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Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis. GENETICS RESEARCH INTERNATIONAL 2016; 2016:7052323. [PMID: 27340568 PMCID: PMC4908241 DOI: 10.1155/2016/7052323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022]
Abstract
Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.
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102
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Population genetic structure and identification of loci under selection in the invasive tunicate, Botryllus schlosseri, using newly developed EST-SSRs. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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103
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Development of microsatellite markers for Manilkara maxima T.D. Penn. (Sapotaceae) and their use in conservation genetics. Mol Biol Rep 2016; 43:451-5. [PMID: 27061192 DOI: 10.1007/s11033-016-3981-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/03/2016] [Indexed: 10/22/2022]
Abstract
Manilkara maxima is an endemic tree species of the Atlantic Forest in southern Bahia, Brazil. It is considered important for forest conservation due to its mutualistic interactions with endemic and endangered animals. Our aim was to develop microsatellite markers to estimate genetic diversity in order to provide information for effectiveness of future conservation programs. We used next generation sequencing technology to develop the first specific microsatellite markers for M. maxima. Seventeen new microsatellite loci were applied in 72 individuals sampled in three natural populations. On average, the number of alleles per loci was 8.8. The expected heterozygosity varied between 0.72 and 0.77, indicating that the developed set of molecular markers is useful for genetic diversity studies. Additionally, the estimated value for the combined probability of exclusion (Q) was greater than 0.999, which indicates the powerful of these molecular tools for paternity and kinship analysis. Our results demonstrate that the set of microsatellites developed in this work is a powerful tool for population genetics, molecular ecology and conservation biology purposes.
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104
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Balao F, Tannhäuser M, Lorenzo MT, Hedrén M, Paun O. Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex. Heredity (Edinb) 2016; 116:351-61. [PMID: 26604189 PMCID: PMC4787024 DOI: 10.1038/hdy.2015.98] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 10/17/2015] [Accepted: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.
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Affiliation(s)
- F Balao
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Tannhäuser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M T Lorenzo
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Hedrén
- Department of Biology, Lund University, Lund, Sweden
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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105
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Kang SW, Patnaik BB, Hwang HJ, Park SY, Wang TH, Park EB, Chung JM, Song DK, Patnaik HH, Lee JB, Kim C, Kim S, Park HS, Lee JS, Han YS, Lee YS. De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology. Int J Mol Sci 2016; 17:379. [PMID: 26999110 PMCID: PMC4813237 DOI: 10.3390/ijms17030379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/05/2016] [Accepted: 03/09/2016] [Indexed: 12/24/2022] Open
Abstract
Aegista chejuensis and Aegista quelpartensis (Family-Bradybaenidae) are endemic to Korea, and are considered vulnerable due to declines in their population. The limited genetic resources for these species restricts the ability to prioritize conservation efforts. We sequenced the transcriptomes of these species using Illumina paired-end technology. Approximately 257 and 240 million reads were obtained and assembled into 198,531 and 230,497 unigenes for A. chejuensis and A. quelpartensis, respectively. The average and N50 unigene lengths were 735.4 and 1073 bp, respectively, for A. chejuensis, and 705.6 and 1001 bp, respectively, for A. quelpartensis. In total, 68,484 (34.5%) and 77,745 (33.73%) unigenes for A. chejuensis and A. quelpartensis, respectively, were annotated to databases. Gene Ontology terms were assigned to 23,778 (11.98%) and 26,396 (11.45) unigenes, for A. chejuensis and A. quelpartensis, respectively, while 5050 and 5838 unigenes were mapped to 117 and 124 pathways in the Kyoto Encyclopedia of Genes and Genomes database. In addition, we identified and annotated 9542 and 10,395 putative simple sequence repeats (SSRs) in unigenes from A. chejuensis and A. quelpartensis, respectively. We designed a list of PCR primers flanking the putative SSR regions. These microsatellites may be utilized for future phylogenetics and conservation initiatives.
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Affiliation(s)
- Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha 751024, India.
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Hongray Howrelia Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Jae Bong Lee
- Korea Zoonosis Research Institute (KOZRI), Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do 54528, Korea.
| | - Changmu Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Soonok Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD. 621-6 Banseok-dong, Yuseong-gu, Daejeon 34069, Korea.
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do 243341, Korea.
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea.
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
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106
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McAssey EV, Gudger EG, Zuellig MP, Burke JM. Population Genetics of the Rubber-Producing Russian Dandelion (Taraxacum kok-saghyz). PLoS One 2016; 11:e0146417. [PMID: 26727474 PMCID: PMC4703197 DOI: 10.1371/journal.pone.0146417] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/16/2015] [Indexed: 11/19/2022] Open
Abstract
The Russian dandelion, Taraxacum kok-saghyz (TKS), is a perennial species native to Central Asia that produces high quality, natural rubber. Despite its potential to help maintain a stable worldwide rubber supply, little is known about genetic variation in this species. To facilitate future germplasm improvement efforts, we developed simple-sequence repeat (SSR) markers from available expressed-sequence tag (EST) data and used them to investigate patterns of population genetic diversity in this nascent crop species. We identified numerous SSRs (1,510 total) in 1,248 unigenes from a larger set of 6,960 unigenes (derived from 16,441 ESTs) and designed PCR primers targeting 767 of these loci. Screening of a subset of 192 of these primer pairs resulted in the identification of 48 pairs that appeared to produce single-locus polymorphisms. We then used the most reliable 17 of these primer pairs to genotype 176 individuals from 17 natural TKS populations. We observed an average of 4.8 alleles per locus with population-level expected heterozygosities ranging from 0.28 to 0.50. An average pairwise FST of 0.11 indicated moderate but statistically significant levels of genetic differentiation, though there was no clear geographic patterning to this differentiation. We also tested these 17 primer pairs in the widespread common dandelion, T. officinale, and a majority successfully produced apparently single-locus amplicons. This result demonstrates the potential utility of these markers for genetic analyses in other species in the genus.
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Affiliation(s)
- Edward V. McAssey
- University of Georgia, Department of Plant Biology, Miller Plant Sciences Building, Athens, GA 30602, United States of America
| | - Ethan G. Gudger
- University of Georgia, Department of Plant Biology, Miller Plant Sciences Building, Athens, GA 30602, United States of America
| | - Matthew P. Zuellig
- University of Georgia, Department of Genetics, Davidson Life Sciences Building, Athens, GA 30602, United States of America
| | - John M. Burke
- University of Georgia, Department of Plant Biology, Miller Plant Sciences Building, Athens, GA 30602, United States of America
- * E-mail:
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107
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Chapuis MP, Plantamp C, Streiff R, Blondin L, Piou C. Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations. Mol Ecol 2015; 24:6107-19. [PMID: 26562076 DOI: 10.1111/mec.13465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 01/21/2023]
Abstract
Unravelling variation among taxonomic orders regarding the rate of evolution in microsatellites is crucial for evolutionary biology and population genetics research. The mean mutation rate of microsatellites tends to be lower in arthropods than in vertebrates, but data are scarce and mostly concern accumulation of mutations in model species. Based on parent-offspring segregations and a hierarchical Bayesian model, the mean rate of mutation in the orthopteran insect Schistocerca gregaria was estimated at 2.1e(-4) per generation per untranscribed dinucleotide locus. This is close to vertebrate estimates and one order of magnitude higher than estimates from species of other arthropod orders, such as Drosophila melanogaster and Daphnia pulex. We also found evidence of a directional bias towards expansions even for long alleles and exceptionally large ranges of allele sizes. Finally, at transcribed microsatellites, the mean rate of mutation was half the rate found at untranscribed loci and the mutational model deviated from that usually considered, with most mutations involving multistep changes that avoid disrupting the reading frame. Our direct estimates of mutation rate were discussed in the light of peculiar biological and genomic features of S. gregaria, including specificities in mismatch repair and the dependence of its activity to allele length. Shedding new light on the mutational dynamics of grasshopper microsatellites is of critical importance for a number of research fields. As an illustration, we showed how our findings improve microsatellite application in population genetics, by obtaining a more precise estimation of S. gregaria effective population size from a published data set based on the same microsatellites.
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Affiliation(s)
- M-P Chapuis
- CIRAD, UMR CBGP, Montpellier, F-34398, France
| | - C Plantamp
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Villeurbanne, 69622, France
| | - R Streiff
- INRA, UMR CBGP, Montpellier, F-34398, France.,INRA, UMR DGIMI, Montpellier, F-34000, France
| | - L Blondin
- CIRAD, UPR B-AMR, Montpellier, F-34398, France
| | - C Piou
- CIRAD, UMR CBGP, Montpellier, F-34398, France
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108
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De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora). Int J Mol Sci 2015; 16:29047-59. [PMID: 26690126 PMCID: PMC4691086 DOI: 10.3390/ijms161226139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/13/2015] [Accepted: 11/26/2015] [Indexed: 01/28/2023] Open
Abstract
Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora.
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109
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Garzón-Martínez GA, Osorio-Guarín JA, Delgadillo-Durán P, Mayorga F, Enciso-Rodríguez FE, Landsman D, Mariño-Ramírez L, Barrero LS. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers. ACTA ACUST UNITED AC 2015; 4:29-37. [PMID: 26550601 DOI: 10.1016/j.plgene.2015.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies.
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Affiliation(s)
- Gina A Garzón-Martínez
- Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia
| | - Jaime A Osorio-Guarín
- Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia
| | - Paola Delgadillo-Durán
- Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia
| | - Franklin Mayorga
- Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia
| | - Felix E Enciso-Rodríguez
- Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, United States of America, Bethesda, MD, USA
| | - Leonardo Mariño-Ramírez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, United States of America, Bethesda, MD, USA
| | - Luz Stella Barrero
- Tibaitatá Research Center, Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogotá, Colombia ; Agrobiodiversity Department, National Direction of Research and Development, CORPOICA
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110
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Ding Y, Zhang J, Lu Y, Lin E, Lou L, Tong Z. Development of EST-SSR markers and analysis of genetic diversity in natural populations of endemic and endangered plant Phoebe chekiangensis. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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111
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Zhao YM, Zhou T, Li ZH, Zhao GF. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae). Molecules 2015; 20:21214-31. [PMID: 26633323 PMCID: PMC6332360 DOI: 10.3390/molecules201219758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/16/2023] Open
Abstract
Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288) were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. A total of 3891 simple sequence repeats (SSRs) were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research.
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Affiliation(s)
- Yue-Mei Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
- College of Biopharmaceutical and Food Engineering, Shangluo University, Beixin Street, Shangluo 726000, China.
| | - Tao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
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112
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De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing. Mol Genet Genomics 2015; 291:849-62. [DOI: 10.1007/s00438-015-1147-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/13/2015] [Indexed: 01/08/2023]
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113
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Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.). Int J Genomics 2015; 2015:679548. [PMID: 26664999 PMCID: PMC4668317 DOI: 10.1155/2015/679548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/21/2015] [Indexed: 11/17/2022] Open
Abstract
Perilla frutescens is valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses of P. frutescens are limited due to a lack of gene annotations and characterization. A full-length cDNA library from P. frutescens leaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as primer pairs. This study is the first to report comparative genomics and EST-SSR markers from P. frutescens will help gene discovery and provide an important source for functional genomics and molecular genetic research in this interesting medicinal plant.
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114
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Lin Y, Chen Y, Xiong W, Zhan A. Genomewide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex. Mol Ecol Resour 2015; 16:784-93. [PMID: 26505988 DOI: 10.1111/1755-0998.12481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 09/23/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
Abstract
The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genomewide genetic markers are still lacking. Here, we characterized a large set of genomewide gene-associated microsatellite markers for C. intestinalis spA (=C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N = 24-48), and Cape Town, South Africa (N = 24-33). The number of alleles, observed heterozygosity and expected heterozygosity ranged from 2 to 11, 0 to 0.833 and 0.021 to 0.818, and from 2 to 10, 0 to 0.879 and 0.031 to 0.845 for the Spanish and African populations, respectively. When all microsatellites were tested for cross-species utility, only 60 loci (25.8%) could be successfully amplified and all loci were polymorphic in C. intestinalis spB. A high level of genomewide polymorphism is likely responsible for the low transferability. The large set of microsatellite markers characterized here is expected to provide a useful genomewide resource for ecological and evolutionary studies using C. intestinalis as a model.
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Affiliation(s)
- Yaping Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
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Bushakra JM, Lewers KS, Staton ME, Zhebentyayeva T, Saski CA. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.). BMC PLANT BIOLOGY 2015; 15:258. [PMID: 26499487 PMCID: PMC4620654 DOI: 10.1186/s12870-015-0629-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/28/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. METHODS Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs. Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. RESULTS To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. CONCLUSION This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.
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Affiliation(s)
- Jill M Bushakra
- USDA-ARS, National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR, 97333-2521, USA.
| | - Kim S Lewers
- USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD, 20705-2350, USA.
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 EJ Chapman Drive, 370 PBB, Knoxville, TN, 37996, USA.
| | - Tetyana Zhebentyayeva
- Genomics & Computational Biology Laboratory, Biosystems Research Complex, Clemson University, 51 New Cherry St., 304, Clemson, SC, 29634, USA.
| | - Christopher A Saski
- Genomics & Computational Biology Laboratory, Biosystems Research Complex, Clemson University, 51 New Cherry St., 304, Clemson, SC, 29634, USA.
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Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants. BMC Genomics 2015; 16:781. [PMID: 26463180 PMCID: PMC4603344 DOI: 10.1186/s12864-015-2031-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. METHODS Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. RESULTS We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. CONCLUSIONS The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.
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Kanduma EG, Mwacharo JM, Mwaura S, Njuguna JN, Nzuki I, Kinyanjui PW, Githaka N, Heyne H, Hanotte O, Skilton RA, Bishop RP. Multi-locus genotyping reveals absence of genetic structure in field populations of the brown ear tick (Rhipicephalus appendiculatus) in Kenya. Ticks Tick Borne Dis 2015; 7:26-35. [PMID: 26278352 DOI: 10.1016/j.ttbdis.2015.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 10/23/2022]
Abstract
Rhipicephalus appendiculatus is an important tick vector of several pathogens and parasitizes domestic and wild animals across eastern and southern Africa. However, its inherent genetic variation and population structure is poorly understood. To investigate whether mammalian host species, geographic separation and resulting reproductive isolation, or a combination of these, define the genetic structure of R. appendiculatus, we analyzed multi-locus genotype data from 392 individuals from 10 geographic locations in Kenya generated in an earlier study. These ticks were associated with three types of mammalian host situations; (1) cattle grazing systems, (2) cattle and wildlife co-grazing systems (3) wildlife grazing systems without livestock. We also analyzed data from 460 individuals from 10 populations maintained as closed laboratory stocks and 117 individuals from five other species in the genus Rhipicephalus. The pattern of genotypes observed indicated low levels of genetic differentiation between the ten field populations (FST=0.014±0.002) and a lack of genetic divergence corresponding to the degree of separation of the geographic sampling locations. There was also no clear association of particular tick genotypes with specific host species. This is consistent with tick dispersal over large geographic ranges and lack of host specificity. In contrast, the 10 laboratory populations (FST=0.248±0.015) and the five other species of Rhipicephalus (FST=0.368±0.032) were strongly differentiated into distinct genetic groups. Some laboratory bred populations diverged markedly from their field counterparts in spite of originally being sampled from the same geographic locations. Our results demonstrate a lack of defined population genetic differentiation in field populations of the generalist R. appendiculatus in Kenya, which may be a result of the frequent anthropogenic movement of livestock and mobility of its several wildlife hosts between different locations.
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Affiliation(s)
- Esther G Kanduma
- Biosciences eastern and central Africa - International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, 00100 Nairobi, Kenya; Department of Biochemistry, School of Medicine, University of Nairobi, P.O. Box 30197, Nairobi, Kenya.
| | - Joram M Mwacharo
- Centre for Genetics and Genomics, School of Life Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK; International Centre for Agricultural Research in Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Stephen Mwaura
- International Livestock Research Institute (ILRI), P. O. Box 30709, 00100 Nairobi, Kenya
| | - Joyce N Njuguna
- Biosciences eastern and central Africa - International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, 00100 Nairobi, Kenya
| | - Inosters Nzuki
- Biosciences eastern and central Africa - International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, 00100 Nairobi, Kenya
| | - Peter W Kinyanjui
- Department of Biochemistry, School of Medicine, University of Nairobi, P.O. Box 30197, Nairobi, Kenya
| | - Naftaly Githaka
- International Livestock Research Institute (ILRI), P. O. Box 30709, 00100 Nairobi, Kenya
| | - Heloise Heyne
- Parasites, Vectors, & Vector-Borne Diseases Progamme, ARC-Onderstepoort Veterinary Institute, Pretoria, South Africa
| | - Olivier Hanotte
- Centre for Genetics and Genomics, School of Life Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Robert A Skilton
- Biosciences eastern and central Africa - International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, 00100 Nairobi, Kenya
| | - Richard P Bishop
- International Livestock Research Institute (ILRI), P. O. Box 30709, 00100 Nairobi, Kenya
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Genetic diversity and structure of Pinus dabeshanensis revealed by expressed sequence tag-simple sequence repeat (EST-SSR) markers. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Cai C, Yang Y, Cheng L, Tong C, Feng J. Development and assessment of EST-SSR marker for the genetic diversity among tobaccos (Nicotiana tabacum L.). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415020064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Souframanien J, Reddy KS. De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L.) Hepper]. PLoS One 2015; 10:e0128748. [PMID: 26042595 PMCID: PMC4456365 DOI: 10.1371/journal.pone.0128748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 05/01/2015] [Indexed: 12/02/2022] Open
Abstract
Black gram [V. mungo (L.) Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS) were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO) functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were identified, of which majority of TCS are grouped into purine metabolism (678) followed by pyrimidine metabolism (263). A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35%) followed by di-nucleotide repeats (32%). PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Tri-nucleotide repeats (57.3%) were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.
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Affiliation(s)
- J. Souframanien
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- * E-mail:
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Jo KM, Jo Y, Chu H, Lian S, Cho WK. Development of EST-derived SSR markers using next-generation sequencing to reveal the genetic diversity of 50 chrysanthemum cultivars. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Mao Y, Zhang Y, Xu C, Qiu Y. Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae. Mol Ecol Resour 2015; 16:228-41. [PMID: 25879377 DOI: 10.1111/1755-0998.12415] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/09/2015] [Accepted: 04/14/2015] [Indexed: 12/13/2022]
Abstract
Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53,929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.
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Affiliation(s)
- Yunrui Mao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yonghua Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuan Xu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yingxiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Development and characterization of polymorphic genic-SSR markers in Larix kaempferi. Molecules 2015; 20:6060-7. [PMID: 25856058 PMCID: PMC6272221 DOI: 10.3390/molecules20046060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 03/24/2015] [Accepted: 03/26/2015] [Indexed: 12/05/2022] Open
Abstract
New simple sequence repeat (SSR) markers were developed in the Japanese larch (Larix kaempferi) using unigene sequences for further genetic diversity studies and the genetic improvement of breeding programs. One thousand two handred and thirty five (1235) primer pairs were tested and 165 successfully identified in L. kaempferi. Out of the amplified candidate markers, 145 (90.6%) exhibited polymorphism among 24 individuals of L. kaempferi, with the number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) averaging at 4.510, 0.487, 0.518 and 0.459, respectively. Cross-species amplification of randomly selection of 30 genic-SSRs among the 145 polymorphic ones showed that 80.0% of the SSRs could be amplified in Larix olgensis, 86.7% could be amplified in Larix principi-rupprechtii and 83.0% could be amplified in Larix gmelinii. High rates of cross-species amplification were observed. The genic-SSRs developed herein would be a valuable resource for genetic analysis of Larix kaempferi and related species, and also have the potential to facilitate the genetic improvement and breeding of larch.
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Vartia S, Collins PC, Cross TF, Fitzgerald RD, Gauthier DT, McGinnity P, Mirimin L, Carlsson J. Multiplexing with three-primer PCR for rapid and economical microsatellite validation. Hereditas 2015; 151:43-54. [PMID: 25041267 DOI: 10.1111/hrd2.00044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/20/2014] [Indexed: 02/01/2023] Open
Abstract
The next generation sequencing revolution has enabled rapid discovery of genetic markers, however, development of fully functioning new markers still requires a long and costly process of marker validation. This study reports a rapid and economical approach for the validation and deployment of polymorphic microsatellite markers obtained from a 454 pyrosequencing library of Atlantic cod, Gadus morhua, Linnaeus 1758. Primers were designed from raw reads to amplify specific amplicon size ranges, allowing effective PCR multiplexing. Multiplexing was combined with a three-primer PCR approach using four universal tails to label amplicons with separate fluorochromes. A total of 192 primer pairs were tested, resulting in 73 polymorphic markers. Of these, 55 loci were combined in six multiplex panels each containing between six and eleven markers. Variability of the loci was assessed on G. morhua from the Celtic Sea (n = 46) and the Scotian Shelf (n = 46), two locations that have shown genetic differentiation in previous studies. Multilocus F(ST) between the two samples was estimated at 0.067 (P = 0.001). After three loci potentially under selection were excluded, the global F(ST) was estimated at 0.043 (P = 0.001). Our technique combines three-primer and multiplex PCR techniques, allowing simultaneous screening and validation of relatively large numbers of microsatellite loci.
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Affiliation(s)
- Salla Vartia
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Co. Galway, Ireland; Area 52 Research Group, School of Biology & Environment Science, University College Dublin, Belfield, Dublin, Ireland.
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Nie H, Niu H, Zhao L, Yang F, Yan X, Zhang G. Genetic diversity and structure of Manila clam (Ruditapes philippinarum) populations from Liaodong peninsula revealed by SSR markers. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.12.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Chand SK, Nanda S, Rout E, Joshi RK. Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L. Bioinformation 2015; 11:145-50. [PMID: 25987765 PMCID: PMC4421003 DOI: 10.6026/97320630011145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 02/28/2015] [Indexed: 12/30/2022] Open
Abstract
Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.
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Affiliation(s)
- Subodh Kumar Chand
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Satyabrata Nanda
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Ellojita Rout
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Raj Kumar Joshi
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
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Qiang Y, Xie H, Qiao S, Yuan Y, Liu Y, Shi X, Shu M, Jin J, Shi S, Tan F, Huang Y. Development of microsatellite markers for Carallia brachiata (Rhizophoraceae). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1400125. [PMID: 25798345 PMCID: PMC4356322 DOI: 10.3732/apps.1400125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/03/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed for Carallia brachiata to assess the genetic diversity and structure of this terrestrial species of the Rhizophoraceae. METHODS AND RESULTS Based on transcriptome data for C. brachiata, 40 primer pairs were initially designed and tested, of which 18 were successfully amplified and 11 were polymorphic. For these microsatellites, one to three alleles per locus were identified. The observed and expected heterozygosities ranged from 0 to 0.727 and 0 to 0.520, respectively. In addition, all primers were successfully amplified in two congeners: C. pectinifolia and C. garciniifolia. CONCLUSIONS The microsatellite markers described here will be useful in population genetic studies of C. brachiata and related species, suggesting that developing microsatellite markers from next-generation sequencing data can be efficient for genetic studies across this genus.
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Affiliation(s)
- Yinmeng Qiang
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Hongxian Xie
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Sitan Qiao
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Yang Yuan
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Xianggang Shi
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Mi Shu
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Jianhua Jin
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Suhua Shi
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Fengxiao Tan
- South China Agricultural University, Guangzhou 510642, Guangdong, People’s Republic of China
| | - Yelin Huang
- Guangdong Provincial Key Laboratory of Plant Resources and State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
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Shirasawa K, Hand ML, Henderson ST, Okada T, Johnson SD, Taylor JM, Spriggs A, Siddons H, Hirakawa H, Isobe S, Tabata S, Koltunow AMG. A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts. ANNALS OF BOTANY 2015; 115:567-80. [PMID: 25538115 PMCID: PMC4343286 DOI: 10.1093/aob/mcu249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. METHODS RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. KEY RESULTS A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. CONCLUSIONS A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Melanie L Hand
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Steven T Henderson
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Takashi Okada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Susan D Johnson
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Jennifer M Taylor
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Andrew Spriggs
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Hayley Siddons
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Anna M G Koltunow
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
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Chapman MA. Transcriptome sequencing and marker development for four underutilized legumes. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1400111. [PMID: 25699221 PMCID: PMC4332146 DOI: 10.3732/apps.1400111] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/24/2015] [Indexed: 05/26/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Combating threats to food and nutrition security in the context of climate change and global population increase is one of the highest priorities of major international organizations. Hundreds of species are grown on a small scale in some of the most drought/flood-prone regions of the world and as such may harbor some of the most environmentally tolerant crops (and alleles). • METHODS AND RESULTS In this study, transcriptomes were sequenced, assembled, and annotated for four underutilized legume crops. Microsatellite markers were identified in each species, as well as a conserved orthologous set of markers for cross-family phylogenetics and comparative mapping, which were ground-truthed on a panel of diverse legume germplasm. • CONCLUSIONS An understanding of these underutilized legumes will inform crop selection and breeding by allowing the investigation of genetic variation and the genetic basis of adaptive traits to be established.
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Affiliation(s)
- Mark A. Chapman
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Centre for Underutilised Crops, University of Southampton, Southampton SO17 1BJ, United Kingdom
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130
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Vijayakumar P, Raut AA, Kumar P, Sharma D, Mishra A. De novo assembly and analysis of crow lungs transcriptome. Genome 2015; 57:499-506. [PMID: 25633965 DOI: 10.1139/gen-2014-0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1,510,303 high-quality sequence reads with 581,198,230 bases was de novo assembled into 22,169 isotigs (isotig represents an individual transcript) and 784,009 singletons. Using these isotigs and 581,681 length-filtered (greater than 300 bp) singletons, 20,010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46,604 (70.29%) and 51,642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20,599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species.
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Affiliation(s)
- Periyasamy Vijayakumar
- a High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal-462021, Madhya Pradesh, India
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131
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Sahu J, Das Talukdar A, Devi K, Choudhury MD, Barooah M, Modi MK, Sen P. E-Microsatellite Markers for Centella asiatica (Gotu Kola) Genome: Validation and Cross-Transferability in Apiaceae Family for Plant Omics Research and Development. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:52-65. [DOI: 10.1089/omi.2014.0113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jagajjit Sahu
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
- Department of Life Science and Bioinformatics, Assam University, Assam, India
| | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Assam, India
| | - Kamalakshi Devi
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | | | - Madhumita Barooah
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | - Mahendra Kumar Modi
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | - Priyabrata Sen
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
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132
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Xiao Y, Zhou L, Xia W, Mason AS, Yang Y, Ma Z, Peng M. Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis). BMC PLANT BIOLOGY 2014; 14:384. [PMID: 25522814 PMCID: PMC4279980 DOI: 10.1186/s12870-014-0384-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/12/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND The oil palm (Elaeis guineensis, 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical species. Developing molecular markers related to cold tolerance would be helpful for molecular breeding of cold tolerant Elaeis guineensis. RESULTS In total, 5791 gene-based SSRs were identified in 51,452 expressed sequences from Elaeis guineensis transcriptome data: approximately one SSR was detected per 10 expressed sequences. Of these 5791 gene-based SSRs, 916 were derived from expressed sequences up- or down-regulated at least two-fold in response to cold stress. A total of 182 polymorphic markers were developed and characterized from 442 primer pairs flanking these cold-responsive SSR repeats. The polymorphic information content (PIC) of these polymorphic SSR markers across 24 lines of Elaeis guineensis varied from 0.08 to 0.65 (mean = 0.31 ± 0.12). Using in-silico mapping, 137 (75.3%) of the 182 polymorphic SSR markers were located onto the 16 Elaeis guineensis chromosomes. Total coverage of 473 Mbp was achieved, with an average physical distance of 3.4 Mbp between adjacent markers (range 96 bp - 20.8 Mbp). Meanwhile, Comparative analysis of transcriptome under cold stress revealed that one ICE1 putative ortholog, five CBF putative orthologs, 19 NAC transcription factors and four cold-induced orhologs were up-regulated at least two fold in response to cold stress. Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers. CONCLUSIONS In the present study, a series of SSR markers were developed based on sequences differentially expressed in response to cold stress. These EST-SSR markers would be particularly useful for gene mapping and population structure analysis in Elaeis guineensis. Meanwhile, the EST-SSR loci were inducible expressed in response to low temperature, which may have potential application in identifying trait-associated markers in oil palm in the future.
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Affiliation(s)
- Yong Xiao
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Lixia Zhou
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Wei Xia
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Annaliese S Mason
- />School of Agriculture and Food Sciences and Centre for Integrative Legume Research, the University of Queensland, 4072 Brisbane, Australia
| | - Yaodong Yang
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Zilong Ma
- />Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan 571101 P. R. China
| | - Ming Peng
- />Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan 571101 P. R. China
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133
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Li X, Jin F, Jin L, Jackson A, Huang C, Li K, Shu X. Development of Cymbidium ensifolium genic-SSR markers and their utility in genetic diversity and population structure analysis in cymbidiums. BMC Genet 2014; 15:124. [PMID: 25481640 PMCID: PMC4276258 DOI: 10.1186/s12863-014-0124-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/30/2014] [Indexed: 11/17/2022] Open
Abstract
Background Cymbidium is a genus of 68 species in the orchid family, with extremely high ornamental value. Marker-assisted selection has proven to be an effective strategy in accelerating plant breeding for many plant species. Analysis of cymbidiums genetic background by molecular markers can be of great value in assisting parental selection and breeding strategy design, however, in plants such as cymbidiums limited genomic resources exist. In order to obtain efficient markers, we deep sequenced the C. ensifolium transcriptome to identify simple sequence repeats derived from gene regions (genic-SSR). Result The 7,936 genic-SSR markers were identified. A total of 80 genic-SSRs were selected, and primers were designed according to their flanking sequences. Of the 80 genic-SSR primer sets, 62 were amplified in C. ensifolium successfully, and 55 showed polymorphism when cross-tested among 9 Cymbidium species comprising 59 accessions. Unigenes containing the 62 genic-SSRs were searched against Non-redundant (Nr), Gene Ontology database (GO), eukaryotic orthologous groups (KOGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The search resulted in 53 matching Nr sequences, of which 39 had GO terms, 18 were assigned to KOGs, and 15 were annotated with KEGG. Genetic diversity and population structure were analyzed based on 55 polymorphic genic-SSR data among 59 accessions. The genetic distance averaged 0.3911, ranging from 0.016 to 0.618. The polymorphic index content (PIC) of 55 polymorphic markers averaged 0.407, ranging from 0.033 to 0.863. A model-based clustering analysis revealed that five genetic groups existed in the collection. Accessions from the same species were typically grouped together; however, C. goeringii accessions did not always form a separate cluster, suggesting that C. goeringii accessions were polyphyletic. Conclusion The genic-SSR identified in this study constitute a set of markers that can be applied across multiple Cymbidium species and used for the evaluation of genetic relationships as well as qualitative and quantitative trait mapping studies. Genic-SSR’s coupled with the functional annotations provided by the unigenes will aid in mapping candidate genes of specific function. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0124-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaobai Li
- Zhejiang Academy of Agricultural Sciences, Shiqiao Road 139, Hangzhou, 310021, People's Republic of China.
| | - Feng Jin
- Hubei University, College of Life Sciences, Wuhan, 430062, People's Republic of China.
| | - Liang Jin
- Zhejiang Academy of Agricultural Sciences, Shiqiao Road 139, Hangzhou, 310021, People's Republic of China.
| | - Aaron Jackson
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, 72160, USA.
| | - Cheng Huang
- Agricultural Technology Extension Stations, Shaoxing County Agricultural Bureau, Shaoxing, 312000, Peoples Republic of China.
| | - Kehu Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
| | - Xiaoli Shu
- State Key Lab of Rice Biology, International Atomic Energy Agency Collaborating Center, Zhejiang University, Hangzhou, 310029, Peoples Republic of China.
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134
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Second generation genetic linkage map for the gilthead sea bream Sparus aurata L. Mar Genomics 2014; 18 Pt A:77-82. [DOI: 10.1016/j.margen.2014.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 12/21/2022]
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135
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Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants. Int J Genomics 2014; 2014:863948. [PMID: 25389527 PMCID: PMC4217358 DOI: 10.1155/2014/863948] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/31/2014] [Accepted: 09/22/2014] [Indexed: 12/20/2022] Open
Abstract
Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%. Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.
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136
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Wolko Ł, Bocianowski J, Antkowiak W, Słomski R. Genetic diversity and population structure of wild pear (Pyrus pyraster (L.) Burgsd.) in Poland. Open Life Sci 2014. [DOI: 10.1515/biol-2015-0003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractIn order to provide molecular characteristics
of wild pear (P. pyraster) resources, six populations
(192 accessions) from different regions of Poland were
investigated with 17 SSR loci. Each of the SSR loci used
was polymorphic, with a mean of 19.5 alleles per locus
and a mean PIC of 0.806. Both the high heterozygosity (Ho
= 0.751) and low Fis (0.007) indicated that the wild pear
populations maintain a relatively high level of diversity,
while the mean Findex of 0.039 and the number of migrants
per generation (Nm = 6.996) revealed a high gene flow and
weak inter-population differentiation. AMOVA analysis
located polymorphisms mainly within populations (96%).
Genetic relations between populations did not show
correlations with geographical distances. The dispersal
influence of gene flow could be the reason of the disrupted
relationship within populations and the low interpopulation
differentiation. We did not find any evidence
to support the hypothesis about influence of interspecies
hybridization with pear cultivars on the level of wild pear
population diversity.
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Affiliation(s)
- Łukasz Wolko
- 1Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, 60-637 Poznan, Poland
| | - Jan Bocianowski
- 2Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, 60-637 Poznan, Poland
| | - Wojciech Antkowiak
- 3Department of Botany, Poznan University of Life Sciences, 60-625 Poznan, Poland
| | - Ryszard Słomski
- 1Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, 60-637 Poznan, Poland
- 4Institute of Human Genetics, Polish Academy of Sciences, 60-493 Poznań, Poland
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137
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Developing conversed microsatellite markers and their implications in evolutionary analysis of the Bemisia tabaci complex. Sci Rep 2014; 4:6351. [PMID: 25220501 PMCID: PMC4163675 DOI: 10.1038/srep06351] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 08/22/2014] [Indexed: 12/27/2022] Open
Abstract
The study of population genetics among the Bemisia tabaci complex is limited due to the lack of conserved molecular markers. In this study, 358, 433 and 322 new polynucleotide microsatellites are separately identified from the transcriptome sequences of three cryptic species of the B. tabaci complex. The cross species transferability of 57 microsatellites was then experimentally validated. The results indicate that these markers are conserved and have high inter-taxon transferability. Thirteen markers were employed to assess the genetic relationships among six cryptic species of the B. tabaci complex. To our surprise, the inferred phylogeny was consistent with that of mitochondrial COI sequences, indicating that microsatellites have the potential to distinguish species of the B. tabaci complex. Our results demonstrate that development of microsatellites from transcriptome data is a fast and cost-effective approach. These markers can be used to analyze the population genetics and evolutionary patterns of the B. tabaci complex.
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138
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He G, Barkley NA, Zhao Y, Yuan M, Prakash CS. Phylogenetic relationships of species of genus Arachis based on genic sequences. Genome 2014; 57:327-34. [PMID: 25211395 DOI: 10.1139/gen-2014-0037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Arachis (Fabaceae), which originated in South America, consists of 80 species. Based on morphological traits and cross-compatibility among the species, the genus is divided into nine taxonomic sections. Arachis is the largest section including the economically valuable cultivated peanut (A. hypogaea). Seven genic sequences were utilized to better understand the phylogenetic relationships between species of genus Arachis. Our study displayed four clades of species of Arachis. Arachis triseminata was genetically isolated from all other species of Arachis studied, and it formed the basal clade with A. retusa and A. dardani from the most ancient sections Extranervosae and Heteranthae, respectively. Species of section Arachis formed a separated single clade from all other species, within which species having B and D genome clustered in one subgroup and three species characterized with an A genome grouped together in another subgroup. A divergent clade including species from five sections was sister to the clade of section Arachis. Between the sister clades and the basal clade there was a clade containing species from the more advanced sections. Phylogenetic relationships of all the species of Arachis using multiple genic sequences were similar to the phylogenies produced with single-copy genes.
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Affiliation(s)
- Guohao He
- a Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088, USA
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139
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Characterization of the global transcriptome for cotton (Gossypium hirsutum L.) anther and development of SSR marker. Gene 2014; 551:206-13. [PMID: 25178523 DOI: 10.1016/j.gene.2014.08.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 08/26/2014] [Accepted: 08/29/2014] [Indexed: 11/20/2022]
Abstract
Cotton is an important fiber plant, and it's attractive to elucidate the molecular mechanism of anther development due to the close relationship between the anther fertility and boll-setting, and also fiber yield. In the present paper, 47.2 million paired-end reads with average length of 82.87 bp from the anthers of TM-1 (Gossypium hirsutum L.), a genetic standard line, were generated through transcriptome sequencing, and 210,965 unigenes of more than 100 bp were obtained. BLAST, KEGG, COG, and GO analyses showed that the genes were enriched in the processes of transcription, translation, and post-translation as well as hormone signal transduction, the transcription factor families, and cell wall-related genes mainly participating in cell expansion and carbohydrate metabolism. Further analysis identified 11,153 potential SSRs. A suit of 5122 primer pair sequences were designed, and 82 of 300 randomly selected primer pairs produced reproducible amplicons that were polymorphic among 22 cotton accessions from G. hirsutum, Gossypium barbadense and Gossypium arboreum. The UPGMA clustering analysis further confirmed high quality and effectiveness of these novel SSR markers. The present study provided insights into the transcriptome profile of the cotton and established a public information platform for functional genomics and molecular breeding.
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140
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Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil MDR. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC PLANT BIOLOGY 2014; 14:220. [PMID: 25143005 PMCID: PMC4160553 DOI: 10.1186/s12870-014-0220-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). RESULTS Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. CONCLUSIONS Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
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Affiliation(s)
- Sonali Sachin Ranade
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
| | - Yao-Cheng Lin
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Andrea Zuccolo
- />Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy
- />Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
| | - Yves Van de Peer
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- />Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa
| | - María del Rosario García-Gil
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
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141
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Russell JR, Hedley PE, Cardle L, Dancey S, Morris J, Booth A, Odee D, Mwaura L, Omondi W, Angaine P, Machua J, Muchugi A, Milne I, Kindt R, Jamnadass R, Dawson IK. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. PLoS One 2014; 9:e102502. [PMID: 25025376 PMCID: PMC4099372 DOI: 10.1371/journal.pone.0102502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/18/2014] [Indexed: 01/24/2023] Open
Abstract
The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.
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Affiliation(s)
- Joanne R. Russell
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Peter E. Hedley
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Linda Cardle
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Siobhan Dancey
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
- College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Jenny Morris
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Allan Booth
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - David Odee
- Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya
- Centre for Ecology & Hydrology at Edinburgh, Centre for Ecology & Hydrology, Penicuik, Scotland, United Kingdom
| | - Lucy Mwaura
- Headquarters, World Agroforestry Centre, Nairobi, Kenya
| | - William Omondi
- Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya
| | - Peter Angaine
- Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya
| | - Joseph Machua
- Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya
| | - Alice Muchugi
- Headquarters, World Agroforestry Centre, Nairobi, Kenya
| | - Iain Milne
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Roeland Kindt
- Headquarters, World Agroforestry Centre, Nairobi, Kenya
| | | | - Ian K. Dawson
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
- Headquarters, World Agroforestry Centre, Nairobi, Kenya
- * E-mail:
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142
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Sakaguchi S, Ito M. Development and characterization of EST-SSR markers for the Solidago virgaurea complex (Asteraceae) in the Japanese archipelago. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1400035. [PMID: 25202641 PMCID: PMC4103478 DOI: 10.3732/apps.1400035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/27/2014] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) for the Solidago virgaurea complex, an ecologically and morphologically diverse species complex in the Japanese archipelago, to elucidate population genetic structure and examine taxonomic boundaries. • METHODS AND RESULTS Utilizing the RNA sequencing data obtained by next-generation sequencing techniques, 15 polymorphic EST-SSR markers with three to 14 alleles were developed, most of which were transferable to different Solidago species native to Eurasia and North America. • CONCLUSIONS The EST-SSR markers developed in this study may be useful for elucidating the population structure and taxonomic delimitation of the species complex, as well as for investigating the population genetics and reproductive ecology of Solidago species.
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Affiliation(s)
- Shota Sakaguchi
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, Meguro, Tokyo 153-0041, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Chiyoda, Tokyo 102-8472, Japan
| | - Motomi Ito
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, Meguro, Tokyo 153-0041, Japan
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143
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The first set of expressed sequence tags (EST) from the medicinal mushroom Agaricus subrufescens delivers resource for gene discovery and marker development. Appl Microbiol Biotechnol 2014; 98:7879-92. [PMID: 24917377 DOI: 10.1007/s00253-014-5844-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
Agaricus subrufescens is one of the most important culinary-medicinal cultivable mushrooms with potentially high-added-value products and extended agronomical valorization. The development of A. subrufescens-related technologies is hampered by, among others, the lack of suitable molecular tools. Thus, this mushroom is considered as a genomic orphan species with a very limited number of available molecular markers or sequences. To fill this gap, this study reports the generation and analysis of the first set of expressed sequence tags (EST) for A. subrufescens. cDNA fragments obtained from young sporophores (SP) and vegetative mycelium in liquid culture (CL) were sequenced using 454 pyrosequencing technology. After assembly process, 4,989 and 5,125 sequences were obtained in SP and CL libraries, respectively. About 87% of the EST had significant similarity with Agaricus bisporus-predicted proteins, and 79% correspond to known proteins. Functional categorization according to Gene Ontology could be assigned to 49% of the sequences. Some gene families potentially involved in bioactive compound biosynthesis could be identified. A total of 232 simple sequence repeats (SSRs) were identified, and a set of 40 EST-SSR polymorphic markers were successfully developed. This EST dataset provides a new resource for gene discovery and molecular marker development. It constitutes a solid basis for further genetic and genomic studies in A. subrufescens.
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144
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Derakhshan E, Majidi M, Sharafi Y, Mirlohi A. Discrimination and genetic diversity of cultivated and wild safflowers (Carthamus spp.) using EST-microsatellites markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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145
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Conflict in outcomes for conservation based on population genetic diversity and genetic divergence approaches: a case study in the Japanese relictual conifer Sciadopitys verticillata (Sciadopityaceae). CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0615-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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146
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Transcriptome analysis of the Portunus trituberculatus: de novo assembly, growth-related gene identification and marker discovery. PLoS One 2014; 9:e94055. [PMID: 24722690 PMCID: PMC3983128 DOI: 10.1371/journal.pone.0094055] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/11/2014] [Indexed: 11/19/2022] Open
Abstract
Background The swimming crab, Portunus trituberculatus, is an important farmed species in China, has been attracting extensive studies, which require more and more genome background knowledge. To date, the sequencing of its whole genome is unavailable and transcriptomic information is also scarce for this species. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for major tissues of Portunus trituberculatus by the Illumina paired-end sequencing technology. Results Total RNA was isolated from eyestalk, gill, heart, hepatopancreas and muscle. Equal quantities of RNA from each tissue were pooled to construct a cDNA library. Using the Illumina paired-end sequencing technology, we generated a total of 120,137 transcripts with an average length of 1037 bp. Further assembly analysis showed that all contigs contributed to 87,100 unigenes, of these, 16,029 unigenes (18.40% of the total) can be matched in the GenBank non-redundant database. Potential genes and their functions were predicted by GO, KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes with fundamental roles in growth and muscle development, including actin, myosin, tropomyosin, troponin and other potentially important candidate genes were identified for the first time in this specie. Furthermore, 22,673 SSRs and 66,191 high-confidence SNPs were identified in this EST dataset. Conclusion The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in Portunus trituberculatus. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will be essential for accelerating aquaculture breeding programs with this species.
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147
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Brouillette LC, Mason CM, Shirk RY, Donovan LA. Adaptive differentiation of traits related to resource use in a desert annual along a resource gradient. THE NEW PHYTOLOGIST 2014; 201:1316-1327. [PMID: 24325125 DOI: 10.1111/nph.12628] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/21/2013] [Indexed: 05/15/2023]
Abstract
• Plant resource-use traits are generally hypothesized to be adaptively differentiated for populations distributed along resource gradients. Although nutrient limitations are expected to select for resource-conservative strategies, water limitations may select for either resource-conservative or -acquisitive strategies. We test whether population differentiation reflects local adaptation for traits associated with resource-use strategies in a desert annual (Helianthus anomalus) distributed along a gradient of positively covarying water and nutrient availability. • We compared quantitative trait variation (Q(ST)) with neutral genetic differentiation (F(ST)), in a common garden glasshouse study, for leaf economics spectrum (LES) and related traits: photosynthesis (A(mass), A(area)), leaf nitrogen (N(mass), N(area)), leaf lifetime (LL), leaf mass per area (LMA), leaf water content (LWC), water-use efficiency (WUE, estimated as δ(13)C) and days to first flower (DFF). • Q(ST)-F(ST) differences support adaptive differentiation for Amass , N(mass), N(area), LWC and DFF. The trait combinations associated with drier and lower fertility sites represent correlated trait evolution consistent with the more resource-acquisitive end of the LES. There was no evidence for adaptive differentiation for A(area), LMA and WUE. • These results demonstrate that hot dry environments can selectively favor correlated evolution of traits contributing to a resource-acquisitive and earlier reproduction 'escape' strategy, despite lower fertility.
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Affiliation(s)
- Larry C Brouillette
- Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
| | - Chase M Mason
- Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
| | - Rebecca Y Shirk
- Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
| | - Lisa A Donovan
- Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
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148
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Kaur S, Cogan NOI, Stephens A, Noy D, Butsch M, Forster JW, Materne M. EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:703-13. [PMID: 24370962 DOI: 10.1007/s00122-013-2252-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/13/2013] [Indexed: 05/24/2023]
Abstract
Large-scale SNP discovery and dense genetic mapping in a lentil intraspecific cross permitted identification of a single chromosomal region controlling tolerance to boron toxicity, an important breeding objective. Lentil (Lens culinaris Medik.) is a highly nutritious food legume crop that is cultivated world-wide. Until recently, lentil has been considered a genomic 'orphan' crop, limiting the feasibility of marker-assisted selection strategies in breeding programs. The present study reports on the identification of single-nucleotide polymorphisms (SNPs) from transcriptome sequencing data, utilisation of expressed sequence tag (EST)-derived simple sequence repeat (SSR) and SNP markers for construction of a gene-based genetic linkage map, and identification of markers in close linkage to major QTLs for tolerance to boron (B) toxicity. A total of 2,956 high-quality SNP markers were identified from a lentil EST database. Sub-sets of 546 SSRs and 768 SNPs were further used for genetic mapping of an intraspecific mapping population (Cassab × ILL2024) that exhibits segregation for B tolerance. Comparative analysis of the lentil linkage map with the sequenced genomes of Medicago truncatula Gaertn., soybean (Glycine max [L.] Merr.) and Lotus japonicus L. indicated blocks of conserved macrosynteny, as well as a number of rearrangements. A single genomic region was found to be associated with variation for B tolerance in lentil, based on evaluation performed over 2 years. Comparison of flanking markers to genome sequences of model species (M. truncatula, soybean and Arabidopsis thaliana) identified candidate genes that are functionally associated with B tolerance, and could potentially be used for diagnostic marker development in lentil.
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Affiliation(s)
- Sukhjiwan Kaur
- Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, VIC, 3083, Australia
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149
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Ma H, Jiang W, Liu P, Feng N, Ma Q, Ma C, Li S, Liu Y, Qiao Z, Ma L. Identification of transcriptome-derived microsatellite markers and their association with the growth performance of the mud crab (Scylla paramamosain). PLoS One 2014; 9:e89134. [PMID: 24551232 PMCID: PMC3923883 DOI: 10.1371/journal.pone.0089134] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 01/20/2014] [Indexed: 11/18/2022] Open
Abstract
Microsatellite markers from a transcriptome sequence library were initially isolated, and their genetic variation was characterized in a wild population of the mud crab (Scylla paramamosain). We then tested the association between these microsatellite markers and the growth performance of S. paramamosain. A total of 129 polymorphic microsatellite markers were identified, with an observed heterozygosity ranging from 0.19 to 1.00 per locus, an expected heterozygosity ranging from 0.23 to 0.96 per locus, and a polymorphism information content (PIC) ranging from 0.21 to 0.95 per locus. Of these microsatellite markers, 30 showed polymorphism in 96 full-sib individuals of a first generation family. Statistical analysis indicated that three microsatellite markers were significantly associated with 12 growth traits of S. paramamosain. Of these three markers, locus Scpa36 was significantly associated with eight growth traits, namely, carapace length, abdomen width (AW), body height (BH), fixed finger length of the claw, fixed finger width of the claw, fixed finger height of the claw, meropodite length of pereiopod 2, and meropodite length of pereiopod 3 (MLP3) (P<0.05). Locus Scpa75 was significantly associated with five growth traits, namely, internal carapace width, AW, carapace width at spine 8, distance between lateral spine 2 (DLS2), and MLP3 (P<0.05). Locus Spm30 was significantly associated with BH, DLS2, and body weight (P<0.05). Further analysis suggested a set of genotypes (BC at Scpa36, BC and BD at Scpa75, and AC at Spm30) that have great potential in the selection of S. paramamosain for growth traits. These findings will facilitate the development of population conservation genetics and molecular marker-assisted selective breeding of S. paramamosain and other closely related species.
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Affiliation(s)
- Hongyu Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Wei Jiang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Ping Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Nana Feng
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Qunqun Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Chunyan Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Shujuan Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Yuexing Liu
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Zhenguo Qiao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Lingbo Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
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150
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Song SL, Lim PE, Phang SM, Lee WW, Hong DD, Prathep A. Development of chloroplast simple sequence repeats (cpSSRs) for the intraspecific study of Gracilaria tenuistipitata (Gracilariales, Rhodophyta) from different populations. BMC Res Notes 2014; 7:77. [PMID: 24490797 PMCID: PMC3922622 DOI: 10.1186/1756-0500-7-77] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/14/2014] [Indexed: 11/26/2022] Open
Abstract
Background Gracilaria tenuistipitata is an agarophyte with substantial economic potential because of its high growth rate and tolerance to a wide range of environment factors. This red seaweed is intensively cultured in China for the production of agar and fodder for abalone. Microsatellite markers were developed from the chloroplast genome of G. tenuistipitata var. liui to differentiate G. tenuistipitata obtained from six different localities: four from Peninsular Malaysia, one from Thailand and one from Vietnam. Eighty G. tenuistipitata specimens were analyzed using eight simple sequence repeat (SSR) primer-pairs that we developed for polymerase chain reaction (PCR) amplification. Findings Five mononucleotide primer-pairs and one trinucleotide primer-pair exhibited monomorphic alleles, whereas the other two primer-pairs separated the G. tenuistipitata specimens into two main clades. G. tenuistipitata from Thailand and Vietnam were grouped into one clade, and the populations from Batu Laut, Middle Banks and Kuah (Malaysia) were grouped into another clade. The combined dataset of these two primer-pairs separated G. tenuistipitata obtained from Kelantan, Malaysia from that obtained from other localities. Conclusions Based on the variations in repeated nucleotides of microsatellite markers, our results suggested that the populations of G. tenuistipitata were distributed into two main geographical regions: (i) populations in the west coast of Peninsular Malaysia and (ii) populations facing the South China Sea. The correct identification of G. tenuistipitata strains with traits of high economic potential will be advantageous for the mass cultivation of seaweeds.
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Affiliation(s)
| | - Phaik-Eem Lim
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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