201
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Engelbrecht J, Duong TA, Berg NVD. New microsatellite markers for population studies of Phytophthora cinnamomi, an important global pathogen. Sci Rep 2017; 7:17631. [PMID: 29247246 PMCID: PMC5732169 DOI: 10.1038/s41598-017-17799-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/29/2017] [Indexed: 01/31/2023] Open
Abstract
Phytophthora cinnamomi is the causal agent of root rot, canker and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses but also threatens natural ecosystems. In South Africa, P. cinnamomi affects eucalyptus, avocado, macadamia and indigenous fynbos. Despite being one of the most important plant pathogens with a global distribution, little information is available regarding origin, invasion history and population biology. This is partly due to the limited number of molecular markers available for studying P. cinnamomi. Using available genome sequences for three isolates of P. cinnamomi, sixteen polymorphic microsatellite markers were developed as a set of multiplexable markers for both PCR and Gene Scan assays. The application of these markers on P. cinnamomi populations from avocado production areas in South Africa revealed that they were all polymorphic in these populations. The markers developed in this study represent a valuable resource for studying the population biology and movement of P. cinnamomi and will aid in the understanding of the origin and invasion history of this important species.
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Affiliation(s)
- J Engelbrecht
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.
| | - T A Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - N V D Berg
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
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202
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Rai MK, Shekhawat JK, Kataria V, Shekhawat N. De novo assembly of leaf transcriptome, functional annotation and genomic resources development in Prosopis cineraria , a multipurpose tree of Indian Thar Desert. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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203
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Kang SW, Patnaik BB, Park SY, Hwang HJ, Chung JM, Sang MK, Min HR, Park JE, Seong J, Jo YH, Noh MY, Lee JD, Jung KY, Park HS, Han YS, Lee JS, Lee YS. Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics. Genes Genomics 2017; 40:333-347. [PMID: 29892840 DOI: 10.1007/s13258-017-0620-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/26/2017] [Indexed: 11/29/2022]
Abstract
Ellobium chinense (Pfeiffer, 1854) is a brackish pulmonate species that inhabits the bases of mangrove trees and is most commonly found in salt grass meadows. Threats to mangrove ecosystems due to habitat degradation and overexploitation have threatened the species with extinction. In South Korea, E. chinense has been assessed as vulnerable, but there are limited data on its population structure and distribution. The nucleotide and protein sequences for this species are not available in databases, which limits the understanding of adaptation-related traits. We sequenced an E. chinense cDNA library using the Illumina platform, and the subsequent bioinformatics analysis yielded 227,032 unigenes. Of these unigenes, 69,088 were annotated to matched protein and nucleotide sequences in databases, for an annotation rate of 30.42%. Among the predominant gene ontology terms, cellular and metabolic processes (under the biological process category), membrane and cell (under the cellular component category), and binding and catalytic activity (under the molecular function category) were noteworthy. In addition, 4850 unigenes were distributed to 15 Kyoto Encyclopaedia of Genes and Genomes based enrichment categories. Among the candidate genes related to adaptation, angiotensin I converting enzyme, adenylate cyclase activating polypeptide, and AMP-activated protein kinase were the most prominent. A total of 15,952 simple sequence repeats (SSRs) were identified in sequences of > 1 kb in length. The di- and trinucleotide repeat motifs were the most common. Among the repeat motif types, AG/CT, AC/GT, and AAC/GTT dominated. Our study provides the first comprehensive genomics dataset for E. chinense, which favors conservation programs for the restoration of the species and provides sufficient evidence for genetic variability among the wild populations.
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Affiliation(s)
- Se Won Kang
- Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181, Ipsin-gil, Jungeup-si, Jeollabuk-do, 56212, South Korea
| | - Bharat Bhusan Patnaik
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha, 751024, India
| | - So Young Park
- Nakdonggang National Institute of Biological Resources, Biodiversity Conservation and Climate Change Division, 137, Donam-2-gil, Sangju-si, Gyeongsangbuk-do, 37242, South Korea
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Min Kyu Sang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Hye Rin Min
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jie Eun Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jiyeon Seong
- Genomic Informatics Center, Hankyong National University, 327 Chungang-ro, Anseong-si, Kyonggi-do, 17579, South Korea
| | - Yong Hun Jo
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Mi Young Noh
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Jong Dae Lee
- Department of Environmental Health Science, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Ki Yoon Jung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea
| | - Yeon Soo Han
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 243341, South Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea.
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204
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Easton J, Gonzalez-Pena V, Yergeau D, Ma X, Gawad C. Genome-wide segregation of single nucleotide and structural variants into single cancer cells. BMC Genomics 2017; 18:906. [PMID: 29178827 PMCID: PMC5702214 DOI: 10.1186/s12864-017-4286-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/08/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Single-cell genome sequencing provides high-resolution details of the clonal genomic modifications that occur during cancer initiation, progression, and ongoing evolution as patients undergo treatment. One limitation of current single-cell sequencing strategies is a suboptimal capacity to detect all classes of single-nucleotide and structural variants in the same cells. RESULTS Here we present a new approach for determining comprehensive variant profiles of single cells using a microfluidic amplicon-based strategy to detect structural variant breakpoint sequences instead of using relative read depth to infer copy number changes. This method can reconstruct the clonal architecture and mutational history of a malignancy using all classes and sizes of somatic variants, providing more complete details of the temporal changes in mutational classes and processes that led to the development of a malignant neoplasm. Using this approach, we interrogated cells from a patient with leukemia, determining that processes producing structural variation preceded single nucleotide changes in the development of that malignancy. CONCLUSIONS All classes and sizes of genomic variants can be efficiently detected in single cancer cells using our new method, enabling the ordering of distinct classes of mutations during tumor evolution.
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Affiliation(s)
- John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | | | - Donald Yergeau
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.,Buffalo Institute for Genomics and Data Analytics, University at Buffalo, Buffalo, NY, 14260, USA.,Present address: Buffalo Institute for Genomics and Data Analytics CBLS, 701 Ellicott St, Buffalo, NY, 14203, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charles Gawad
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA. .,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA. .,Present address: MS 1260, Room IA6042, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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205
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Development and validation of a multiple locus variable number tandem repeat analysis (MLVA) scheme for Fusobacterium necrophorum. Vet Microbiol 2017; 213:108-113. [PMID: 29291993 DOI: 10.1016/j.vetmic.2017.11.017] [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: 04/04/2017] [Revised: 09/26/2017] [Accepted: 11/17/2017] [Indexed: 11/21/2022]
Abstract
Fusobacterium necrophorum is associated with various diseases in humans and animals. Reservoirs (sites where the pathogen persists in the absence of disease) of F. necrophorum are believed to be present in healthy individuals e.g. tonsillar epithelium, or their environment e.g. soil, but for most diseases the reservoir sites are unknown. Strain typing of F. necrophorum would facilitate linking specific reservoirs with a specific disease. The aim of this study was to develop multiple locus variable number tandem repeat analysis (MLVA) as a strain typing technique for F. necrophorum, and to test the use of this scheme to analyse both isolates and mixed communities of bacteria. Seventy-three tandem repeat regions were identified in the F. necrophorum genome; three of these loci were suitable and developed as a MLVA scheme. The MLVA scheme was sensitive, specific, and discriminatory for both isolates and communities of F. necrophorum. The MLVA scheme strain typed 46/52F. necrophorum isolates including isolates of both subspecies and from different countries, host species and sample sites within host. There were 12 unique MLVA strain types that clustered by subspecies. The MLVA scheme characterised the F. necrophorum community in DNA from 32/49 foot- and 28/33 mouth swabs from sheep. There were 17 community types in total. In 31/32 foot swabs, single strains of F. necrophorum were detected while in the 28 mouth swabs there were up to a maximum of 8 strains of F. necrophorum detected. The results demonstrate the potential for this method to elucidate reservoirs of F. necrophorum.
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206
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Zhong S, Su Y, Mao Y, Liu M, Wang J, Zhang Q. Development and characterization of 24 SNP markers in Kuruma shrimp (Marsupenaeus japonicus) by illumina sequencing. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0913-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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207
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Fine mapping and candidate gene analysis of the virescent gene v 1 in Upland cotton (Gossypium hirsutum). Mol Genet Genomics 2017; 293:249-264. [PMID: 29052764 DOI: 10.1007/s00438-017-1383-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 10/13/2017] [Indexed: 01/12/2023]
Abstract
The young leaves of virescent mutants are yellowish and gradually turn green as the plants reach maturity. Understanding the genetic basis of virescent mutants can aid research of the regulatory mechanisms underlying chloroplast development and chlorophyll biosynthesis, as well as contribute to the application of virescent traits in crop breeding. In this study, fine mapping was employed, and a recessive gene (v 1) from a virescent mutant of Upland cotton was narrowed to an 84.1-Kb region containing ten candidate genes. The GhChlI gene encodes the cotton Mg-chelatase I subunit (CHLI) and was identified as the candidate gene for the virescent mutation using gene annotation. BLAST analysis showed that the GhChlI gene has two copies, Gh_A10G0282 and Gh_D10G0283. Sequence analysis indicated that the coding region (CDS) of GhChlI is 1269 bp in length, with three predicted exons and one non-synonymous nucleotide mutation (G1082A) in the third exon of Gh_D10G0283, with an amino acid (AA) substitution of arginine (R) to lysine (K). GhChlI-silenced TM-1 plants exhibited a lower GhChlI expression level, a lower chlorophyll content, and the virescent phenotype. Analysis of upstream regulatory elements and expression levels of GhChlI showed that the expression quantity of GhChlI may be normal, and with the development of the true leaf, the increase in the Gh_A10G0282 dosage may partially make up for the deficiency of Gh_D10G0283 in the v 1 mutant. Phylogenetic analysis and sequence alignment revealed that the protein sequence encoded by the third exon of GhChlI is highly conserved across diverse plant species, in which AA substitutions among the completely conserved residues frequently result in changes in leaf color in various species. These results suggest that the mutation (G1082A) within the GhChlI gene may cause a functional defect of the GhCHLI subunit and thus the virescent phenotype in the v1 mutant. The GhChlI mutation not only provides a tool for understanding the associations of CHLI protein function and the chlorophyll biosynthesis pathway but also has implications for cotton breeding.
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208
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Wang Y, Xie J, Zhang H, Guo B, Ning S, Chen Y, Lu P, Wu Q, Li M, Zhang D, Guo G, Zhang Y, Liu D, Zou S, Tang J, Zhao H, Wang X, Li J, Yang W, Cao T, Yin G, Liu Z. Mapping stripe rust resistance gene YrZH22 in Chinese wheat cultivar Zhoumai 22 by bulked segregant RNA-Seq (BSR-Seq) and comparative genomics analyses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2191-2201. [PMID: 28711956 DOI: 10.1007/s00122-017-2950-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 05/22/2023]
Abstract
A stripe rust resistance gene YrZH22 was mapped by combined BSR-Seq and comparative genomics analyses to a 5.92 centimorgan (cM) genetic interval spanning a 4 Mb physical genomic region on wheat chromosome 4BL1. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases of wheat and severely threatens wheat production worldwide. The widely grown Chinese wheat cultivar Zhoumai 22 is highly resistant to the current prevailing PST race CYR34 (V26). Genetic analysis of F5:6 and F6:7 recombinant inbred line (RIL) populations indicated that adult-plant stripe rust resistance in Zhoumai 22 is controlled by a single gene, temporarily designated YrZH22. By applying bulked segregant RNA-Seq (BSR-Seq), 7 SNP markers were developed and SNP mapping showed that YrZH22 is located between markers WGGB105 and WGGB112 on chromosome arm 4BL. The corresponding genomic regions of the Chinese Spring 4BL genome assembly and physical map of Aegilops tauschii 4DL were selected for comparative genomics analyses to develop nine new polymorphic markers that were used to construct a high-resolution genetic linkage map of YrZH22. YrZH22 was delimited in a 5.92 cM genetic interval between markers WGGB133 and WGGB146, corresponding to 4.1 Mb genomic interval in Chinese Spring 4BL and a 2.2 Mb orthologous genomic region in Ae. tauschii 4DL. The genetic linkage map of YrZH22 will be valuable for fine mapping and positional cloning of YrZH22, and can be used for marker-assisted selection in wheat breeding.
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Affiliation(s)
- Yong Wang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jingzhong Xie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huaizhi Zhang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Bingmin Guo
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yongxing Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ping Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiuhong Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Miaomiao Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Deyun Zhang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Guanghao Guo
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Yan Zhang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Shaokui Zou
- Zhoukou Academy of Agriculture Sciences, Zhoukou, 466001, Henan, China
| | - Jianwei Tang
- Zhoukou Academy of Agriculture Sciences, Zhoukou, 466001, Henan, China
| | - Hong Zhao
- Wheat Institute, Henan Academy of Agriculture Sciences, Zhengzhou, 450002, Henan, China
| | - Xicheng Wang
- Wheat Institute, Henan Academy of Agriculture Sciences, Zhengzhou, 450002, Henan, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agriculture Sciences, Chengdu, 610066, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agriculture Sciences, Chengdu, 610066, China
| | - Tingjie Cao
- Wheat Institute, Henan Academy of Agriculture Sciences, Zhengzhou, 450002, Henan, China.
| | - Guihong Yin
- Zhoukou Academy of Agriculture Sciences, Zhoukou, 466001, Henan, China.
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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209
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Sandhu M, Sureshkumar V, Prakash C, Dixit R, Solanke AU, Sharma TR, Mohapatra T, S V AM. RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. BMC Bioinformatics 2017; 18:432. [PMID: 28964253 PMCID: PMC5622590 DOI: 10.1186/s12859-017-1846-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Background Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. Results RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. Conclusions The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201 Electronic supplementary material The online version of this article (10.1186/s12859-017-1846-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maninder Sandhu
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - V Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Rekha Dixit
- Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India.,Current address: Department of biotechnology, Keralverma faculty of science, Swami Vivekanand Subharti University, Meerut, 250005, Uttar Pradesh, India
| | - Amolkumar U Solanke
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - Amitha Mithra S V
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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210
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Zhang J, Liu W, Lu Y, Liu Q, Yang X, Li X, Li L. A resource of large-scale molecular markers for monitoring Agropyron cristatum chromatin introgression in wheat background based on transcriptome sequences. Sci Rep 2017; 7:11942. [PMID: 28931929 PMCID: PMC5607264 DOI: 10.1038/s41598-017-12219-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 09/01/2017] [Indexed: 12/22/2022] Open
Abstract
Agropyron cristatum is a wild grass of the tribe Triticeae and serves as a gene donor for wheat improvement. However, very few markers can be used to monitor A. cristatum chromatin introgressions in wheat. Here, we reported a resource of large-scale molecular markers for tracking alien introgressions in wheat based on transcriptome sequences. By aligning A. cristatum unigenes with the Chinese Spring reference genome sequences, we designed 9602 A. cristatum expressed sequence tag-sequence-tagged site (EST-STS) markers for PCR amplification and experimental screening. As a result, 6063 polymorphic EST-STS markers were specific for the A. cristatum P genome in the single-receipt wheat background. A total of 4956 randomly selected polymorphic EST-STS markers were further tested in eight wheat variety backgrounds, and 3070 markers displaying stable and polymorphic amplification were validated. These markers covered more than 98% of the A. cristatum genome, and the marker distribution density was approximately 1.28 cM. An application case of all EST-STS markers was validated on the A. cristatum 6 P chromosome. These markers were successfully applied in the tracking of alien A. cristatum chromatin. Altogether, this study provided a universal method of large-scale molecular marker development to monitor wild relative chromatin in wheat.
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Affiliation(s)
- Jinpeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqing Lu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qunxing Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinming Yang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuquan Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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211
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Shrestha SK, Lamour K, Young-Kelly H. Genome sequences and SNP analyses of Corynespora cassiicola from cotton and soybean in the southeastern United States reveal limited diversity. PLoS One 2017; 12:e0184908. [PMID: 28910414 PMCID: PMC5599035 DOI: 10.1371/journal.pone.0184908] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 09/01/2017] [Indexed: 12/17/2022] Open
Abstract
Corynespora cassiicola attackes diverse agriculturally important plants, including soybean and cotton, in the US. It is a reemerge pathogen on cotton in southeastern US. Whole genome sequences of four cotton and one soybean isolate from Tennessee were used to develop single nucleotide polymorphism markers for cotton isolates. Cotton isolates had little diversity at the genome level and very little differentiation from the soybean isolate. Analysis of 75 isolates from cotton and soybean, using targeted-sequencing of 22 polymorphic SNP sites, revealed eight multi-locus genotypes and it appears a single clonal lineage predominates across the southeastern region. The cotton and soybean genome sequences were significantly different from the public reference genome derived from a rubber isolate and the utility of these novel resources will be discussed.
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Affiliation(s)
- Sandesh K. Shrestha
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, United States of America
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, United States of America
| | - Heather Young-Kelly
- Department of Entomology and Plant Pathology, The University of Tennessee, Jackson, TN, United States of America
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212
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RNA-seq of Rice Yellow Stem Borer Scirpophaga incertulas Reveals Molecular Insights During Four Larval Developmental Stages. G3-GENES GENOMES GENETICS 2017; 7:3031-3045. [PMID: 28717048 PMCID: PMC5592929 DOI: 10.1534/g3.117.043737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The yellow stem borer (YSB), Scirpophaga incertulas, is a prominent pest in rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on the biology and mechanisms underlying the growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome analysis at the first, third, fifth, and seventh larval developmental stages employing Illumina Hi-seq. High-quality reads (HQR) of ∼229 Mb were assembled into 24,775 transcripts with an average size of 1485 bp. Genes associated with various metabolic processes, i.e., detoxification mechanism [CYP450, GSTs, and carboxylesterases (CarEs)], RNA interference (RNAi) machinery (Dcr-1, Dcr-2, Ago-1, Ago-2, Sid-1, Sid-2, Sid-3, and Sid-1-related gene), chemoreception (CSPs, GRs, OBPs, and ORs), and regulators [transcription factors (TFs) and hormones] were differentially regulated during the developmental stages. Identification of stage-specific transcripts made it possible to determine the essential processes of larval development. Comparative transcriptome analysis revealed that YSB has not evolved much with respect to the detoxification mechanism, but showed the presence of distinct RNAi machinery. The presence of strong specific visual recognition coupled with chemosensory mechanisms supports the monophagous nature of YSB. Designed expressed sequenced tags-simple-sequence repeats (EST-SSRs) will facilitate accurate estimation of the genetic diversity of YSB. This is the first report on characterization of the YSB transcriptome and the identification of genes involved in key processes, which will help researchers and industry to devise novel pest control strategies. This study also opens up a new avenue to develop next-generation resistant rice using RNAi or genome editing approaches.
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213
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SNP discovery in spotted halibut (Verasper variegatus) using restriction site-associated DNA sequencing(RAD-seq). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0837-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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214
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Pandey MK, Khan AW, Singh VK, Vishwakarma MK, Shasidhar Y, Kumar V, Garg V, Bhat RS, Chitikineni A, Janila P, Guo B, Varshney RK. QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:927-941. [PMID: 28028892 PMCID: PMC5506652 DOI: 10.1111/pbi.12686] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 05/12/2023]
Abstract
Rust and late leaf spot (LLS) are the two major foliar fungal diseases in groundnut, and their co-occurrence leads to significant yield loss in addition to the deterioration of fodder quality. To identify candidate genomic regions controlling resistance to rust and LLS, whole-genome resequencing (WGRS)-based approach referred as 'QTL-seq' was deployed. A total of 231.67 Gb raw and 192.10 Gb of clean sequence data were generated through WGRS of resistant parent and the resistant and susceptible bulks for rust and LLS. Sequence analysis of bulks for rust and LLS with reference-guided resistant parent assembly identified 3136 single-nucleotide polymorphisms (SNPs) for rust and 66 SNPs for LLS with the read depth of ≥7 in the identified genomic region on pseudomolecule A03. Detailed analysis identified 30 nonsynonymous SNPs affecting 25 candidate genes for rust resistance, while 14 intronic and three synonymous SNPs affecting nine candidate genes for LLS resistance. Subsequently, allele-specific diagnostic markers were identified for three SNPs for rust resistance and one SNP for LLS resistance. Genotyping of one RIL population (TAG 24 × GPBD 4) with these four diagnostic markers revealed higher phenotypic variation for these two diseases. These results suggest usefulness of QTL-seq approach in precise and rapid identification of candidate genomic regions and development of diagnostic markers for breeding applications.
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Affiliation(s)
- Manish K. Pandey
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Manish K. Vishwakarma
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Vinay Kumar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Vanika Garg
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Ramesh S. Bhat
- Department of BiotechnologyUniversity of Agricultural SciencesDharwadIndia
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Baozhu Guo
- Crop Protection and Management Research UnitUSDA‐Agricultural Research ServiceTiftonGAUSA
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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215
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Zhang H, Kong F, Wang X, Liang L, Schoen CD, Feng J, Wang Z. Tetra-primer ARMS PCR for rapid detection and characterisation of Plasmopara viticola phenotypes resistant to carboxylic acid amide fungicides. PEST MANAGEMENT SCIENCE 2017; 73:1655-1660. [PMID: 27990754 DOI: 10.1002/ps.4506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 12/06/2016] [Accepted: 12/10/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND The occurrence of Plasmopara viticola populations resistant to carboxylic acid amide (CAA) fungicides is becoming a serious problem in the control of grapevine downy mildew worldwide. The resistance is caused by point mutations in the PvCesA3 gene. These isolates with this mutation have been detected mainly by determining the minimum inhibitory concentration of fungicides, which is always time consuming and inefficient. RESULTS To establish a suitable method for rapid detection of the G1105S mutation in P. viticola, an efficient and simple molecular method was developed, based on tetra-primer ARMS PCR. A set of four primers were designed and optimised to distinguish the different genotypes within one step. Only 2 h was required from the sampling of symptoms to the phenotyping of fungicide resistance. Using this method, CAA-resistant P. viticola were identified for the first time in China. Also, the finding of sensitive heterozygotes indicated that the resistant allele is spreading in the population in Ziyuan. CONCLUSION This new method proved to be useful as an early warning system for resistance outbreaks of P. viticola to CAA fungicides in the field and may be helpful in decisions concerning rotation of different fungicide groups. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Fanfang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xina Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Lisha Liang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
- Guilin Municipal Bureau of Forestry, Guangxi, China
| | - Cor D Schoen
- Wageningen Plant Research, Wageningen, The Netherlands
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Zhongyue Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
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216
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Legoff J, Resche-Rigon M, Bouquet J, Robin M, Naccache SN, Mercier-Delarue S, Federman S, Samayoa E, Rousseau C, Piron P, Kapel N, Simon F, Socié G, Chiu CY. The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease. Nat Med 2017; 23:1080-1085. [PMID: 28759053 DOI: 10.1038/nm.4380] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 06/29/2017] [Indexed: 12/13/2022]
Abstract
Much attention has been focused on the role of the bacterial microbiome in human health, but the virome is understudied. Although previously investigated in individuals with inflammatory bowel diseases or solid-organ transplants, virome dynamics in allogeneic hematopoietic stem cell transplantation (HSCT) and enteric graft-versus-host disease (GVHD) remain unexplored. Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of vertebrate viral sequences following transplantation (P = 0.02). Increases in both the rates of detection (P < 0.0001) and number of sequences (P = 0.047) of persistent DNA viruses (anelloviruses, herpesviruses, papillomaviruses and polyomaviruses) over time were observed in individuals with enteric GVHD relative to those without, a finding accompanied by a reduced phage richness (P = 0.01). Picobirnaviruses were detected in 18 individuals (40.9%), more frequently before or within a week after transplant than at later time points (P = 0.008). In a time-dependent Cox proportional-hazards model, picobirnaviruses were predictive of the occurrence of severe enteric GVHD (hazard ratio, 2.66; 95% confidence interval (CI) = 1.46-4.86; P = 0.001), and correlated with higher fecal levels of two GVHD severity markers, calprotectin and α1-antitrypsin. These results reveal a progressive expansion of vertebrate viral infections over time following HSCT, and they suggest an unexpected association of picobirnaviruses with early post-transplant GVHD.
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Affiliation(s)
- Jérôme Legoff
- University of Paris Diderot, Sorbonne Paris Cité, Inserm U941, Microbiology Laboratory, Hôpital Saint-Louis, APHP, Paris, France.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Matthieu Resche-Rigon
- University of Paris Diderot, Sorbonne Paris Cité, Inserm U1153, ECSTRA Team, Biostatistics Unit, APHP, Hôpital Saint-Louis, Paris, France
| | - Jerome Bouquet
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Marie Robin
- University of Paris Descartes, EA4065, Microbiology Laboratory, Hôpital Saint-Louis, APHP, Paris, France
| | - Samia N Naccache
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Séverine Mercier-Delarue
- University of Paris Diderot, Sorbonne Paris Cité, Inserm U941, Microbiology Laboratory, Hôpital Saint-Louis, APHP, Paris, France
| | - Scot Federman
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Erik Samayoa
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Clotilde Rousseau
- University of Paris Descartes, EA4065, Microbiology Laboratory, Hôpital Saint-Louis, APHP, Paris, France
| | - Prescillia Piron
- University of Paris Diderot, Sorbonne Paris Cité, Inserm U1153, ECSTRA Team, Biostatistics Unit, APHP, Hôpital Saint-Louis, Paris, France
| | - Nathalie Kapel
- Laboratoire de Coprologie Fonctionnelle, APHP, GH Pitié-Salpêtrière Charles Foix, EA4065, Université Paris Descartes, Paris, France
| | - François Simon
- University of Paris Diderot, Sorbonne Paris Cité, Inserm U941, Microbiology Laboratory, Hôpital Saint-Louis, APHP, Paris, France
| | - Gérard Socié
- University of Paris Diderot, Sorbonne Paris Cité, Paris, France, and Hematology and Transplantation, INSERM Unité Mixte de Recherche Scientifique 1160, Paris, France
| | - Charles Y Chiu
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA.,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California, USA
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217
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Jeon K, Min B, Park JS, Kang YK. Simultaneous Methylation-Level Assessment of Hundreds of CpG Sites by Targeted Bisulfite PCR Sequencing (TBPseq). Front Genet 2017; 8:97. [PMID: 28751909 PMCID: PMC5507944 DOI: 10.3389/fgene.2017.00097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 12/23/2022] Open
Abstract
Methylated-DNA sequencing technologies are producing vast amounts of methylome data from cancer samples, from which cancer-associated differentially methylated CpG sites (cDMCs) are continuously identified and filed. The inclusion of as many cDMCs as possible helps improve the accuracy of cancer diagnosis and sometimes identify cancer subtypes. However, the lack of an established method for the analysis of 100s of cDMCs practically impedes their robust use in clinical medicine. Here, we tested the availability of targeted bisulfite-PCR-sequencing (TBPseq) technology for the assessment of methylation levels of a myriad of CpGs scattered over the genome. In randomly selected 46 cancer cell lines, multiplexed PCR yielded a variety of amplicons harboring 246 CpGs residing at promoters of 97 cancer-associated genes, all of which were sequenced in the same flow cell. Clustering analysis of the TBPseq-assessed methylation levels of target CpGs showed that the lung and liver cancer cell lines correlated relatively strongly with each other while they weakly correlated with colon cancer cells. CpGs at the LIFR gene promoter, which are known to be hypermethylated in colon cancers, indeed were heavily methylated in the tested colon cancer cells. Moreover, the LIFR promoter hypermethylation was found in colon cancer cells only, but not in biliary tract, liver, lung, and stomach cancers cell lines. A meta-analysis with public cancer methylome data verified the colon cancer specificity of LIFR promoter methylation. These results demonstrate that our TBPseq-based methylation assessment could be considered an effective, accurate, and competitive method to simultaneously examine a large number of target cDMCs and patient samples.
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Affiliation(s)
- Kyuheum Jeon
- Development and Differentiation Research CenterKorea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, Korea University of Science and TechnologyDaejeon, South Korea
| | - Byungkuk Min
- Development and Differentiation Research CenterKorea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea
| | - Jung S Park
- Development and Differentiation Research CenterKorea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea
| | - Yong-Kook Kang
- Development and Differentiation Research CenterKorea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, Korea University of Science and TechnologyDaejeon, South Korea
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218
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Hammaker D, Whitaker JW, Maeshima K, Boyle DL, Ekwall AKH, Wang W, Firestein GS. LBH Gene Transcription Regulation by the Interplay of an Enhancer Risk Allele and DNA Methylation in Rheumatoid Arthritis. Arthritis Rheumatol 2017; 68:2637-2645. [PMID: 27159840 DOI: 10.1002/art.39746] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/03/2016] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To identify nonobvious therapeutic targets for rheumatoid arthritis (RA), we performed an integrative analysis incorporating multiple "omics" data and the Encyclopedia of DNA Elements (ENCODE) database for potential regulatory regions. This analysis identified the limb bud and heart development (LBH) gene, which has risk alleles associated with RA/celiac disease and lupus, and can regulate cell proliferation in RA. We identified a novel LBH transcription enhancer with an RA risk allele (rs906868 G [Ref]/T) 6 kb upstream of the LBH gene with a differentially methylated locus. The confluence of 3 regulatory elements, rs906868, an RA differentially methylated locus, and a putative enhancer, led us to investigate their effects on LBH regulation in fibroblast-like synoviocytes (FLS). METHODS We cloned the 1.4-kb putative enhancer with either the rs906868 Ref allele or single-nucleotide polymorphism (SNP) variant into reporter constructs. The constructs were methylated in vitro and transfected into cultured FLS by nucleofection. RESULTS We found that both variants increased transcription, thereby confirming the region's enhancer function. Unexpectedly, the transcriptional activity of the Ref risk allele was significantly lower than that of the SNP variant and is consistent with low LBH levels as a risk factor for aggressive FLS behavior. Using RA FLS lines with a homozygous Ref or SNP allele, we confirmed that homozygous Ref lines expressed lower LBH messenger RNA levels than did the SNP lines. Methylation significantly reduced enhancer activity for both alleles, indicating that enhancer function is dependent on its methylation status. CONCLUSION This study shows how the interplay between genetics and epigenetics can affect expression of LBH in RA.
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Affiliation(s)
| | | | | | | | - Anna-Karin H Ekwall
- Anna-Karin H. Ekwall, MD, PhD: The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Wei Wang
- University of California at San Diego, La Jolla
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219
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Hazra A, Dasgupta N, Sengupta C, Das S. Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits. BMC Res Notes 2017; 10:261. [PMID: 28683768 PMCID: PMC5501407 DOI: 10.1186/s13104-017-2577-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/28/2017] [Indexed: 11/10/2022] Open
Abstract
Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified. Micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and thus effects on related phenotype. Present study deals with identification of the microsatellite motifs within the reported and predicted miRNA precursors that are effectively followed by designing of primers from SSR flanking regions in order to PCR validation. In addition to the earlier reports, two new miRNAs are predicting here from tea expressed tag sequence database. Furthermore, 18 SSR motifs are found to be in 13 of all 33 predicted miRNAs. Trinucleotide motifs are most abundant among all followed by dinucleotides. Since, miRNA based SSR markers are evidenced to have significant role on genetic fingerprinting study, these outcomes would pave the way in developing novel markers for tagging tea specific agronomic traits as well as substantiating non-conventional breeding program.
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Affiliation(s)
- Anjan Hazra
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India.,Department of Botany, University of Kalyani, Nadia, Kalyani, 741235, India
| | - Nirjhar Dasgupta
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India
| | - Chandan Sengupta
- Department of Botany, University of Kalyani, Nadia, Kalyani, 741235, India
| | - Sauren Das
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India.
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220
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Li Y, Harris-Shultz K, Wang H, Wadl PA, Ji P. Population Structure and Genetic Diversity of Phytophthora nicotianae from Tobacco in Georgia. PLANT DISEASE 2017; 101:1113-1118. [PMID: 30682967 DOI: 10.1094/pdis-01-17-0142-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Black shank, caused by Phytophthora nicotianae, occurs worldwide and is responsible for significant yield loss in tobacco production in Georgia. Management of the disease has primarily relied on utilization of tobacco cultivars with resistance to race 0 of the pathogen and application of the fungicide mefenoxam. Races of P. nicotianae currently prevalent in tobacco production in Georgia, their sensitivity to mefenoxam, and genetic diversity of the pathogen are largely unknown. To determine population structure and genetic diversity of the pathogen, simple sequence repeat (SSR) markers were used. Three races of P. nicotianae (races 0, 1, and 3) were isolated from infected tobacco plants, with race 3 identified in Georgia for the first time. The majority of isolates were identified as A2 mating type and all isolates were sensitive or intermediately sensitive to mefenoxam at 1 or 10 μg/ml, with effective concentration of mefenoxam for 50% mycelial growth reduction values ranging from <0.01 to 0.12 μg/ml. Bayesian and unweighted pair group method with arithmetic means analyses of 59 isolates using SSR markers grouped the isolates in two major groups. Group I contained 20 isolates, of which 19 isolates were collected from Berrien County. Group II contained 39 isolates collected from Bacon, Cook, Tift, and Toombs Counties as well as one sample from Berrien County. Genetic diversity of the isolates was associated with geographical location of collection, and isolates in group I were primarily (75%) race 1, whereas isolates in group II were primarily (69%) race 0. The presence of a single pathogen mating type at most of the locations implies low probability of sexual recombination that may have contributed to the low genetic diversity at a particular geographical location. Sensitivity of the isolates to mefenoxam indicates that the fungicide remains to be a potent tool for growers to combat the disease. Information generated in the study advances our knowledge about diversity and population structure of P. nicotianae, which facilitates development and implementation of effective disease management programs.
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Affiliation(s)
- Yonggang Li
- Agricultural College, Northeast Agricultural University, Harbin 150030, China; and Department of Plant Pathology, University of Georgia, Tifton 31794
| | - Karen Harris-Shultz
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Crop Genetics and Breeding Research Unit, Tifton, GA 31793
| | - Hongliang Wang
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Crop Genetics and Breeding Research Unit, Tifton, GA 31793
| | - Phillip A Wadl
- USDA-ARS, U.S. Vegetable Laboratory, Charleston, SC 29414
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton
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221
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Klindworth DL, Saini J, Long Y, Rouse MN, Faris JD, Jin Y, Xu SS. Physical mapping of DNA markers linked to stem rust resistance gene Sr47 in durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1135-1154. [PMID: 28286900 DOI: 10.1007/s00122-017-2875-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 02/07/2017] [Indexed: 06/06/2023]
Abstract
Markers linked to stem rust resistance gene Sr47 were physically mapped in three small Aegilops speltoides chromosomal bins. Five markers, including two PCR-based SNP markers, were validated for marker-assisted selection. In durum wheat (Triticum turgidum subsp. durum), the gene Sr47 derived from Aegilops speltoides conditions resistance to race TTKSK (Ug99) of the stem rust pathogen (Puccinia graminis f. sp. tritici). Sr47 is carried on small interstitial translocation chromosomes (Ti2BL-2SL-2BL·2BS) in which the Ae. speltoides chromosome 2S segments are divided into four bins in genetic stocks RWG35, RWG36, and RWG37. Our objective was to physically map molecular markers to bins and to determine if any of the molecular markers would be useful in marker-assisted selection (MAS). Durum cultivar Joppa was used as the recurrent parent to produce three BC2F2 populations. Each BC2F2 plant was genotyped with markers to detect the segment carrying Sr47, and stem rust testing of BC2F3 progeny with race TTKSK confirmed the genotyping. Forty-nine markers from published sources, four new SSR markers, and five new STARP (semi-thermal asymmetric reverse PCR) markers, were evaluated in BC2F2 populations for assignment of markers to bins. Sr47 was mapped to bin 3 along with 13 markers. No markers were assigned to bin 1; however, 7 and 13 markers were assigned to bins 2 and 4, respectively. Markers Xrwgs38a, Xmag1729, Xwmc41, Xtnac3119, Xrwgsnp1, and Xrwgsnp4 were found to be useful for MAS of Sr47. However, STARP markers Xrwgsnp1 and Xrwgsnp4 can be used in gel-free systems, and are the preferred markers for high-throughput MAS. The physical mapping data from this study will also be useful for pyramiding Sr47 with other Sr genes on chromosome 2B.
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Affiliation(s)
- Daryl L Klindworth
- USDA-ARS, Northern Crop Science Laboratory, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Jyoti Saini
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Yunming Long
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Matthew N Rouse
- USDA-ARS, Cereal Disease Laboratory, and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Justin D Faris
- USDA-ARS, Northern Crop Science Laboratory, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Yue Jin
- USDA-ARS, Cereal Disease Laboratory, and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Steven S Xu
- USDA-ARS, Northern Crop Science Laboratory, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.
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Sathyanarayana N, Pittala RK, Tripathi PK, Chopra R, Singh HR, Belamkar V, Bhardwaj PK, Doyle JJ, Egan AN. Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. BMC Genomics 2017; 18:409. [PMID: 28545396 PMCID: PMC5445377 DOI: 10.1186/s12864-017-3780-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/10/2017] [Indexed: 12/14/2022] Open
Abstract
Background The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. Results One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. Conclusions The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3780-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- N Sathyanarayana
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India.
| | - Ranjith Kumar Pittala
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India
| | - Pankaj Kumar Tripathi
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India
| | - Ratan Chopra
- United States Department of Agriculture, Agriculture Research Service, 3810 4th St., Lubbock, TX, 79415, USA
| | - Heikham Russiachand Singh
- Department of Plant Science, McGill University, Raymond Building, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, H9X 3V9, Canada
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Pardeep Kumar Bhardwaj
- Institute of Bioresources and Sustainable Development, ikkim Centre, Tadong-737102, Gangtok, Sikkim, India
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 412 Mann Library, Ithaca, NY, 14853, USA
| | - Ashley N Egan
- Department of Botany, Smithsonian Institution, National Museum of Natural History, US National Herbarium, 10th and Constitution Ave NW, Washington, DC, 20013, USA.
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Leelatanawit R, Saetung T, Phuengwas S, Karoonuthaisiri N, Devahastin S. Selection of reference genes for quantitative real-time PCR in postharvest tomatoes (Lycopersicon esculentum
) treated by continuous low-voltage direct current electricity to increase secondary metabolites. Int J Food Sci Technol 2017. [DOI: 10.1111/ijfs.13477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rungnapa Leelatanawit
- Microarray Laboratory; National Center for Genetic Engineering and Biotechnology (BIOTEC); National Science and Technology Development Agency; Khlong Luang Pathumthani 12120 Thailand
| | - Thunyarat Saetung
- Advanced Food Processing Research Laboratory; Department of Food Engineering; Faculty of Engineering; King Mongkut's University of Technology Thonburi; Tungkru Bangkok 10140 Thailand
| | - Sudtida Phuengwas
- Microarray Laboratory; National Center for Genetic Engineering and Biotechnology (BIOTEC); National Science and Technology Development Agency; Khlong Luang Pathumthani 12120 Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Laboratory; National Center for Genetic Engineering and Biotechnology (BIOTEC); National Science and Technology Development Agency; Khlong Luang Pathumthani 12120 Thailand
| | - Sakamon Devahastin
- Advanced Food Processing Research Laboratory; Department of Food Engineering; Faculty of Engineering; King Mongkut's University of Technology Thonburi; Tungkru Bangkok 10140 Thailand
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Evangelisti E, Gogleva A, Hainaux T, Doumane M, Tulin F, Quan C, Yunusov T, Floch K, Schornack S. Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors. BMC Biol 2017; 15:39. [PMID: 28494759 PMCID: PMC5427549 DOI: 10.1186/s12915-017-0379-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped in understanding how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce. RESULTS We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features. CONCLUSIONS These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection-relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.
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Affiliation(s)
| | - Anna Gogleva
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Thomas Hainaux
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
- Present address: Université Libre de Bruxelles, Bruxelles, Belgium
| | - Mehdi Doumane
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
- Present address: École Normale Supérieure de Lyon, Lyon, France
| | - Frej Tulin
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Clément Quan
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Temur Yunusov
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
| | - Kévin Floch
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK
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Novák K, Pikousová J, Czerneková V, Mátlová V. Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform. Anim Biotechnol 2017; 28:228-236. [PMID: 28489974 DOI: 10.1080/10495398.2017.1279170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. High-throughput sequencing of pooled PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a significant portion of the known diversity in the global breed panel and presumably exceeding diversity in production populations. Notably, the ancient Czech Red breed appeared to possess greater haplotype diversity than the Czech Red Pied breed, a Simmental variant, although the haplotype frequencies might have been distorted by significant crossbreeding and bottlenecks in the history of Czech Red cattle. The differences in haplotype frequencies validated the phenotypic distinctness of the local breeds. Due to the availability of Czech Red Pied production herds, the effect of intensive breeding on TLR diversity can be evaluated in this model. The advantages of the Pacific Biosciences technology for the resequencing of long PCR fragments with subsequent direct phasing were independently validated.
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Affiliation(s)
- Karel Novák
- a Institute of Animal Science , Prague-Uhříněves , Czech Republic
| | - Jitka Pikousová
- a Institute of Animal Science , Prague-Uhříněves , Czech Republic
| | | | - Věra Mátlová
- a Institute of Animal Science , Prague-Uhříněves , Czech Republic
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226
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Campa A, Ferreira JJ. Gene coding for an elongation factor is involved in resistance against powdery mildew in common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:849-860. [PMID: 28233030 DOI: 10.1007/s00122-017-2864-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/24/2017] [Indexed: 05/29/2023]
Abstract
Genetic control of the resistance response against powdery mildew in common bean was studied combining genetic, genomic and transcriptomic analyses. A candidate resistance gene in cultivar Porrillo Sintetico was proposed. The species causing the fungal disease powdery mildew (PM) in the local common bean crop was identified as Erysiphe polygoni through the molecular analysis of the internal transcribed spacer region. A genetic analysis of the resistance in cultivar Porrillo Sintetico was conducted using different F2:3 populations, and a dominant gene conferring total resistance against a local PM isolate was physically located between 84,188 and 218,664 bp of chromosome Pv04. An in silico analysis of this region, based on the common bean reference sequence, revealed four genes candidate to be involved in the resistance reaction. Relative expression levels of these genes after PM infection showed a significant over-expression of the candidate gene Phvul.004G001500 in the resistant genotype Porrillo Sintetico. This gene was re-sequenced in the parental genotypes X2776 and Porrillo Sintetico to explain their different phenotypic responses against PM. Several substitutions where identified in exon regions, all of them synonymous, so differences in the produced amino acid sequence were not expected. However, a total of 37 mutations were identified in non-coding regions of the gene sequence, suggesting that intron variation could be responsible for the different gene expression levels after PM infection. No evidence of other regulatory mechanisms, such as alternative splicing or methylation, was identified. Candidate resistance gene Phvul.004G001500 codes for an elongation factor that is not a typical gene related to recognition of specific pathogens in plants, suggesting its involvement in the resistance through plant immune system.
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Affiliation(s)
- Ana Campa
- Plant Genetics, Area of Horticultural and Forest Crops, SERIDA, Asturias, Spain.
| | - Juan José Ferreira
- Plant Genetics, Area of Horticultural and Forest Crops, SERIDA, Asturias, Spain
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227
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Protasio AV, van Dongen S, Collins J, Quintais L, Ribeiro DM, Sessler F, Hunt M, Rinaldi G, Collins JJ, Enright AJ, Berriman M. MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005559. [PMID: 28542189 PMCID: PMC5459504 DOI: 10.1371/journal.pntd.0005559] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/05/2017] [Accepted: 04/05/2017] [Indexed: 01/06/2023] Open
Abstract
Schistosomes are parasitic helminths that cause schistosomiasis, a disease affecting circa 200 million people, primarily in underprivileged regions of the world. Schistosoma mansoni is the most experimentally tractable schistosome species due to its ease of propagation in the laboratory and the high quality of its genome assembly and annotation. Although there is growing interest in microRNAs (miRNAs) in trematodes, little is known about the role these molecules play in the context of developmental processes. We use the completely unaware "miRNA-blind" bioinformatics tool Sylamer to analyse the 3'-UTRs of transcripts differentially expressed between the juvenile and adult stages. We show that the miR-277/4989 family target sequence is the only one significantly enriched in the transition from juvenile to adult worms. Further, we describe a novel miRNA, sma-miR-4989 showing that its proximal genomic location to sma-miR-277 suggests that they form a miRNA cluster, and we propose hairpin folds for both miRNAs compatible with the miRNA pathway. In addition, we found that expression of sma-miR-277/4989 miRNAs are up-regulated in adults while their predicted targets are characterised by significant down-regulation in paired adult worms but remain largely undisturbed in immature "virgin" females. Finally, we show that sma-miR-4989 is expressed in tegumental cells located proximal to the oesophagus gland and also distributed throughout the male worms' body. Our results indicate that sma-miR-277/4989 might play a dominant role in post-transcriptional regulation during development of juvenile worms and suggest an important role in the sexual development of female schistosomes.
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Affiliation(s)
- Anna V. Protasio
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Stijn van Dongen
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Julie Collins
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Leonor Quintais
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Diogo M. Ribeiro
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Florian Sessler
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Martin Hunt
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gabriel Rinaldi
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - James J. Collins
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Anton J. Enright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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228
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Spina EJ, Guzman E, Zhou H, Kosik KS, Smith WC. A microRNA-mRNA expression network during oral siphon regeneration in Ciona. Development 2017; 144:1787-1797. [PMID: 28432214 DOI: 10.1242/dev.144097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/10/2017] [Indexed: 12/14/2022]
Abstract
Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in Ciona robusta, and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed, we also identified 57 novel microRNAs, several of which are among the most highly differentially expressed. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGFβ during early regrowth, and negative regulation of extracellular proteases in late stage regeneration. Consistent with the expression results, we found that inhibition of TGFβ signaling blocked OS regeneration. A correlation network was subsequently inferred for all predicted microRNA-mRNA target pairs expressed during regeneration. Network-based clustering associated transcripts into 22 non-overlapping groups, the functional analysis of which showed enrichment of stress response, signaling pathway and extracellular protease categories that could be related to specific microRNAs. Predicted targets of the miR-9 cluster suggest a role in regulating differentiation and the proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle.
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Affiliation(s)
- Elijah J Spina
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elmer Guzman
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Hongjun Zhou
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Kenneth S Kosik
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - William C Smith
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA .,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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229
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O’Halloran DM. phylo-node: A molecular phylogenetic toolkit using Node.js. PLoS One 2017; 12:e0175480. [PMID: 28410421 PMCID: PMC5391935 DOI: 10.1371/journal.pone.0175480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 03/27/2017] [Indexed: 12/05/2022] Open
Abstract
Background Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. Results To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. Conclusions phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.
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Affiliation(s)
- Damien M. O’Halloran
- Department of Biological Sciences, The George Washington University, Washington, DC, United States of America
- Institute for Neuroscience, The George Washington University, Washington, DC, United States of America
- * E-mail:
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Hong SR, Jung SE, Lee EH, Shin KJ, Yang WI, Lee HY. DNA methylation-based age prediction from saliva: High age predictability by combination of 7 CpG markers. Forensic Sci Int Genet 2017; 29:118-125. [PMID: 28419903 DOI: 10.1016/j.fsigen.2017.04.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
DNA methylation is currently one of the most promising age-predictive biomarkers. Many studies have reported DNA methylation-based age predictive models, but most of these are based on DNA methylation patterns from blood. Only a few studies have examined age-predictive DNA patterns in saliva, which is one of the most frequently-encountered body fluids at crime scenes. In this study, we generated genome-wide DNA methylation profiles of saliva from 54 individuals and identified CpG markers that showed a high correlation between methylation and age. Because the age-associated marker candidates from saliva differed from those of blood, we investigated DNA methylation patterns of 6 age-associated CpG marker candidates (cg00481951, cg19671120, cg14361627, cg08928145, cg12757011, and cg07547549 of the SST, CNGA3, KLF14, TSSK6, TBR1, and SLC12A5 genes, respectively) in addition to a cell type-specific CpG marker (cg18384097 of the PTPN7 gene) in an independent set of saliva samples obtained from 226 individuals aged 18 to 65 years. Multiplex methylation SNaPshot reactions were used to generate the data. We then generated a linear regression model with age information and the methylation profile from the 113 training samples. The model exhibited a 94.5% correlation between predicted and chronological age with a mean absolute deviation (MAD) from chronological age of 3.13 years. In subsequent validation using 113 test samples, we also observed a high correlation between predicted and chronological age (Spearman's rho=0.952, MAD from chronological age=3.15years). The model composed of 7 selected CpG sites enabled age prediction in saliva with high accuracy, which will be useful in saliva analysis for investigative leads.
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Affiliation(s)
- Sae Rom Hong
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Sang-Eun Jung
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Eun Hee Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Woo Ick Yang
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea.
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Leelatanawit R, Uawisetwathana U, Klanchui A, Khudet J, Phomklad S, Wongtriphop S, Jiravanichpaisal P, Karoonuthaisiri N. Transcriptomic Analysis of Male Black Tiger Shrimp (Penaeus monodon) After Polychaete Feeding to Enhance Testicular Maturation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:125-135. [PMID: 28246982 DOI: 10.1007/s10126-017-9738-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
To reveal molecular mechanism of how polychaetes enhanced reproductive maturation in the male black tiger shrimp (Penaeus monodon), transcriptomic profiles of male reproductive organs (testes and vas deferens) between polychaete-fed and commercial pellet-fed male brooders were compared using cDNA microarray. The overall profiles were distinguishingly different between the two feed groups as well as between testes and vas deferens. Additionally, six of 11 differentially expressed gene identified by the microarray (HNRPUL1 and GCP4 in testes, MAT2B, CDC16, and CSN5 in vas deferens, and SLD5 in both organs) were validated by quantitative real-time PCR (qPCR) and found to exhibit significantly higher expression levels in polychaete-fed shrimp than those in commercial pellet-fed shrimp. From microarray and qPCR results, the differentially expressed transcripts in both testes and vas deferens between different feeds belonged to DNA replication and microtubule nucleation pathways. Interestingly, while the transcripts involved in nutrient uptake and nucleotide biosynthesis were increased only in testes, those involved in protein refolding and apoptosis were increased only in vas deferens. These findings suggest that polychaetes may enhance spermatogenesis by increasing spermatogonia proliferation in testes and by regulating mature spermatozoa in vas deferens.
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Affiliation(s)
- Rungnapa Leelatanawit
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand.
| | - Umaporn Uawisetwathana
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Amornpan Klanchui
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Jutatip Khudet
- Shrimp Genetic Improvement Center (SGIC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Surat Thani, Thailand
| | - Suwanchai Phomklad
- Shrimp Genetic Improvement Center (SGIC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Surat Thani, Thailand
| | - Somjai Wongtriphop
- Shrimp Genetic Improvement Center (SGIC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Surat Thani, Thailand
| | - Pikul Jiravanichpaisal
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
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STITCHER 2.0: primer design for overlapping PCR applications. Sci Rep 2017; 7:45349. [PMID: 28358011 PMCID: PMC5371788 DOI: 10.1038/srep45349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/22/2017] [Indexed: 12/04/2022] Open
Abstract
Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to ‘stitch’ individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user’s input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html.
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Shen C, Jin X, Zhu D, Lin Z. Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq. BMC Genomics 2017; 18:247. [PMID: 28330454 PMCID: PMC5363057 DOI: 10.1186/s12864-017-3643-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 03/18/2017] [Indexed: 11/10/2022] Open
Abstract
Background Cotton (Gossypium spp.), as the world’s most utilized textile fibre source, is an important, economically valuable crop worldwide. Understanding the genomic variation of tetraploid cotton species is important for exploitation of the excellent characteristics of wild cotton and for improving the diversity of cotton in breeding. However, the discovery of DNA polymorphisms in tetraploid cotton genomes has lagged behind other important crops. Results A total of 111,795,823 reads, 467,735 specific length amplified fragment (SLAF) tags and 139,176 high-quality DNA polymorphisms were identified using specific length amplified fragment sequencing (SLAF-seq), including 132,880 SNPs and 6,296 InDels between the reference genome (TM-1) and the five tetraploid cotton species. Intriguingly, gene ontology (GO) enrichment analysis revealed that a number of significant terms were related to reproduction in G. barbadense acc. 3–79. Based on the new data sets, we reconstructed phylogenetic trees that showed a high concordance to the phylogeny of diploid and polyploid cottons. A large amount of interspecific genetic variations were identified, and some of them were validated by the single-strand conformation polymorphism (SSCP) method, which will be applied in introgression genetics and breeding with G. hirsutum cv. Emian22 as the receptor and the other species as donors. Conclusions Using SLAF-seq, a large number of DNA polymorphisms were identified. The comprehensive analysis of DNA polymorphisms provided invaluable insights into the different tetraploid cotton species. More importantly, the identification of numerous interspecific genetic variations provides the basis and is very practical for future introgression breeding. The results presented herein provide a valuable genomic resource for new insights into the genetics and breeding of cotton. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3643-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xin Jin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - De Zhu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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RNA-Seq reveals the molecular mechanism of trapping and killing of root-knot nematodes by nematode-trapping fungi. World J Microbiol Biotechnol 2017; 33:65. [DOI: 10.1007/s11274-017-2232-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 02/17/2017] [Indexed: 12/22/2022]
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235
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Tortajada-Genaro LA, Puchades R, Maquieira Á. Primer design for SNP genotyping based on allele-specific amplification—Application to organ transplantation pharmacogenomics. J Pharm Biomed Anal 2017; 136:14-21. [DOI: 10.1016/j.jpba.2016.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/22/2016] [Accepted: 12/23/2016] [Indexed: 12/12/2022]
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Rodrigues-Luiz GF, Cardoso MS, Valdivia HO, Ayala EV, Gontijo CMF, Rodrigues TDS, Fujiwara RT, Lopes RS, Bartholomeu DC. TipMT: Identification of PCR-based taxon-specific markers. BMC Bioinformatics 2017; 18:104. [PMID: 28187714 PMCID: PMC5303226 DOI: 10.1186/s12859-017-1485-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 01/11/2017] [Indexed: 12/02/2022] Open
Abstract
Background Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity. Results Here, we report the development of a Tool for Identification of Primers for Multiple Taxa (TipMT), which is a web application to search and design primers for genotyping based on genomic data. The tool identifies and targets single sequence repeats (SSR) or orthologous/taxa-specific genes for genotyping using Multiplex PCR. This pipeline was applied to the genomes of four species of Leishmania (L. amazonensis, L. braziliensis, L. infantum and L. major) and validated by PCR using artificial genomic DNA mixtures of the Leishmania species as templates. This experimental validation demonstrates the reliability of TipMT because amplification profiles showed discrimination of genomic DNA samples from Leishmania species. Conclusions The TipMT web tool allows for large-scale identification and design of taxon-specific primers and is freely available to the scientific community at http://200.131.37.155/tipMT/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1485-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriela F Rodrigues-Luiz
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana S Cardoso
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hugo O Valdivia
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edward V Ayala
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Thiago de S Rodrigues
- Departamento de Computação, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ricardo T Fujiwara
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Robson S Lopes
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Departamento de Computação, Universidade Federal do Mato Grosso, Barra do Garças, Mato Grosso, Brazil
| | - Daniella C Bartholomeu
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Development of Anonymous Nuclear Loci for Pterospora andromedea (Monotropoideae) Using Illumina and Ion Torrent Sequencing Data. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0686-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wingo TS, Kotlar A, Cutler DJ. MPD: multiplex primer design for next-generation targeted sequencing. BMC Bioinformatics 2017; 18:14. [PMID: 28056760 PMCID: PMC5217220 DOI: 10.1186/s12859-016-1453-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background Targeted resequencing offers a cost-effective alternative to whole-genome and whole-exome sequencing when investigating regions known to be associated with a trait or disease. There are a number of approaches to targeted resequencing, including microfluidic PCR amplification, which may be enhanced by multiplex PCR. Currently, there is no open-source software that can design next-generation multiplex PCR experiments that ensures primers are unique at a genome-level and efficiently pools compatible primers. Results We present MPD, a software package that automates the design of multiplex PCR primers for next-generation sequencing. The core of MPD is implemented in C for speed and uses a hashed genome to ensure primer uniqueness, avoids placing primers over sites of known variation, and efficiently pools compatible primers. A JavaScript web application (http://multiplexprimer.io) utilizing the MPD Perl package provides a convenient platform for users to make designs. Using a realistic set of genes identified by genome-wide association studies (GWAS), we achieve 90% coverage of all exonic regions using stringent design criteria. Using the first 47 primer pools for wet-lab validation, we sequenced ~25Kb at 99.7% completeness with a mean coverage of 300X among 313 samples simultaneously and identified 224 variants. The number and nature of variants we observe are consistent with high quality sequencing. Conclusions MPD can successfully design multiplex PCR experiments suitable for next-generation sequencing, and simplifies retooling targeted resequencing pipelines to focus on new targets as new genetic evidence emerges.
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Affiliation(s)
- Thomas S Wingo
- Division of Neurology, Atlanta VA Medical Center, Decatur, 30033, GA, USA. .,Department of Neurology, Emory University School of Medicine, Atlanta, 30322, GA, USA. .,Department of Human Genetics, Emory University School of Medicine, 615 Michael Street NE, Atlanta, GA, 30322, USA.
| | - Alex Kotlar
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street NE, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street NE, Atlanta, GA, 30322, USA
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PCR-Based Detection Methods for Single-Nucleotide Polymorphism or Mutation: Real-Time PCR and Its Substantial Contribution Toward Technological Refinement. Adv Clin Chem 2017; 80:45-72. [PMID: 28431642 DOI: 10.1016/bs.acc.2016.11.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses. PCR-based methods for SNP/mutation detection are broadly categorized into two types-(1) polymorphic or mutant allele-directed specific analysis using primers matched with substituted nucleotide or using oligonucleotides to block or clamp the nontargeted template, and (2) melting curve analysis, which is combined with the real-time PCR techniques using hydrolysis probes, hybridization probes, or double-stranded DNA-binding fluorescent dyes. Innovative and novel approaches as well as technical improvements have made SNP- or mutation-detection methods increasingly more sophisticated. These advances include DNA/RNA preparation and subsequent amplification steps, and miniaturization of PCR instruments such that testing may be performed with relative ease in clinical laboratories or as a point-of-care test in clinical settings.
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Ammar MH, Khan AM, Migdadi HM, Abdelkhalek SM, Alghamdi SS. Faba bean drought responsive gene identification and validation. Saudi J Biol Sci 2017; 24:80-89. [PMID: 28053575 PMCID: PMC5199002 DOI: 10.1016/j.sjbs.2016.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/08/2016] [Accepted: 05/15/2016] [Indexed: 11/16/2022] Open
Abstract
This study was carried out to identify drought-responsive genes in a drought tolerant faba bean variety (Hassawi 2) using a suppressive subtraction hybridization approach (SSH). A total of 913 differentially expressed clones were sequenced from a differential cDNA library that resulted in a total of 225 differentially expressed ESTs. The genes of mitochondrial and chloroplast origin were removed, and the remaining 137 EST sequences were submitted to the gene bank EST database (LIBEST_028448). A sequence analysis identified 35 potentially drought stress-related ESTs that regulate ion channels, kinases, and energy production and utilization and transcription factors. Quantitative PCR on Hassawi 2 genotype confirmed that more than 65% of selected drought-responsive genes were drought-related. Among these induced genes, the expression levels of eight highly up-regulated unigenes were further analyzed across 38 selected faba bean genotypes that differ in their drought tolerance levels. These unigenes included ribulose 1,5-bisphosphate carboxylase (rbcL) gene, non-LTR retroelement reverse related, probable cyclic nucleotide-gated ion channel, polyubiquitin, potassium channel, calcium-dependent protein kinase and putative respiratory burst oxidase-like protein C and a novel unigene. The expression patterns of these unigenes were variable across 38 genotypes however, it was found to be very high in tolerant genotype. The up-regulation of these unigenes in majority of tolerant genotypes suggests their possible role in drought tolerance. The identification of possible drought responsive candidate genes in Vicia faba reported here is an important step toward the development of drought-tolerant genotypes that can cope with arid environments.
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Affiliation(s)
- Megahed H. Ammar
- Legume Research Group, Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- Rice Research and Training Center, Sakha, 33717 KafrEl-Sheikh, Egypt
| | - Altaf M. Khan
- Legume Research Group, Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Hussein M. Migdadi
- Legume Research Group, Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Samah M. Abdelkhalek
- Botany and Microbiology Department, College of Science, King Saud University, Saudi Arabia
- Rice Research and Training Center, Sakha, 33717 KafrEl-Sheikh, Egypt
| | - Salem S. Alghamdi
- Legume Research Group, Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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241
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Pieck ML, Ruck A, Farman ML, Peterson GL, Stack JP, Valent B, Pedley KF. Genomics-Based Marker Discovery and Diagnostic Assay Development for Wheat Blast. PLANT DISEASE 2017; 101:103-109. [PMID: 30682315 DOI: 10.1094/pdis-04-16-0500-re] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Wheat blast has emerged as a major threat to wheat production in South America. Although originally restricted to Brazil, the disease has since been observed in the neighboring countries of Argentina, Bolivia, and Paraguay and recently the pathogen, Magnaporthe oryzae Triticum pathotype, was isolated from infected wheat in Bangladesh. There is growing concern that the pathogen may continue to spread to other parts of the world, including the United States, where several M. oryzae pathotypes are endemic. M. oryzae pathotypes are morphologically indistinguishable and, therefore, must be characterized genotypically. Symptoms of wheat blast include bleaching of the head, which closely resembles the symptoms of Fusarium head blight, further complicating efforts to monitor for the presence of the pathogen in the field. We used a genomics-based approach to identify molecular markers unique to the Triticum pathotype of M. oryzae. One of these markers, MoT3, was selected for the development of a polymerase chain reaction (PCR)-based diagnostic assay that was evaluated for specificity using DNA from 284 M. oryzae isolates collected from a diverse array of host species. Conventional PCR primers were designed to amplify a 361-bp product, and the protocol consistently amplified from as little as 0.1 ng of purified DNA. The specificity of the MoT3-based assay was also evaluated using Fusarium spp. DNA, from which no amplicons were detected.
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Affiliation(s)
- Michael L Pieck
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit (FDWSRU)
| | - Amy Ruck
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit (FDWSRU)
| | - Mark L Farman
- Department of Plant Pathology, University of Kentucky, Lexington 40546
| | | | - James P Stack
- Department of Plant Pathology, Kansas State University, Throckmorton Plant Sciences Center, Manhattan 66506
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Throckmorton Plant Sciences Center, Manhattan 66506
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Aravind J, Rinku S, Pooja B, Shikha M, Kaliyugam S, Mallikarjuna MG, Kumar A, Rao AR, Nepolean T. Identification, Characterization, and Functional Validation of Drought-responsive MicroRNAs in Subtropical Maize Inbreds. FRONTIERS IN PLANT SCIENCE 2017; 8:941. [PMID: 28626466 PMCID: PMC5454542 DOI: 10.3389/fpls.2017.00941] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
MicroRNA-mediated gene regulation plays a crucial role in controlling drought tolerance. In the present investigation, 13 drought-associated miRNA families consisting of 65 members and regulating 42 unique target mRNAs were identified from drought-associated microarray expression data in maize and were subjected to structural and functional characterization. The largest number of members (14) was found in the zma-miR166 and zma-miR395 families, with several targets. However, zma-miR160, zma-miR390, zma-miR393, and zma-miR2275 each showed a single target. Twenty-three major drought-responsive cis-regulatory elements were found in the upstream regions of miRNAs. Many drought-related transcription factors, such as GAMYB, HD-Zip III, and NAC, were associated with the target mRNAs. Furthermore, two contrasting subtropical maize genotypes (tolerant: HKI-1532 and sensitive: V-372) were used to understand the miRNA-assisted regulation of target mRNA under drought stress. Approximately 35 and 31% of miRNAs were up-regulated in HKI-1532 and V-372, respectively. The up-regulation of target mRNAs was as high as 14.2% in HKI-1532 but was only 2.38% in V-372. The expression patterns of miRNA-target mRNA pairs were classified into four different types: Type I- up-regulation, Type II- down-regulation, Type III- neutral regulation, and Type IV- opposite regulation. HKI-1532 displayed 46 Type I, 13 Type II, and 23 Type III patterns, whereas V-372 had mostly Type IV interactions (151). A low level of negative regulations of miRNA associated with a higher level of mRNA activity in the tolerant genotype helped to maintain crucial biological functions such as ABA signaling, the auxin response pathway, the light-responsive pathway and endosperm expression under stress conditions, thereby leading to drought tolerance. Our study identified candidate miRNAs and mRNAs operating in important pathways under drought stress conditions, and these candidates will be useful in the development of drought-tolerant maize hybrids.
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Affiliation(s)
- Jayaraman Aravind
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- Division of Germplasm Conservation, National Bureau of Plant Genetic ResourcesNew Delhi, India
| | - Sharma Rinku
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- Department of Life Sciences, Shiv Nadar UniversityGautam Buddha Nagar, India
| | - Banduni Pooja
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | - Mittal Shikha
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | - Shiriga Kaliyugam
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Arun Kumar
- National Phytotron Facility, Indian Agricultural Research InstituteNew Delhi, India
| | - Atmakuri Ramakrishna Rao
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research InstituteNew Delhi, India
| | - Thirunavukkarasu Nepolean
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- *Correspondence: Thirunavukkarasu Nepolean ;
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Zhao Y, Keremane M, Prakash CS, He G. Characterization and Amplification of Gene-Based Simple Sequence Repeat (SSR) Markers in Date Palm. Methods Mol Biol 2017; 1638:259-271. [PMID: 28755229 DOI: 10.1007/978-1-4939-7159-6_21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The paucity of molecular markers limits the application of genetic and genomic research in date palm (Phoenix dactylifera L.). Availability of expressed sequence tag (EST) sequences in date palm may provide a good resource for developing gene-based markers. This study characterizes a substantial fraction of transcriptome sequences containing simple sequence repeats (SSRs) from the EST sequences in date palm. The EST sequences studied are mainly homologous to those of Elaeis guineensis and Musa acuminata. A total of 911 gene-based SSR markers, characterized with functional annotations, have provided a useful basis not only for discovering candidate genes and understanding genetic basis of traits of interest but also for developing genetic and genomic tools for molecular research in date palm, such as diversity study, quantitative trait locus (QTL) mapping, and molecular breeding. The procedures of DNA extraction, polymerase chain reaction (PCR) amplification of these gene-based SSR markers, and gel electrophoresis of PCR products are described in this chapter.
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Affiliation(s)
- Yongli Zhao
- Department of Agricultural and Environmental Science, College of Agriculture, Environment, and Nutrition Sciences, Tuskegee University, 1200 W. Montgomery Rd, Tuskegee, AL, 36088, USA
| | | | | | - Guohao He
- Department of Agricultural and Environmental Science, College of Agriculture, Environment, and Nutrition Sciences, Tuskegee University, 1200 W. Montgomery Rd, Tuskegee, AL, 36088, USA.
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Ponyared P, Ponsawat J, Tongsima S, Seresangtakul P, Akkasaeng C, Tantisuwichwong N. ESAP plus: a web-based server for EST-SSR marker development. BMC Genomics 2016; 17:1035. [PMID: 28155670 PMCID: PMC5260030 DOI: 10.1186/s12864-016-3328-4] [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] [Indexed: 11/14/2022] Open
Abstract
Background Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. Results A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface. Conclusions ESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3328-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Piyarat Ponyared
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Jiradej Ponsawat
- Department of Computer Engineering, Faculty of Engineering, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, 12120, Thailand
| | - Pusadee Seresangtakul
- Department of Computer Science, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chutipong Akkasaeng
- Department of Plant Science and Agricultural Resources, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
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Rausch V, Peccerella T, Lackner C, Yagmur E, Seitz HK, Longerich T, Mueller S. Primary liver injury and delayed resolution of liver stiffness after alcohol detoxification in heavy drinkers with the PNPLA3 variant I148M. World J Hepatol 2016; 8:1547-1556. [PMID: 28050235 PMCID: PMC5165268 DOI: 10.4254/wjh.v8.i35.1547] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 07/15/2016] [Accepted: 09/18/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the influence of PNPLA3 genotype in heavy drinkers on serum markers and liver stiffness (LS) during alcohol withdrawal and its association with histology.
METHODS Caucasian heavy drinkers (n = 521) with a mean alcohol consumption of 192.1 g/d (median alcohol consumption: 169.0 g/d; 95%CI: 179.0-203.3) were enrolled at the Salem Medical Center, University of Heidelberg. LS was measured by transient elastography (Fibroscan, Echosens SA, Paris, France). LS and serum markers were prospectively studied in these patients with all stages of alcoholic liver disease (steatosis, steatohepatitis, fibrosis) prior and after alcohol detoxification with a mean observation interval of 6.2 ± 3.2 d. A liver biopsy with histological analysis including the Kleiner score was obtained in 80 patients.
RESULTS The PNPLA3 rs738409 genotype distribution for CC, CG and GG was 39.2%, 52.6% and 8.2%. GG genotype primarily correlated with histological steatohepatitis (r = 0.404, P < 0.005), ballooning (r = 0.319, P < 0.005) and less with steatosis (r = 0.264, P < 0.05). Mean LS was lowest in CC carriers (13.1 kPa) as compared to CG and GG carriers (17.6 and 17.2 kPa). Notably, LS primarily correlated with fibrosis stage (r = 0.828, P < 0.005), ballooning (r = 0.516, P < 0.005), steatohepatitis (r = 0.319, P < 0.005) but not with steatosis. After alcohol withdrawal, LS did not change in CC carriers, significantly decreased in CG-carriers from 17.6 to 12.7 kPa but to a lesser extent in GG carriers from 17.6 to 14.5 kPa. This was due to prolonged resolution of inflammation with significantly elevated aspartate transaminase levels after alcohol withdrawal in GG carriers. Non-invasive fibrosis assessment by LS in all patients showed a significantly higher F0 rate as compared to the biopsy cohort (47% vs 6%) with 3.8% more CC carriers while 3.7% less were seen in the F4 cirrhosis group. Thus, about 20% of patients with alcoholic liver cirrhosis would be attributable to PNPLA3 G variants. The OR to develop cirrhosis corrected for age, gender and body mass index was 1.295 (95%CI: 0.787-2.131) for CG + GG carriers.
CONCLUSION In heavy drinkers, PNPLA3 GG primarily correlates with ballooning/steatohepatitis but not steatosis resulting in a delayed inflammation-associated resolution of LS. Consequently, sustained ballooning-associated LS elevation seems to be a potential risk factor for fibrosis progression in PNPLA3 GG carriers.
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Development and characterization of 23 microsatellite markers for the endangered beetle Carabus lafossei (Coleoptera, Carabidae). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0660-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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QU CHUNMEI, LIANG XUFANG, HUANG WEI, ZHAO CHENG, CAO LIANG, YANG MIN, TIAN CHANGXU. Development and characterization of twenty-nine novel polymorphic microsatellite loci in the mandarin fish Siniperca chuatsi. J Genet 2016. [DOI: 10.1007/s12041-013-0221-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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248
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Aykanat T, Lindqvist M, Pritchard VL, Primmer CR. From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar. JOURNAL OF FISH BIOLOGY 2016; 89:2658-2679. [PMID: 27709620 DOI: 10.1111/jfb.13149] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included the sdy partial gene product to determine genetic sex, as well as three additional modules comprising SNPs for assessing neutral genetic variation (NSNP = 150), examining functional genetic variation associated with sea age at maturity (NSNP = 5), and for performing genetic subpopulation assignment (NSNP = 61). The assay was primarily developed to monitor long-term genetic changes in S. salar from the Teno River, but modules are likely suitable for application in a wide range of S. salar populations. Furthermore, the fast and versatile assay development pipeline offers a strategy for developing targeted sequencing assays in any species.
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Affiliation(s)
- T Aykanat
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - M Lindqvist
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - V L Pritchard
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - C R Primmer
- Department of Biology, University of Turku, Turku, 20014, Finland
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249
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De novo SNP markers development for the Neotropical gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing-based genotyping. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0584-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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250
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Kleppe L, Edvardsen RB, Furmanek T, Andersson E, Juanchich A, Wargelius A. bmp15l,figla,smc1bl, andlarp6lare preferentially expressed in germ cells in Atlantic salmon (Salmo salarL.). Mol Reprod Dev 2016; 84:76-87. [DOI: 10.1002/mrd.22755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/02/2016] [Indexed: 11/11/2022]
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