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Safaa H, Khaled R, Isaac S, Mostafa R, Ragab M, Elsayed DAA, Helal M. Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks. J Genet Eng Biotechnol 2023; 21:105. [PMID: 37856056 PMCID: PMC10587045 DOI: 10.1186/s43141-023-00556-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. RESULTS The total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. CONCLUSION The current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.
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Affiliation(s)
- Hosam Safaa
- Department of Biology, College of Science, University of Bisha, P.O. Box 551, 61922, Bisha, Saudi Arabia.
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Rawan Khaled
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Suzy Isaac
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Rofida Mostafa
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Mohamed Ragab
- Poultry Production Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
- Animal Breeding and Genetics Department, National Institute for Agricultural and Food Research and Technology (INIA), 28040, Madrid, Spain
| | - Dalia A A Elsayed
- Department of Poultry Breeding, Agriculture Research Center, Animal Production Research Institute, Dokki, Giza, Egypt
| | - Mostafa Helal
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
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Huang J, Lu Z, Lin C, Xu W, Liu Y. Comprehensive Comparative Analyses of Aspidistra Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny. Genes (Basel) 2023; 14:1894. [PMID: 37895243 PMCID: PMC10606303 DOI: 10.3390/genes14101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Limestone karsts are renowned for extremely high species richness and endemism. Aspidistra (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of Aspidistra species are mainly based on their specialized and diverse floral structures. Aspidistra plants have inconspicuous flowers, and the similarity in vegetative morphology often leads to difficulties in species discrimination. Chloroplast genomes possess variable genetic information and offer the potential for interspecies identification. However, as yet there is little information about the interspecific diversity and evolution of the plastid genomes of Aspidistra. In this study, we reported chloroplast (cp) genomes of seven Aspidistra species (A. crassifila, A. dolichanthera, A. erecta, A. longgangensis, A. minutiflora, A. nankunshanensis, and A. retusa). These seven highly-conserved plastid genomes all have a typical quartile structure and include a total of 113 unique genes, comprising 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Additionally, we conducted a comprehensive comparative analysis of Aspidistra cp genomes. We identified eight divergent hotspot regions (trnC-GCA-petN, trnE-UUC-psbD, accD-psaI, petA-psbJ, rpl20-rps12, rpl36-rps8, ccsA-ndhD and rps15-ycf1) that serve as potential molecular markers. Our newly generated Aspidistra plastomes enrich the resources of plastid genomes of karst plants, and an investigation into the plastome diversity offers novel perspectives on the taxonomy, phylogeny and evolution of Aspidistra species.
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Affiliation(s)
- Jie Huang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China; (J.H.); (Z.L.); (Y.L.)
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Zhaocen Lu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China; (J.H.); (Z.L.); (Y.L.)
| | - Chunrui Lin
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China; (J.H.); (Z.L.); (Y.L.)
| | - Weibin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Yan Liu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China; (J.H.); (Z.L.); (Y.L.)
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Hiremath V, Singh KP, Jain N, Swaroop K, Jain PK, Panwar S, Sinha N. Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus ( Gladiolus × grandiflorus L.) genotypes. PeerJ 2023; 11:e15820. [PMID: 37701831 PMCID: PMC10493085 DOI: 10.7717/peerj.15820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/10/2023] [Indexed: 09/14/2023] Open
Abstract
Background Genetic analysis of gladiolus germplasm using simple sequence repeat (SSR) markers is largely missing due to scarce genomic information. Hence, microsatellites identified for related genera or species may be utilized to understand the genetic diversity and assess genetic relationships among cultivated gladiolus varieties. Methods In the present investigation, we screened 26 genomic SSRs (Gladiolus palustris, Crocus sativus, Herbertia zebrina, Sysirinchium micranthum), 14 chloroplast SSRs (Gladiolus spp., chloroplast DNA regions) and 25 Iris Expressed Sequence Tags (ESTs) derived SSRs across the 84 gladiolus (Gladiolus × grandiflorus L.) genotypes. Polymorphic markers detected from amplified SSRs were used to calculate genetic diversity estimates, analyze population structure, cluster analysis and principal coordinate analysis (PCoA). Results A total of 41 SSRs showed reproducible amplification pattern among the selected gladiolus cultivars. Among these, 17 highly polymorphic SSRs revealed a total of 58 polymorphic alleles ranging from two to six with an average of 3.41 alleles per marker. Polymorphic information content (PIC) values ranged from 0.11 to 0.71 with an average value of 0.48. A total of 4 SSRs were selectively neutral based on the Ewens-Watterson test. Hence, 66.66% of Gladiolus palustris, 48% of Iris spp. EST, 71.42% of Crocus sativus SSRs showed cross-transferability among the gladiolus genotypes. Analysis of genetic structure of 84 gladiolus genotypes revealed two subpopulations; 35 genotypes were assigned to subpopulation 1, 37 to subpopulation 2 and the remaining 12 genotypes could not be attributed to either subpopulation. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations, whereas 36.55% of variation among individuals within the total population. The least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation between two subpopulations was observed. The grouping pattern of population structure was consistent with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on simple matching dissimilarity coefficient and PCoA. Conclusion SSR markers from the present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement. Genetic relationships assessed among the genotypes of respective clusters may assist the breeders in selecting desirable parents for crossing.
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Affiliation(s)
- Varun Hiremath
- Division of Floriculture and Landscaping, Indian Agricultural Research Institute, New Delhi, India
| | - Kanwar Pal Singh
- Division of Floriculture and Landscaping, Indian Agricultural Research Institute, New Delhi, India
| | - Neelu Jain
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Kishan Swaroop
- Division of Floriculture and Landscaping, Indian Agricultural Research Institute, New Delhi, India
| | | | - Sapna Panwar
- Division of Floriculture and Landscaping, Indian Agricultural Research Institute, New Delhi, India
| | - Nivedita Sinha
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
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Lu CT, Yang MJ, Luo MX, Wang JC. Aspidistradaibuensis var. longkiauensis, a new variety of Aspidistra (Asparagaceae) from Taiwan, identified through morphological and genetic analyses. PHYTOKEYS 2023; 222:129-151. [PMID: 37215050 PMCID: PMC10194778 DOI: 10.3897/phytokeys.222.100885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/12/2023] [Indexed: 05/24/2023]
Abstract
Aspidistra Ker Gawl. is one of the the most diverse and fastest-growing genera of angiosperm. Most Aspidistra species have been discovered in a limited area or a single site through morphological comparison. Because of the lack of population studies, morphological variation within species and the boundaries of some species remain unclear. In recent years, combining genetic and morphological markers has become a powerful approach for species delimitation. In this study, we performed population sampling and integrated morphometrics and microsatellite genetic diversity analyses to determine the species diversity of Aspidistra in Taiwan. We identified three species, namely Aspidistraattenuata Hayata; A.daibuensisHayatavar.daibuensis; A.mushaensisHayatavar.mushaensis; and reduced A.longiconnectiva C.T.Lu, K.C.Chuang & J.C.Wang to the variety level, and described a new variety, A.daibuensisHayatavar.longkiauensis. The description, diagnosis, distribution, and photographs of this new variety as well as a key to the known Taiwanese Aspidistra are provided.
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Affiliation(s)
- Chang-Tse Lu
- Department of Biological Resources, National Chiayi University, 300 Syuefu Rd., Chiayi City 60004, TaiwanNational Chiayi UniversityChiayiTaiwan
| | - Ming-Jen Yang
- Department of Life Science, National Taiwan Normal University, 88 Ting-Chow Rd., Sec 4, Wenshan, Taipei City 11677, TaiwanNational Taiwan Normal UniversityTaipeiTaiwan
| | - Min-Xin Luo
- Department of Life Science, National Taiwan Normal University, 88 Ting-Chow Rd., Sec 4, Wenshan, Taipei City 11677, TaiwanNational Taiwan Normal UniversityTaipeiTaiwan
| | - Jenn-Che Wang
- Department of Life Science, National Taiwan Normal University, 88 Ting-Chow Rd., Sec 4, Wenshan, Taipei City 11677, TaiwanNational Taiwan Normal UniversityTaipeiTaiwan
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Ma M, Meng H, Lei E, Wang T, Zhang W, Lu B. De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae). BMC PLANT BIOLOGY 2022; 22:467. [PMID: 36171538 PMCID: PMC9519402 DOI: 10.1186/s12870-022-03827-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/30/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers. RESULTS A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species. CONCLUSIONS Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.
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Affiliation(s)
- Mengli Ma
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe University, Mengzi, 661199, China
| | - Hengling Meng
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe University, Mengzi, 661199, China
| | - En Lei
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661199, China
| | - Tiantao Wang
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661199, China
| | - Wei Zhang
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe University, Mengzi, 661199, China
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661199, China
| | - Bingyue Lu
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe University, Mengzi, 661199, China.
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661199, China.
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Adedze YMN, Lu X, Xia Y, Sun Q, Nchongboh CG, Alam MA, Liu M, Yang X, Zhang W, Deng Z, Li W, Si L. Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber. Sci Rep 2021; 11:3872. [PMID: 33594240 PMCID: PMC7886880 DOI: 10.1038/s41598-021-83313-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Insertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.
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Affiliation(s)
- Yawo Mawunyo Nevame Adedze
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China.
| | - Xia Lu
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Yingchun Xia
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Qiuyue Sun
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Chofong G Nchongboh
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Brunswick, Germany
| | - Md Amirul Alam
- Faculty of Sustainable Agriculture, Horticulture and Landscaping Program, University Malaysia Sabah, Sandakan Campus, 90509, Sandakan, Sabah, Malaysia
| | - Menghua Liu
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Xue Yang
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Wenting Zhang
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Zhijun Deng
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Wenhu Li
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Longting Si
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
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Vu DD, Shah SNM, Pham MP, Bui VT, Nguyen MT, Nguyen TPT. De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. BMC PLANT BIOLOGY 2020; 20:358. [PMID: 32727354 PMCID: PMC7391578 DOI: 10.1186/s12870-020-02571-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 07/23/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. RESULTS In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. CONCLUSION Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.
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Affiliation(s)
- Dinh Duy Vu
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University Dera Ismail Khan, Dera Ismail Khan, Pakistan
| | - Mai Phuong Pham
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Van Thang Bui
- College of Forestry Biotechnology, Vietnam National University of Forestry, Xuan Mai, Hanoi, Vietnam
| | - Minh Tam Nguyen
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi Phuong Trang Nguyen
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, , Cau Giay, Hanoi, Vietnam.
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Aiello D, Ferradini N, Torelli L, Volpi C, Lambalk J, Russi L, Albertini E. Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare. PLANTS (BASEL, SWITZERLAND) 2020; 9:E175. [PMID: 32024130 PMCID: PMC7076658 DOI: 10.3390/plants9020175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/30/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites-also known as simple sequence repeats (SSRs)-are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.
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Affiliation(s)
- Domenico Aiello
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Nicoletta Ferradini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Lorenzo Torelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Chiara Volpi
- Enza Zaden Italia Research S.r.l. SS., 01016 Tarquinia, Italy;
| | - Joep Lambalk
- Enza Zaden, Research and Development B.V. P.O. Box 7, 1600AA Enkhuizen, The Netherlands;
| | - Luigi Russi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
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Bernard AM, Richards VP, Stanhope MJ, Shivji MS. Transcriptome-Derived Microsatellites Demonstrate Strong Genetic Differentiation in Pacific White Sharks. J Hered 2019; 109:771-779. [PMID: 30204894 DOI: 10.1093/jhered/esy045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/08/2018] [Indexed: 01/25/2023] Open
Abstract
Recent advances in genome-scale sequencing technology have allowed the development of high resolution genetic markers for the study of nonmodel taxa. In particular, transcriptome sequencing has proven to be highly useful in generating genomic markers for use in population genetic studies, allowing for insight into species connectivity, as well as local adaptive processes as many transcriptome-derived markers are found within or associated with functional genes. Herein, we developed a set of 30 microsatellite markers from a heart transcriptome for the white shark (Carcharodon carcharias), a widely distributed and globally vulnerable marine predator. Using these markers as well as 10 published anonymous genomic microsatellite loci, we provide 1) the first nuclear genetic assessment of the cross-Pacific connectivity of white sharks, and 2) a comparison of the levels of inferred differentiation across microsatellite marker sets (i.e., transcriptome vs. anonymous) to assess their respective utility to elucidate the population genetic dynamics of white sharks. Significant (FST = 0.083, P = 0.05; G″ST = 0.200; P = 0.001) genetic differentiation was found between Southwestern Pacific (n = 19) and Northeastern Pacific (n = 20) white sharks, indicating restricted, cross Pacific gene flow in this species. Transcriptome-derived microsatellite marker sets identified much higher (up to 2×) levels of genetic differentiation than anonymous genomic markers, underscoring potential utility of transcriptome markers in identifying subtle population genetic differences within highly vagile, globally distributed marine species.Subject areas: Population structure and phylogeography; Conservation genetics and biodiversity.
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Affiliation(s)
- Andrea M Bernard
- Save Our Seas Shark Research Center & Guy Harvey Research Institute, Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, North Ocean Drive, Dania Beach, FL
| | - Vincent P Richards
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Mahmood S Shivji
- Save Our Seas Shark Research Center & Guy Harvey Research Institute, Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, North Ocean Drive, Dania Beach, FL
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10
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De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway. Sci Rep 2019; 9:14876. [PMID: 31619732 PMCID: PMC6795813 DOI: 10.1038/s41598-019-51355-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/16/2019] [Indexed: 01/06/2023] Open
Abstract
Gymnema sylvestre is a highly valuable medicinal plant in traditional Indian system of medicine and used in many polyherbal formulations especially in treating diabetes. However, the lack of genomic resources has impeded its research at molecular level. The present study investigated functional gene profile of G. sylvestre via RNA sequencing technology. The de novo assembly of 88.9 million high quality reads yielded 23,126 unigenes, of which 18116 were annotated against databases such as NCBI nr database, gene ontology (GO), KEGG, Pfam, CDD, PlantTFcat, UniProt & GreeNC. Total 808 unigenes mapped to 78 different Transcription Factor families, whereas 39 unigenes assigned to CYP450 and 111 unigenes coding for enzymes involved in the biosynthesis of terpenoids including transcripts for synthesis of important compounds like Vitamin E, beta-amyrin and squalene. Among them, presence of six important enzyme coding transcripts were validated using qRT-PCR, which showed high expression of enzymes involved in methyl-erythritol phosphate (MEP) pathway. This study also revealed 1428 simple sequence repeats (SSRs), which may aid in molecular breeding studies. Besides this, 8 putative long non-coding RNAs (lncRNAs) were predicted from un-annotated sequences, which may hold key role in regulation of essential biological processes in G. sylvestre. The study provides an opportunity for future functional genomic studies and to uncover functions of the lncRNAs in G. sylvestre.
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Lu R, Xu W, Lu Q, Li P, Losh J, Hina F, Li E, Qiu Y. Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae. PLANT DIVERSITY 2018; 40:253-264. [PMID: 30740572 PMCID: PMC6317509 DOI: 10.1016/j.pld.2018.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/21/2023]
Abstract
The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA)-Eastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study, we sequenced the floral and leaf transcriptomes of the zygomorphic flowered C roomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala (ChFlower), flowers of C. japonica (CjFlower), and leaves of C. japonica (CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes (SCNGs) and 21,460 expression sequence tags-simple sequence repeats (EST-SSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade (SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.
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Affiliation(s)
- Ruisen Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wuqin Xu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qixiang Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jocelyn Losh
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Faiza Hina
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Enxiang Li
- College of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Yingxiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Corresponding author.
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12
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De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae). Genes (Basel) 2018; 9:genes9080378. [PMID: 30060522 PMCID: PMC6115825 DOI: 10.3390/genes9080378] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
Acer miaotaiense (P. C. Tsoong) is a rare and highly endangered plant in China. Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species. Here, 93,305 unigenes were obtained by multiple assembled contigs with a transcriptome sequencing program. Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic (average number of alleles (Na) = 8, expected heterozygosity (He) = 0.635, polymorphism information content (PIC) = 0.604) and were further used for population genetic analysis. All 261 samples were grouped into two genetic clusters by UPGMA, a principal component analyses and a STRUCTURE analyses. A moderate level of genetic differentiation (genetic differentiation index (Fst) = 0.059–0.116, gene flow = 1.904–3.993) among the populations and the major genetic variance (81.01%) within populations were revealed by the AMOVA. Based on the results, scientific conservation strategies should be established using in situ and ex situ conservation strategies. The study provides useful genetic information for the protection of precious wild resources and for further research on the origin and evolution of this endangered plant and its related species.
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Barboza K, Beretta V, Kozub PC, Salinas C, Morgenfeld MM, Galmarini CR, Cavagnaro PF. Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae. Mol Genet Genomics 2018; 293:1091-1106. [PMID: 29705936 DOI: 10.1007/s00438-018-1442-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/25/2018] [Indexed: 02/04/2023]
Abstract
Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized-along with 112 previously developed SSRs-at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the Allium species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of Allium species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across Allium species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2-5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of Allium transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other Allium.
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Affiliation(s)
- Karina Barboza
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
| | - Vanesa Beretta
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
| | - Perla C Kozub
- Facultad de Ciencias Agrarias (FCA), Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Cecilia Salinas
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
| | - Mauro M Morgenfeld
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Claudio R Galmarini
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
- Facultad de Ciencias Agrarias, Instituto de Horticultura, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Pablo F Cavagnaro
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina.
- Facultad de Ciencias Agrarias, Instituto de Horticultura, Universidad Nacional de Cuyo, Mendoza, Argentina.
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Lopez L, Wolf EM, Pires JC, Edger PP, Koch MA. Molecular Resources from Transcriptomes in the Brassicaceae Family. FRONTIERS IN PLANT SCIENCE 2017; 8:1488. [PMID: 28900436 PMCID: PMC5581910 DOI: 10.3389/fpls.2017.01488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family. Moreover, we selected the genus Cochlearia to test the transferability and polymorphism of these markers among species. Additionally, we annotated Cochlearia pyrenaica transcriptome in order to identify the position of each of the mined SSRs. While we introduce a new set of tools that will further enable evolutionary studies across the Brassicaceae, we also discuss some broader aspects of SSR evolution. Overall, we developed 2012 ready-to-use SSR markers with their respective primers in 19 Brassicaceae species and a high quality annotated transcriptome for C. pyrenaica. As indicated by our transferability test with the genus Cochlearia these SSRs are transferable to species within the genus increasing exponentially the number of targeted species. Also, our polymorphism results showed substantial levels of variability for these markers. Finally, despite its complex evolutionary history, SSR evolution across the Brassicaceae family is highly conserved and we found no deviation from patterns reported in other Angiosperms.
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Affiliation(s)
- Lua Lopez
- Biodiversity and Plant Systematics, Centre of Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Eva M. Wolf
- Biodiversity and Plant Systematics, Centre of Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - J. Chris Pires
- Division of Biological Sciences, University of MissouriColumbia, MO, United States
| | - Patrick P. Edger
- Department of Horticulture, Michigan State UniversityEast Lansing, MI, United States
- Ecology, Evolutionary Biology and Behavior, Michigan State UniversityEast Lansing, MI, United States
| | - Marcus A. Koch
- Biodiversity and Plant Systematics, Centre of Organismal Studies, University of HeidelbergHeidelberg, Germany
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Duan X, Wang K, Su S, Tian R, Li Y, Chen M. De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae). PLoS One 2017; 12:e0172513. [PMID: 28212394 PMCID: PMC5315398 DOI: 10.1371/journal.pone.0172513] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/05/2017] [Indexed: 11/21/2022] Open
Abstract
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.
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Affiliation(s)
- Xinle Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China.,College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Sha Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Ruizheng Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yuting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Maohua Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
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16
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Zhang Y, Zhang X, Wang YH, Shen SK. De Novo Assembly of Transcriptome and Development of Novel EST-SSR Markers in Rhododendron rex Lévl. through Illumina Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 8:1664. [PMID: 29018469 PMCID: PMC5622969 DOI: 10.3389/fpls.2017.01664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/11/2017] [Indexed: 05/18/2023]
Abstract
Transcriptome sequences generated by next-generation sequencing (NGS) technologies can be utilized to rapidly detect and characterize a large number of gene-based microsatellites from different plants. Rhododendron rex Lévl. is a perennial woody species from the family Ericaceae and an endangered plant with high ornamental value endemic to Southwestern China. Nevertheless, the genetic and genomic information of R. rex remain unknown. In this study, we performed transcriptome sequencing for R. rex leaf samples, and generated large transcript sequences for functional characterization and development gene-associated SSR markers. A total of 164,242 unigenes were assembled and 115,089 (70.07%) unigenes were successfully annotated in public databases. In addition, a total of 15,314 potential EST-SSRs were identified, and the frequency of SSRs in the R. rex unigenes was 9.32%, with an average of one EST-SSR per 5.65 kb. The most abundant type was repeated di-nucleotide (54.63%), followed by mono- (26.03%) and tri-nucleotide (18.51%) repeats. Based on the SSR-containing sequence, 100 primer pairs were randomly selected and synthesized and used for assessment of the polymorphism. Thirty-six primer pairs were polymorphic and revealed polymorphism among 20 individuals from four R. rex populations. A total of 197 alleles were identified, with an average of 5.472 alleles per locus. The Polymorphism Information Content ranged from 0.154 to 0.870, with a mean of 0.482. The newly developed EST-SSR markers exhibited high transferability (58.33-83.33%) among the six subgenera. Thus, these novel EST-SSR markers developed would provide valuable sequence resources for population structure, genetic diversity analysis, and genetic resource assessments of R. rex and its related species.
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17
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Olsson S, Seoane-Zonjic P, Bautista R, Claros MG, González-Martínez SC, Scotti I, Scotti-Saintagne C, Hardy OJ, Heuertz M. Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers. Mol Ecol Resour 2016; 17:614-630. [PMID: 27718316 DOI: 10.1111/1755-0998.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain
| | - Pedro Seoane-Zonjic
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Rocío Bautista
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France
| | - Ivan Scotti
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Caroline Scotti-Saintagne
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Olivier J Hardy
- Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France.,Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
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Zhu H, Song P, Koo DH, Guo L, Li Y, Sun S, Weng Y, Yang L. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis. BMC Genomics 2016; 17:557. [PMID: 27495254 PMCID: PMC4974753 DOI: 10.1186/s12864-016-2870-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/01/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. RESULTS A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis clustered in another group. Furthermore, structure analysis was consistent with the dendrogram indicating the 134 watermelon accessions were classified into two populations. CONCLUSION The large number of genome wide SSR markers developed herein from the watermelon genome provides a valuable resource for genetic map construction, QTL exploration, map-based gene cloning and marker-assisted selection in watermelon which has a very narrow genetic base and extremely low polymorphism among cultivated lines. Furthermore, the cross-species transferable SSR markers identified herein should also have practical uses in many applications in species of Cucurbitaceae family whose whole genome sequences are not yet available.
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Affiliation(s)
- Huayu Zhu
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Pengyao Song
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Dal-Hoe Koo
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
| | - Luqin Guo
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Yanman Li
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Shouru Sun
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- US Department of Agriculture/Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI 53706 USA
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
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19
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Yin X, Yang Y, Yang Y. Development and characterization of 29 polymorphic EST-SSR markers for Stipa purpurea (Poaceae). APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600027. [PMID: 27610274 PMCID: PMC5001856 DOI: 10.3732/apps.1600027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/12/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using Illumina sequencing for further genetic diversity studies of Stipa purpurea (Poaceae). METHODS AND RESULTS Twenty-nine polymorphic and eight monomorphic EST-SSR loci were developed and characterized in 90 individuals from nine S. purpurea populations. The number of alleles per locus ranged from two to 13, and heterozygosity within populations and total heterozygosity ranged from 0.04-0.76 and from 0.04-0.87, respectively. Of 37 loci, 12 showed interspecific transferability and polymorphism in a related species, S. glareosa. CONCLUSIONS These newly developed EST-SSR primers provide a useful tool to investigate genetic diversity at the population level and to analyze the population structure of S. purpurea.
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Affiliation(s)
- Xin Yin
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People’s Republic of China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yunqiang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People’s Republic of China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People’s Republic of China
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People’s Republic of China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People’s Republic of China
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Chen H, Chen X, Tian J, Yang Y, Liu Z, Hao X, Wang L, Wang S, Liang J, Zhang L, Yin F, Cheng X. Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data. PLoS One 2016; 11:e0151040. [PMID: 26950544 PMCID: PMC4780709 DOI: 10.1371/journal.pone.0151040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022] Open
Abstract
Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
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Affiliation(s)
- Honglin Chen
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- * E-mail: (HLC); (XZC)
| | - Xin Chen
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Jing Tian
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, Hebei, China
| | - Yong Yang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui, China
| | - Zhenxing Liu
- Tangshan Academy of Agricultural Sciences, Tangshan 036001, Hebei, China
| | - Xiyu Hao
- Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Lixia Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Suhua Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Liang
- Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Liya Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui, China
| | - Fengxiang Yin
- Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Xuzhen Cheng
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- * E-mail: (HLC); (XZC)
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Zhou T, Li ZH, Bai GQ, Feng L, Chen C, Wei Y, Chang YX, Zhao GF. Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae). Molecules 2016; 21:166. [PMID: 26907245 PMCID: PMC6272838 DOI: 10.3390/molecules21030166] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 11/16/2022] Open
Abstract
Dipteronia Oliver (Aceraceae) is an endangered Chinese endemic genus consisting of two living species, Dipteronia sinensis and Dipteronia dyeriana. However, studies on the population genetics and evolutionary analyses of Dipteronia have been hindered by limited genomic resources and genetic markers. Here, the generation, de novo assembly and annotation of transcriptome datasets, and a large set of microsatellite or simple sequence repeat (SSR) markers derived from Dipteronia have been described. After Illumina pair-end sequencing, approximately 93.2 million reads were generated and assembled to yield a total of 99,358 unigenes. A majority of these unigenes (53%, 52,789) had at least one blast hit against the public protein databases. Further, 12,377 SSR loci were detected and 4179 primer pairs were designed for experimental validation. Of these 4179 primer pairs, 435 primer pairs were randomly selected to test polymorphism. Our results show that products from 132 primer pairs were polymorphic, in which 97 polymorphic SSR markers were further selected to analyze the genetic diversity of 10 natural populations of Dipteronia. The identification of SSR markers during our research will provide the much valuable data for population genetic analyses and evolutionary studies in Dipteronia.
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Affiliation(s)
- Tao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 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, Xi'an 710069, China.
| | - Guo-Qing Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
- Xi'an Botanical Garden of Shaanxi Province, Xi'an 710061, China.
| | - Li Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Chen Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Yue Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Yong-Xia Chang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 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, Xi'an 710069, China.
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22
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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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23
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Bonatelli IAS, Carstens BC, Moraes EM. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae). PLoS One 2015; 10:e0142602. [PMID: 26561396 PMCID: PMC4641700 DOI: 10.1371/journal.pone.0142602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.
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Affiliation(s)
| | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Evandro M. Moraes
- Department of Biology, Federal University of São Carlos, Sorocaba, São Paulo, Brazil
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24
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Ambreen H, Kumar S, Variath MT, Joshi G, Bali S, Agarwal M, Kumar A, Jagannath A, Goel S. Development of Genomic Microsatellite Markers in Carthamus tinctorius L. (Safflower) Using Next Generation Sequencing and Assessment of Their Cross-Species Transferability and Utility for Diversity Analysis. PLoS One 2015; 10:e0135443. [PMID: 26287743 PMCID: PMC4545945 DOI: 10.1371/journal.pone.0135443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/23/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing. PRINCIPAL FINDINGS Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to cultivated safflower and formed a distinct cluster. The cluster analysis also distinguished diploid and tetraploid wild species of safflower. CONCLUSION Next generation sequencing of safflower genome generated a large set of microsatellite markers. The novel markers developed in this study will add to the existing repertoire of markers and can be used for diversity analysis, synteny studies, construction of linkage maps and marker-assisted selection.
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Affiliation(s)
- Heena Ambreen
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Shivendra Kumar
- Department of Botany, University of Delhi, Delhi, 110007, India
| | | | - Gopal Joshi
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Sapinder Bali
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Amar Kumar
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Arun Jagannath
- Department of Botany, University of Delhi, Delhi, 110007, India
- * E-mail: (SG); (AJ)
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, 110007, India
- * E-mail: (SG); (AJ)
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25
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Wang X, Li J, Li Y. Isolation and characterization of microsatellite markers for an endemic tree in East Asia, Quercus variabilis (Fagaceae). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500032. [PMID: 26082882 PMCID: PMC4467763 DOI: 10.3732/apps.1500032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers of Quercus variabilis (Fagaceae) were isolated for population genetic and landscape genetic studies. METHODS AND RESULTS Roche 454 pyrosequencing combined with the magnetic bead enrichment protocol were used to isolate microsatellite markers for Q. variabilis. A total of 2121 microsatellites were identified from 63,851 individual sequence reads. One hundred microsatellite loci were selected to test primer amplification efficiency among 24 individuals from two wild populations. Among the 100 tested markers, 34 primer pairs were successfully amplified. Of these, 14 yielded polymorphic amplification products, whereas the remaining 20 loci were monomorphic. The number of alleles for polymorphic loci ranged from two to six, and the observed heterozygosity ranged from 0.042 to 0.750. CONCLUSIONS These microsatellite loci will provide useful tools for further population genetic and landscape genetic studies on Q. variabilis.
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Affiliation(s)
- Xian Wang
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, People’s Republic of China
| | - Jing Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, People’s Republic of China
| | - Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, People’s Republic of China
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26
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Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers. PLoS One 2015; 10:e0120273. [PMID: 25830701 PMCID: PMC4382333 DOI: 10.1371/journal.pone.0120273] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 02/02/2015] [Indexed: 11/19/2022] Open
Abstract
Mung bean (Vigna radiate (L.) Wilczek) is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0%) and 23,235 (47.7%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5%) could be classified into gene ontology categories, 18,316 (37.6%) into Swiss-Prot categories and 10,918 (22.4%) into KOG database categories (E-value < 1.0E-5). A total of 6,585 (8.3%) were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR), and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST). A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%), GAA/TTC (12.6%), AAAT/ATTT (6.8%), AAAAT/ATTTT (6.2%) and AAAAAT/ATTTTT (1.9%). A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
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27
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Moodley Y, Masello JF, Cole TL, Calderon L, Munimanda GK, Thali MR, Alderman R, Cuthbert RJ, Marin M, Massaro M, Navarro J, Phillips RA, Ryan PG, Suazo CG, Cherel Y, Weimerskirch H, Quillfeldt P. Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds. Mol Ecol Resour 2015; 15:1046-58. [PMID: 25594938 DOI: 10.1111/1755-0998.12372] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 12/31/2022]
Abstract
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC , even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa.
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Affiliation(s)
- Yoshan Moodley
- Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa.,Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Savoyenstr. 1a, A-1160, Vienna, Austria
| | - Juan F Masello
- Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany
| | - Theresa L Cole
- Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, 6102, Australia
| | - Luciano Calderon
- Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany
| | - Gopi K Munimanda
- Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Savoyenstr. 1a, A-1160, Vienna, Austria
| | - Marco R Thali
- Ecogenics GmbH, Grabenstrasse 11a, 8952, Zurich-Schlieren, Switzerland
| | - Rachael Alderman
- Department of Primary Industries, Parks, Water and Environment, GPO Box 44, Hobart, Tas., 7001, Australia
| | - Richard J Cuthbert
- Royal Society for the Protection of Birds (RSPB), The Lodge, Sandy, Bedfordshire, SG19 2DL, UK
| | - Manuel Marin
- Section of Ornithology, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, 90007, USA.,Feather Link Inc., 1013 Westchester Way, Cincinnati, OH, 45244, USA
| | - Melanie Massaro
- School of Environmental Sciences, Charles Sturt University, PO Box 789, Albury, NSW, 2640, Australia
| | - Joan Navarro
- Department of Conservation Biology, Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio s/n, Seville, 41092, Spain
| | - Richard A Phillips
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Peter G Ryan
- Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa
| | - Cristián G Suazo
- Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, 79360, Villiers-en-Bois, France
| | - Henri Weimerskirch
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, 79360, Villiers-en-Bois, France
| | - Petra Quillfeldt
- Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany
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