regulatory control over transcriptional networks is preserved by selection across deep evolutionary time, yet selection pressures on individual miRNA genes in contemporary populations remain poorly characterized in any organism. Here, we quantify nucleotide variability for 129 miRNAs in the genome of the nematode Caenorhabditis remanei to understand the microevolution of this important class of regulatory genes. Our analysis of three population samples and C. remanei's sister species revealed ongoing natural selection that constrains evolution of all sequence domains within miRNA hairpins. We also show that new miRNAs evolve faster than older miRNAs but that selection nevertheless favors their persistence. Despite the ongoing importance of purging of new mutations, we discover a trove of >400 natural miRNA sequence variants that include single nucleotide polymorphisms in seed motifs, indels that ablate miRNA functional domains, and origination of new miRNAs by duplication. Moreover, we demonstrate substantial nucleotide divergence of pre-miRNA hairpin alleles between populations and sister species. These findings from the first global survey of miRNA microevolution in Caenorhabditis support the idea that changes in gene expression, mediated through divergence in miRNA regulation, can contribute to phenotypic novelty and adaptation to specific environments in the present day as well as the distant past.
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Affiliation(s)
- Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
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Farazi TA, Brown M, Morozov P, ten Hoeve JJ, Ben-Dov IZ, Hovestadt V, Hafner M, Renwick N, Mihailović A, Wessels LF, Tuschl T. Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing. Methods 2012; 58:171-87. [PMID: 22836126 PMCID: PMC3597438 DOI: 10.1016/j.ymeth.2012.07.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/12/2012] [Accepted: 07/16/2012] [Indexed: 11/17/2022] Open
Abstract
The characterization of post-transcriptional gene regulation by small regulatory RNAs of 20-30 nt length, particularly miRNAs and piRNAs, has become a major focus of research in recent years. A prerequisite for the characterization of small RNAs is their identification and quantification across different developmental stages, normal and diseased tissues, as well as model cell lines. Here we present a step-by-step protocol for the bioinformatic analysis of barcoded cDNA libraries for small RNA profiling generated by Illumina sequencing, thereby facilitating miRNA and other small RNA profiling of large sample collections.
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Affiliation(s)
- Thalia A. Farazi
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Miguel Brown
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Pavel Morozov
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Jelle J. ten Hoeve
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Iddo Z. Ben-Dov
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Volker Hovestadt
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Markus Hafner
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Neil Renwick
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Aleksandra Mihailović
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Lodewyk F.A. Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
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Till BJ, Jankowicz-Cieslak J, Sági L, Huynh OA, Utsushi H, Swennen R, Terauchi R, Mba C. Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling. Theor Appl Genet 2010; 121:1381-9. [PMID: 20589365 PMCID: PMC2955235 DOI: 10.1007/s00122-010-1395-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 06/17/2010] [Indexed: 05/02/2023]
Abstract
Musa (banana and plantain) is an important genus for the global export market and in local markets where it provides staple food for approximately 400 million people. Hybridization and polyploidization of several (sub)species, combined with vegetative propagation and human selection have produced a complex genetic history. We describe the application of the Ecotilling method for the discovery and characterization of nucleotide polymorphisms in diploid and polyploid accessions of Musa. We discovered over 800 novel alleles in 80 accessions. Sequencing and band evaluation shows Ecotilling to be a robust and accurate platform for the discovery of polymorphisms in homologous and homeologous gene targets. In the process of validating the method, we identified two single nucleotide polymorphisms that may be deleterious for the function of a gene putatively important for phototropism. Evaluation of heterozygous polymorphism and haplotype blocks revealed a high level of nucleotide diversity in Musa accessions. We further applied a strategy for the simultaneous discovery of heterozygous and homozygous polymorphisms in diploid accessions to rapidly evaluate nucleotide diversity in accessions of the same genome type. This strategy can be used to develop hypotheses for inheritance patterns of nucleotide polymorphisms within and between genome types. We conclude that Ecotilling is suitable for diversity studies in Musa, that it can be considered for functional genomics studies and as tool in selecting germplasm for traditional and mutation breeding approaches.
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Affiliation(s)
- Bradley J Till
- FAO/IAEA Agricultural and Biotechnology Laboratory, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria.
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