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Xue Y, Wang Y, Chen J, Zhang G, Liu W, Wan F, Zhang Y. Disparities in Genetic Diversity Drive the Population Displacement of Two Invasive Cryptic Species of the Bemisia tabaci Complex in China. Int J Mol Sci 2024; 25:7966. [PMID: 39063207 PMCID: PMC11277096 DOI: 10.3390/ijms25147966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Within the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) complex, two cryptic species, namely Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), are important invasive pests affecting global agriculture and horticulture. They were introduced into China sequentially in the mid-1990s and around 2003, respectively. Subsequently, the latter invader MED has outcompeted the earlier invader MEAM1, becoming the dominant population in the field. Although extensive studies have explored the underlying mechanisms driving this shift, the contribution of population genetics remains notably underexplored. In this study, we analyzed the genetic diversity and structure of 22 MED and 8 MEAM1 populations from various regions of China using mitochondrial DNA sequencing and microsatellite genotyping. Our results indicate low and moderate levels of genetic differentiation among geographically separate populations of MED and MEAM1, respectively. Median-joining network analysis of mtCOI gene haplotypes revealed no clear geographic structuring for either, with common haplotypes observed across provinces, although MED had more haplotypes. Comparative analyses revealed that MED presented greater genetic diversity than MEAM1 on the basis of two markers. Furthermore, analysis of molecular variance supported these findings, suggesting that while some genetic variation exists between populations, a significant amount is also present within populations. These findings reveal the population genetics of the two invasive cryptic species of the B. tabaci complex in China and suggest that the disparities in genetic diversity drive the displacement of their populations in the field. This work also provides valuable information on the genetic factors influencing the population dynamics and dominance of these invasive whitefly species.
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Affiliation(s)
- Yantao Xue
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.X.); (Y.W.); (J.C.); (G.Z.); (W.L.); (F.W.)
| | - Yusheng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.X.); (Y.W.); (J.C.); (G.Z.); (W.L.); (F.W.)
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Jiqiang Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.X.); (Y.W.); (J.C.); (G.Z.); (W.L.); (F.W.)
| | - Guifen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.X.); (Y.W.); (J.C.); (G.Z.); (W.L.); (F.W.)
| | - Wanxue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.X.); (Y.W.); (J.C.); (G.Z.); (W.L.); (F.W.)
| | - Fanghao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.X.); (Y.W.); (J.C.); (G.Z.); (W.L.); (F.W.)
| | - Yibo Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.X.); (Y.W.); (J.C.); (G.Z.); (W.L.); (F.W.)
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Purificacion M, Shah RBM, De Meeûs T, Bakar SB, Savantil AB, Yusof MM, Amalin D, Nguyen H, Sulistyowati E, Budiman A, Ekayanti A, Niogret J, Ravel S, Vreysen MJB, Abd-Alla AMM. Development and characterization of microsatellite markers for population genetics of the cocoa pod borer Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae). PLoS One 2024; 19:e0297662. [PMID: 38603675 PMCID: PMC11008836 DOI: 10.1371/journal.pone.0297662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/09/2024] [Indexed: 04/13/2024] Open
Abstract
The cocoa pod borer (CPB) Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae) is one of the major constraints for cocoa production in South East Asia. In addition to cultural and chemical control methods, autocidal control tactics such as the Sterile Insect Technique (SIT) could be an efficient addition to the currently control strategy, however SIT implementation will depend on the population genetics of the targeted pest. The aim of the present work was to search for suitable microsatellite loci in the genome of CPB that is partially sequenced. Twelve microsatellites were initially selected and used to analyze moths collected from Indonesia, Malaysia, and the Philippines. A quality control verification process was carried out and seven microsatellites found to be suitable and efficient to distinguish differences between CPB populations from different locations. The selected microsatellites were also tested against a closely related species, i.e. the lychee fruit borer Conopomorpha sinensis (LFB) from Vietnam and eight loci were found to be suitable. The availability of these novel microsatellite loci will provide useful tools for the analysis of the population genetics and gene flow of these pests, to select suitable CPB strains to implement the SIT.
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Affiliation(s)
- Marynold Purificacion
- Biological Control Research Unit, Center for Natural Science and Environmental Research, De La Salle University, Manila, Philippines
| | - Roslina Binti Mohd Shah
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Thierry De Meeûs
- Intertryp, Univ Montpellier, Cirad, IRD, Montpellier, France
- IRD, UMR Intertryp, Cirad, Campus International de Baillarguet, Montpellier, France
| | | | - Anisah Bintil Savantil
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Meriam Mohd Yusof
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Divina Amalin
- Biological Control Research Unit, Center for Natural Science and Environmental Research, De La Salle University, Manila, Philippines
| | - Hien Nguyen
- Plant Protection Research Institute, Duc Thang, Hanoi, Vietnam
| | | | - Aris Budiman
- Indonesian Coffee and Cocoa Research Institute, Jember, Indonesia
| | - Arni Ekayanti
- Mars Cocoa Research Centre, Mars Wrigley, Sulawesi Selatan, Indonesia
| | - Jerome Niogret
- Mars Wrigley, Centre for Tropical Environmental & Sustainability Science, James Cook University Nguma-bada Campus, Smithfield, Australia
| | - Sophie Ravel
- Intertryp, Univ Montpellier, Cirad, IRD, Montpellier, France
| | - Marc J. B. Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Adly M. M. Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
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Gstöttenmayer F, Moyaba P, Rodriguez M, Mulandane FC, Mucache HN, Neves L, De Beer C, Ravel S, De Meeûs T, Mach RL, Vreysen MJB, Abd-Alla AM. Development and characterization of microsatellite markers for the tsetse species Glossina brevipalpis and preliminary population genetics analyses. Parasite 2023; 30:34. [PMID: 37712836 PMCID: PMC10503490 DOI: 10.1051/parasite/2023038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
Tsetse flies, the vectors of African trypanosomes are of key medical and economic importance and one of the constraints for the development of Africa. Tsetse fly control is one of the most effective and sustainable strategies used for controlling the disease. Knowledge about population structure and level of gene flow between neighbouring populations of the target vector is of high importance to develop appropriate strategies for implementing effective management programmes. Microsatellites are commonly used to identify population structure and assess dispersal of the target populations and have been developed for several tsetse species but were lacking for Glossina brevipalpis. In this study, we screened the genome of G. brevipalpis to search for suitable microsatellite markers and nine were found to be efficient enough to distinguish between different tsetse populations. The availability of these novel microsatellite loci will help to better understand the population biology of G. brevipalpis and to assess the level of gene flow between different populations. Such information will help with the development of appropriate strategies to implement the sterile insect technique (SIT) in the framework of an area-wide integrated pest management (AW-IPM) approach to manage tsetse populations and ultimately address the trypanosomoses problem in these targeted areas.
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Affiliation(s)
- Fabian Gstöttenmayer
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
| | - Percy Moyaba
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
- Epidemiology, Parasites and Vectors, Agricultural Research Council-Onderstepoort Veterinary Research 100 Soutpan Road Private Bag X05 Onderstepoort 0110 South Africa
| | - Montse Rodriguez
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
| | - Fernando C. Mulandane
- University Eduardo Mondlane, Centro de Biotecnologia Av. de Moçambique Km 1.5 Maputo Mozambique
| | - Hermógenes N. Mucache
- University Eduardo Mondlane, Centro de Biotecnologia Av. de Moçambique Km 1.5 Maputo Mozambique
| | - Luis Neves
- University Eduardo Mondlane, Centro de Biotecnologia Av. de Moçambique Km 1.5 Maputo Mozambique
- University of Pretoria, Department of Veterinary Tropical Diseases Private Bag X04 Onderstepoort 0110 South Africa
| | - Chantel De Beer
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
| | - Sophie Ravel
- University of Montpellier, Cirad, IRD, Intertryp Campus International de Baillarguet 34398 Montpellier Cedex 5 France
| | - Thierry De Meeûs
- University of Montpellier, Cirad, IRD, Intertryp Campus International de Baillarguet 34398 Montpellier Cedex 5 France
| | - Robert L. Mach
- Institute of Chemical, Environmental, and Bioscience Engineering, Vienna University of Technology Gumpendorfer Straße 1a 1060 Vienna Austria
| | - Marc J. B. Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
| | - Adly M.M. Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
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Azizi MMF, Lau HY, Abu-Bakar N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 2021. [DOI: 10.1007/s12038-021-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kumar R, Kumar C, Paliwal R, Roy Choudhury D, Singh I, Kumar A, Kumari A, Singh R. Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [ Andrographis paniculata (Burm. F.) Nees]. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1734. [PMID: 33316874 PMCID: PMC7763852 DOI: 10.3390/plants9121734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/05/2020] [Accepted: 11/17/2020] [Indexed: 11/16/2022]
Abstract
Kalmegh (Andrographis paniculata (Burm. F.) Nees) is one of the most important medicinal plants and has been widely explored as traditional medicine. To exploit its natural genetic diversity and initiations of molecular breeding to develop novel cultivars or varieties, developments of genomic resources are essential. Four microsatellite-enriched genomic libraries-(CT)14, (GT)12, (AG)15 and (AAC)8-were constructed using the genomic DNA of A. paniculata. Initially, 183 recombinant colonies were screened for the presence of CT, GT, AG, and AAC microsatellite repeats, out of which 47 clones found positive for the desired simple sequence repeats (SSRs). It was found that few colonies had more than one desirable SSR. Thus, a sum of 67 SSRs were designed and synthesized for their validation among 42 A. paniculata accessions. Out of the 67 SSRs used for genotyping, only 41 were found to be polymorphic. The developed set of g-SSR markers showed substantial genetic variability among the selected A. paniculata accessions, with an average polymorphic information content (PIC) value of 0.32. Neighbor-joining tree analysis, population structure analysis, analysis of molecular variance (AMOVA), and principal coordinate analysis (PCoA) illustrated the considerable genetic diversity among them. The novel g-SSR markers developed in the present study could be important genomic resources for future applications in A. paniculata.
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Affiliation(s)
- Ramesh Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (R.K.); (R.P.); (D.R.C.)
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida 201313, Uttar Pradesh, India;
| | - Chavlesh Kumar
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Ritu Paliwal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (R.K.); (R.P.); (D.R.C.)
| | - Debjani Roy Choudhury
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (R.K.); (R.P.); (D.R.C.)
| | - Isha Singh
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
- School of Biomolecular and Biomedical Sciences, University College of Dublin, D04V1W8 Dublin, Ireland
| | - Ashok Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India;
| | - Abha Kumari
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida 201313, Uttar Pradesh, India;
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (R.K.); (R.P.); (D.R.C.)
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Xu T, Liao Z, Su J. Pattern recognition receptors in grass carp Ctenopharyngodon idella: II. Organization and expression analysis of NOD-like receptors. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 110:103734. [PMID: 32418892 DOI: 10.1016/j.dci.2020.103734] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
Nucleotide-binding domain and leucine-rich repeat containing receptors (NLRs) are a pivotal intracellular pattern recognition receptor family. However, studies on NLR genes in important economic fish grass carp (Ctenopharyngodon idella) are sporadic. The accumulations of genomic resource and transcriptomic sequences make it feasible to conduct a systematic analysis of these genes. In this study, we systematically conducted the genome-wide study of C. idella NLR genes and characterized their phylogeny, gene structure, conserved domain, evolutionary mechanism, and expression profiles post viral or bacterial challenge. A total of 65 NLR genes were identified and clustered into five subfamilies based on structural and phylogenetic features, including eight NODs (NLR-A), five NLRP-like receptors (NLR-B), forty-seven teleost-specific NLRs (NLR-C), two members with a B30.2 domain at the C-terminal (NLR-B30.2), and three additional NLRs (other NLRs). Gene structure analysis showed that NLRs were significantly different, with exon numbers from 3 to 31. Conserved domain analysis showed that most members of C. idella NLRs had additional domains besides the typical NLR domains. Gene duplication analysis indicated that the evolution of the NLR gene family was mainly related to segment duplication. mRNA expression analysis indicated that many members were differently expressed in multiple tissues post grass carp reovirus (GCRV) or Aeromonas hydrophila infection. The expression was particularly enhanced in liver post GCRV infection, and obviously lower post A. hydrophila infection than that post GCRV infection in spleen. These results provide systematic basic data for further functional studies of NLR, and insight into the immune responses of piscine fish NLRs to pathogen infections.
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Affiliation(s)
- Tianbing Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhiwei Liao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Su
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Wang HL, Lei T, Xia WQ, Cameron SL, Liu YQ, Zhang Z, Gowda MMN, De Barro P, Navas-Castillo J, Omongo CA, Delatte H, Lee KY, Patel MV, Krause-Sakate R, Ng J, Wu SL, Fiallo-Olivé E, Liu SS, Colvin J, Wang XW. Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host. Sci Rep 2019; 9:6568. [PMID: 31024030 PMCID: PMC6484021 DOI: 10.1038/s41598-019-42793-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/26/2019] [Indexed: 11/09/2022] Open
Abstract
The 37 currently recognized Bemisia tabaci cryptic species are economically important species and contain both primary and secondary endosymbionts, but their diversity has never been mapped systematically across the group. To achieve this, PacBio sequencing of full-length bacterial 16S rRNA gene amplicons was carried out on 21 globally collected species in the B. tabaci complex, and two samples from B. afer were used here as outgroups. The microbial diversity was first explored across the major lineages of the whole group and 15 new putative bacterial sequences were observed. Extensive comparison of our results with previous endosymbiont diversity surveys which used PCR or multiplex 454 pyrosequencing platforms showed that the bacterial diversity was underestimated. To validate these new putative bacteria, one of them (Halomonas) was first confirmed to be present in MED B. tabaci using Hiseq2500 and FISH technologies. These results confirmed PacBio is a reliable and informative venue to reveal the bacterial diversity of insects. In addition, many new secondary endosymbiotic strains of Rickettsia and Arsenophonus were found, increasing the known diversity in these groups. For the previously described primary endosymbionts, one Portiera Operational Taxonomic Units (OTU) was shared by all B. tabaci species. The congruence of the B. tabaci-host and Portiera phylogenetic trees provides strong support for the hypothesis that primary endosymbionts co-speciated with their hosts. Likewise, a comparison of bacterial alpha diversities, Principal Coordinate Analysis, indistinct endosymbiotic communities harbored by different species and the co-divergence analyses suggest a lack of association between overall microbial diversity with cryptic species, further indicate that the secondary endosymbiont-mediated speciation is unlikely to have occurred in the B. tabaci species group.
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Affiliation(s)
- Hua-Ling Wang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.,Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, United Kingdom
| | - Teng Lei
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Wen-Qiang Xia
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Stephen L Cameron
- Department of Entomology, Purdue University, 901West State Street, West Lafayette, IN, 479074, USA
| | - Yin-Quan Liu
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zhen Zhang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Maruthi M N Gowda
- Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, United Kingdom
| | - Paul De Barro
- CSIRO Ecosystem Sciences, Brisbane, QLD, 4001, Australia
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750, Algarrobo-Costa, Málaga, Spain
| | - Christopher A Omongo
- National Crops Resources Research Institute, Namulonge, P.O. Box, 7084, Kampala, Uganda
| | - Hélène Delatte
- CIRAD, UMR PVBMT CIRAD-Universitéde La Réunion, Pôle de Protection des Plantes, 7 chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Kyeong-Yeoll Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Mitulkumar V Patel
- Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, United Kingdom
| | | | - James Ng
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, 92521, USA
| | - San-Ling Wu
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750, Algarrobo-Costa, Málaga, Spain
| | - Shu-Sheng Liu
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, United Kingdom.
| | - Xiao-Wei Wang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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Microsatellite Borders and Micro-sequence Conservation in Juglans. Sci Rep 2019; 9:3748. [PMID: 30842460 PMCID: PMC6403238 DOI: 10.1038/s41598-019-39793-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022] Open
Abstract
Walnuts (Juglans spp.) are economically important nut and timber species with a worldwide distribution. Using the published Persian walnut genome as a reference for the assembly of short reads from six Juglans species and several interspecific hybrids, we identified simple sequence repeats in 12 Juglans nuclear and organellar genomes. The genome-wide distribution and polymorphisms of nuclear and organellar microsatellites (SSRs) for most Juglans genomes have not been previously studied. We compared the frequency of nuclear SSR motifs and their lengths across Juglans, and identified section-specific chloroplast SSR motifs. Primer pairs were designed for more than 60,000 SSR-containing sequences based on alignment against assembled scaffold sequences. Of the >60,000 loci, 39,000 were validated by e-PCR using unique primer pairs. We identified primers containing 100% sequence identity in multiple species. Across species, sequence identity in the SSR-flanking regions was generally low. Although SSRs are common and highly dispersed in the genome, their flanking sequences are conserved at about 90 to 95% identity within Juglans and within species. In a few rare cases, flanking sequences are identical across species of Juglans. This comprehensive report of nuclear and organellar SSRs in Juglans and the generation of validated SSR primers will be a useful resource for future genetic analyses, walnut breeding programs, high-level taxonomic evaluations, and genomic studies in Juglandaceae.
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Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses. Genes Genomics 2019; 41:467-481. [PMID: 30637579 DOI: 10.1007/s13258-018-00780-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/21/2018] [Indexed: 10/27/2022]
Abstract
BACKGROUND WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. OBJECTIVE In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. METHODS For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. RESULTS We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2-7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress-response pathways. CONCLUSION This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.
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D'Agostino N, Tamburino R, Cantarella C, De Carluccio V, Sannino L, Cozzolino S, Cardi T, Scotti N. The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution. Genes (Basel) 2018; 9:E503. [PMID: 30336638 PMCID: PMC6210379 DOI: 10.3390/genes9100503] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 11/16/2022] Open
Abstract
Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative genomic research in higher plants. Here, we determined the complete nucleotide sequences of the plastomes of eight Capsicum species (eleven genotypes), representing the three main taxonomic groups in the genus and estimated molecular diversity. Comparative analyses highlighted a wide spectrum of variation, ranging from point mutations to small/medium size insertions/deletions (InDels), with accD, ndhB, rpl20, ycf1, and ycf2 being the most variable genes. The global pattern of sequence variation is consistent with the phylogenetic signal. Maximum-likelihood tree estimation revealed that Capsicum chacoense is sister to the baccatum complex. Divergence and positive selection analyses unveiled that protein-coding genes were generally well conserved, but we identified 25 positive signatures distributed in six genes involved in different essential plastid functions, suggesting positive selection during evolution of Capsicum plastomes. Finally, the identified sequence variation allowed us to develop simple PCR-based markers useful in future work to discriminate species belonging to different Capsicum complexes.
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Affiliation(s)
- Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Valentina De Carluccio
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy.
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy.
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
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11
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Macfadyen S, Paull C, Boykin L, De Barro P, Maruthi M, Otim M, Kalyebi A, Vassão D, Sseruwagi P, Tay W, Delatte H, Seguni Z, Colvin J, Omongo C. Cassava whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) in East African farming landscapes: a review of the factors determining abundance. BULLETIN OF ENTOMOLOGICAL RESEARCH 2018; 108:565-582. [PMID: 29433589 PMCID: PMC7672366 DOI: 10.1017/s0007485318000032] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a pest species complex that causes widespread damage to cassava, a staple food crop for millions of households in East Africa. Species in the complex cause direct feeding damage to cassava and are the vectors of multiple plant viruses. Whilst significant work has gone into developing virus-resistant cassava cultivars, there has been little research effort aimed at understanding the ecology of these insect vectors. Here we assess critically the knowledge base relating to factors that may lead to high population densities of sub-Saharan African (SSA) B. tabaci species in cassava production landscapes of East Africa. We focus first on empirical studies that have examined biotic or abiotic factors that may lead to high populations. We then identify knowledge gaps that need to be filled to deliver sustainable management solutions. We found that whilst many hypotheses have been put forward to explain the increases in abundance witnessed since the early 1990s, there are little published data and these tend to have been collected in a piecemeal manner. The most critical knowledge gaps identified were: (i) understanding how cassava cultivars and alternative host plants impact population dynamics and natural enemies; (ii) the impact of natural enemies in terms of reducing the frequency of outbreaks and (iii) the use and management of insecticides to delay the development of resistance. In addition, there are several fundamental methodologies that need to be developed and deployed in East Africa to address some of the more challenging knowledge gaps.
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Affiliation(s)
- S. Macfadyen
- CSIRO, Clunies Ross St. Acton, ACT, 2601, Australia
- Author for correspondence Phone: +61 (02) 62464432 Fax: +61 (02) 62464094
| | - C. Paull
- CSIRO, Boggo Rd. Dutton Park, QLD, 4001, Australia
| | - L.M. Boykin
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - P. De Barro
- CSIRO, Boggo Rd. Dutton Park, QLD, 4001, Australia
| | - M.N. Maruthi
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, ME4 4TB, UK
| | - M. Otim
- National Crops Resources Research Institute, Kampala, Uganda
| | - A. Kalyebi
- National Crops Resources Research Institute, Kampala, Uganda
- Mikocheni Agricultural Research Institute, P.O. Box 6226 Dar es Salaam, Tanzania
| | - D.G. Vassão
- Max Planck Institute for Chemical Ecology, Hans-Knoell Str. 8 D-07745 Jena, Germany
| | - P. Sseruwagi
- Mikocheni Agricultural Research Institute, P.O. Box 6226 Dar es Salaam, Tanzania
| | - W.T. Tay
- CSIRO, Boggo Rd. Dutton Park, QLD, 4001, Australia
| | - H. Delatte
- CIRAD, UMR PVBMT, Saint Pierre, La Réunion 97410-F, France
| | - Z. Seguni
- Mikocheni Agricultural Research Institute, P.O. Box 6226 Dar es Salaam, Tanzania
| | - J. Colvin
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, ME4 4TB, UK
| | - C.A. Omongo
- National Crops Resources Research Institute, Kampala, Uganda
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12
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Inostroza PA, Vera-Escalona I, Wild R, Norf H, Brauns M. Tandem Action of Natural and Chemical Stressors in Stream Ecosystems: Insights from a Population Genetic Perspective. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7962-7971. [PMID: 29898597 DOI: 10.1021/acs.est.8b01259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Agricultural and urban land use has dramatically increased over the last century and one consequence is the release of anthropogenic chemicals into aquatic ecosystems. One of the rarely studied consequences is the effect of land use change on internal concentrations of organic micropollutants (OMPs) in aquatic invertebrates and its effects on their genotype diversity. Here, we applied population genetic and internal concentrations of OMPs analyses to determine evolutionary implications of chemical pollution on Gammarus pulex populations from a natural and two agricultural streams. Along 14 consecutive months sampled, 26 different OMPs were quantified in G. pulex extracts with the highest number, concentration, and toxic pressure in the anthropogenically stressed stream ecosystems. Our results indicate distinct internal OMP profiles and changes in both genetic variation and genetic structure in streams affected by anthropogenic activity. Genetic variation was attributed to chemical pollution whereas changes in the genetic structure were attributed to environmental disturbances, such as changes in discharge in the impacted stream ecosystems, which worked both independently and in tandem. Finally, we conclude that human-impacted streams are subjected to severe alterations in their population genetic patterns compared to nonimpacted stream ecosystems.
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Affiliation(s)
- Pedro A Inostroza
- Department of River Ecology , Helmholtz Centre for Environmental Research - UFZ , Brückstraße 3A , Magdeburg , Germany
| | - Iván Vera-Escalona
- Department of Biology , Dalhousie University , 1355 Oxford St. , Halifax , Canada
| | - Romy Wild
- Department of River Ecology , Helmholtz Centre for Environmental Research - UFZ , Brückstraße 3A , Magdeburg , Germany
| | - Helge Norf
- Department of River Ecology , Helmholtz Centre for Environmental Research - UFZ , Brückstraße 3A , Magdeburg , Germany
- Department of Aquatic Ecosystem Analysis and Management , Helmholtz Centre for Environmental Research - UFZ , Brückstraße 3A , Magdeburg , Germany
| | - Mario Brauns
- Department of River Ecology , Helmholtz Centre for Environmental Research - UFZ , Brückstraße 3A , Magdeburg , Germany
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13
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Xie W, Chen C, Yang Z, Guo L, Yang X, Wang D, Chen M, Huang J, Wen Y, Zeng Y, Liu Y, Xia J, Tian L, Cui H, Wu Q, Wang S, Xu B, Li X, Tan X, Ghanim M, Qiu B, Pan H, Chu D, Delatte H, Maruthi MN, Ge F, Zhou X, Wang X, Wan F, Du Y, Luo C, Yan F, Preisser EL, Jiao X, Coates BS, Zhao J, Gao Q, Xia J, Yin Y, Liu Y, Brown JK, Zhou XJ, Zhang Y. Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q. Gigascience 2018; 6:1-7. [PMID: 28327996 PMCID: PMC5467035 DOI: 10.1093/gigascience/gix018] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 03/10/2017] [Indexed: 11/15/2022] Open
Abstract
The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 437 kb, and a total length of 658 Mb. Annotation of repetitive elements and coding regions resulted in 265.0 Mb TEs (40.3%) and 20 786 protein-coding genes with putative gene family expansions, respectively. Phylogenetic analysis based on orthologs across 14 arthropod taxa suggested that MED/Q is clustered into a hemipteran clade containing A. pisum and is a sister lineage to a clade containing both R. prolixus and N. lugens. Genome completeness, as estimated using the CEGMA and Benchmarking Universal Single-Copy Orthologs pipelines, reached 96% and 79%. These MED/Q genomic resources lay a foundation for future 'pan-genomic' comparisons of invasive vs. noninvasive, invasive vs. invasive, and native vs. exotic Bemisia, which, in return, will open up new avenues of investigation into whitefly biology, evolution, and management.
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Affiliation(s)
- Wen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | | | - Zezhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Litao Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Xin Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Dan Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ming Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yanan Wen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Yang Zeng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Yating Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Jixing Xia
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Lixia Tian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Hongying Cui
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Qingjun Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Shaoli Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Baoyun Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Xianchun Li
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Xinqiu Tan
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Murad Ghanim
- Department of Entomology, Volcani Center, Bet Dagan 5025001, Israel
| | - Baoli Qiu
- Key Lab of Bio-pesticide Creation and Application, South China Agricultural University, Guangzhou 510642, China
| | - Huipeng Pan
- Key Lab of Bio-pesticide Creation and Application, South China Agricultural University, Guangzhou 510642, China
| | - Dong Chu
- College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
| | | | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK
| | - Feng Ge
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xueping Zhou
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaowei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fanghao Wan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuzhou Du
- School of Horticulture and Plant Protection and Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
| | - Chen Luo
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100089, China
| | - Fengming Yan
- Collaborative Innovation Center of Henan Grain Crops, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Evan L Preisser
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Xiaoguo Jiao
- College of Life Sciences, Hubei University, Wuhan 430062, China
| | - Brad S Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, Ames, IA 50011, USA
| | | | - Qiang Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Ye Yin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Liu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Xuguo Joe Zhou
- Department of Entomology, S-225 Agricultural Science Center North, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Youjun Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
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14
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Deng K, Deng R, Fan J, Chen E. Transcriptome analysis and development of simple sequence repeat (SSR) markers in Zingiber striolatum Diels. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:125-134. [PMID: 29398844 PMCID: PMC5787116 DOI: 10.1007/s12298-017-0485-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/16/2017] [Accepted: 11/06/2017] [Indexed: 05/26/2023]
Abstract
Illumina-based paired-end sequencing technology was used for the high-throughput transcriptome sequencing of combined Zingiber striolatum Diels tissues (i.e., root, stem, leaf, flower, and fruit tissues). More than 130 million sequencing reads were generated, and a de novo assembly yielded 287,959 contigs and 112,107 unigenes with an average length of 1029 and 28,891 bp, respectively. Similarity searches with known sequences led to the identification of 51,804 (46.21%) genes. Of the annotated unigenes, 6867 and 51,987 were assigned to Gene Ontology and Clusters of Orthologous Groups categories, respectively. Additionally, 8384 simple sequence repeats (SSRs) were identified as potential molecular markers in the unigenes. Thirty pairs of polymerase chain reaction primers were designed and used to validate the unigenes and assess the associated genomic polymorphism. The PCR amplification products for 25 primer pairs were of the expected size. These primers may represent usable molecular markers. The thousands of SSR markers identified in the present study may be useful for analyses of genetic diversity, genetic linkage mapping, and the identification and improvement of varieties during the breeding of Z. striolatum Diels. The unigene sequences and SSR markers described herein may serve as valuable resources for future investigations of Z. striolatum Diels.
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Affiliation(s)
- Kuanping Deng
- Zunyi Academy of Agricultural Sciences, Zunyi, 563100 Guizhou China
| | - Renju Deng
- Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou China
| | - Jianxin Fan
- Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou China
| | - Enfa Chen
- Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou China
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15
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Sun X, Cai R, Jin X, Shafer ABA, Hu X, Yang S, Li Y, Qi L, Liu S, Hu D. Blood transcriptomics of captive forest musk deer (Moschus berezovskii) and possible associations with the immune response to abscesses. Sci Rep 2018; 8:599. [PMID: 29330436 PMCID: PMC5766596 DOI: 10.1038/s41598-017-18534-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/13/2017] [Indexed: 12/17/2022] Open
Abstract
Forest musk deer (Moschus berezovskii; FMD) are both economically valuable and highly endangered. A problem for FMD captive breeding programs has been the susceptibility of FMD to abscesses. To investigate the mechanisms of abscess development in FMD, the blood transcriptomes of three purulent and three healthy individuals were generated. A total of ~39.68 Gb bases were generated using Illumina HiSeq 4000 sequencing technology and 77,752 unigenes were identified after assembling. All the unigenes were annotated, with 63,531 (81.71%) mapping to at least one database. Based on these functional annotations, 45,798 coding sequences (CDS) were detected, along with 12,697 simple sequence repeats (SSRs) and 65,536 single nucleotide polymorphisms (SNPs). A total of 113 unigenes were found to be differentially expressed between healthy and purulent individuals. Functional annotation indicated that most of these differentially expressed genes were involved in the regulation of immune system processes, particularly those associated with parasitic and bacterial infection pathways.
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Affiliation(s)
- Xiaoning Sun
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation,Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Ruibo Cai
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation,Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Xuelin Jin
- Shaanxi Institute of Zoology, No. 88 Xing Qing Ave Xian, Shaanxi, 710032, China
| | - Aaron B A Shafer
- Forensic Science and Environmental & Life Sciences, Trent University,1600 West Bank Drive,Peterborough, Ontario, Canada
| | - Xiaolong Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation,Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Shuang Yang
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation,Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Yimeng Li
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation,Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Lei Qi
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation,Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Shuqiang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation,Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China.
| | - Defu Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation,Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China.
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16
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Gaynor KM, Solomon JW, Siller S, Jessell L, Duffy JE, Rubenstein DR. Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes. Mol Ecol Resour 2017; 17:e160-e173. [PMID: 28776934 DOI: 10.1111/1755-0998.12705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/16/2017] [Accepted: 07/25/2017] [Indexed: 11/28/2022]
Abstract
Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.
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Affiliation(s)
- Kaitlyn M Gaynor
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Joseph W Solomon
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Stefanie Siller
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Linnet Jessell
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - J Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian Institution, Washington, DC, USA
| | - Dustin R Rubenstein
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Ornithology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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17
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Genome microsatellite diversity within the Apicomplexa phylum. Mol Genet Genomics 2016; 291:2117-2129. [PMID: 27590734 DOI: 10.1007/s00438-016-1244-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/27/2016] [Indexed: 10/21/2022]
Abstract
The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 apicomplexan organisms that represent four different lineages within the phylum. Only perfect SSRs with at least 12 nucleotides and composed of 2-6 mers were included. To better understand the association of SSR types with the genomic regions, the SSRs were classified accordingly with the genomic location into exon, intron and intergenic categories. Our results showed heterogeneous SSRs density within the studied genomes. However, the most frequent SSRs types were di- and tri-nucleotide repeats. The former was associated with intergenic regions, while the latter was associated with exon regions.
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18
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Song X, Shen F, Huang J, Huang Y, Du L, Wang C, Fan Z, Hou R, Yue B, Zhang X. Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca). J Hered 2016; 107:423-30. [PMID: 27112165 DOI: 10.1093/jhered/esw024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/18/2016] [Indexed: 01/19/2023] Open
Abstract
Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.
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Affiliation(s)
- Xuhao Song
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Fujun Shen
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Jie Huang
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Yan Huang
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Lianming Du
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Chengdong Wang
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Zhenxin Fan
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Rong Hou
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Bisong Yue
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Xiuyue Zhang
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
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Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps. BMC Evol Biol 2016; 16:77. [PMID: 27068234 PMCID: PMC4828801 DOI: 10.1186/s12862-016-0643-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 03/23/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Many species contain evolutionarily distinct groups that are genetically highly differentiated but morphologically difficult to distinguish (i.e., cryptic species). The presence of cryptic species poses significant challenges for the accurate assessment of biodiversity and, if unrecognized, may lead to erroneous inferences in many fields of biological research and conservation. RESULTS We tested for cryptic genetic variation within the broadly distributed alpine mayfly Baetis alpinus across several major European drainages in the central Alps. Bayesian clustering and multivariate analyses of nuclear microsatellite loci, combined with phylogenetic analyses of mitochondrial DNA, were used to assess population genetic structure and diversity. We identified two genetically highly differentiated lineages (A and B) that had no obvious differences in regional distribution patterns, and occurred in local sympatry. Furthermore, the two lineages differed in relative abundance, overall levels of genetic diversity as well as patterns of population structure: lineage A was abundant, widely distributed and had a higher level of genetic variation, whereas lineage B was less abundant, more prevalent in spring-fed tributaries than glacier-fed streams and restricted to high elevations. Subsequent morphological analyses revealed that traits previously acknowledged as intraspecific variation of B. alpinus in fact segregated these two lineages. CONCLUSIONS Taken together, our findings indicate that even common and apparently ecologically well-studied species may consist of reproductively isolated units, with distinct evolutionary histories and likely different ecology and evolutionary potential. These findings emphasize the need to investigate hidden diversity even in well-known species to allow for appropriate assessment of biological diversity and conservation measures.
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Cheng J, Zhao Z, Li B, Qin C, Wu Z, Trejo-Saavedra DL, Luo X, Cui J, Rivera-Bustamante RF, Li S, Hu K. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Sci Rep 2016; 6:18919. [PMID: 26739748 PMCID: PMC4703971 DOI: 10.1038/srep18919] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/30/2015] [Indexed: 02/05/2023] Open
Abstract
The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zicheng Zhao
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Bo Li
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Qin
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Diana L. Trejo-Saavedra
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Xirong Luo
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Rafael F. Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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21
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Liu F, Hu Z, Liu W, Li J, Wang W, Liang Z, Wang F, Sun X. Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development. Sci Rep 2016; 6:18947. [PMID: 26732855 PMCID: PMC4702172 DOI: 10.1038/srep18947] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/01/2015] [Indexed: 11/09/2022] Open
Abstract
Using transcriptome data to mine microsatellite and develop markers has growingly become prevalent. However, characterizing the possible function of microsatellite is relatively rare. In this study, we explored microsatellites in the transcriptome of the brown alga Sargassum thunbergii and characterized the frequencies, distribution, function and evolution, and developed primers to validate these microsatellites. Our results showed that Tri-nucleotide is the most abundant, followed by di- and mono-nucleotide. The length of microsatellite was significantly affected by the repeat motif size. The density of microsatellite in the CDS region is significantly lower than that in the UTR region. The annotation of the transcripts containing microsatellite showed that 573 transcripts have GO terms and can be categorized into 42 groups. Pathways enrichment showed that microsatellites were significantly overrepresented in the genes involved in pathways such as Ubiquitin mediated proteolysis, RNA degradation, Spliceosome, etc. Primers flanking 961 microsatellite loci were designed, and among the 30 pairs of primer selected randomly for availability test, 23 were proved to be efficient. These findings provided new insight into the function and evolution of microsatellite in transcriptome, and the identified microsatellite loci within the annotated gene will be useful for developing functional markers in S. thunbergii.
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Affiliation(s)
- Fuli Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zimin Hu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Wenhui Liu
- Qinghai Environment Monitoring Centre, Xining, 810007, China
| | - Jingjing Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Wenjun Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Zhourui Liang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Feijiu Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiutao Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
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Ke F, You S, He W, Liu T, Vasseur L, Douglas CJ, You M. Genetic differentiation of the regional Plutella xylostella populations across the Taiwan Strait based on identification of microsatellite markers. Ecol Evol 2015; 5:5880-91. [PMID: 26811762 PMCID: PMC4717340 DOI: 10.1002/ece3.1850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 12/12/2022] Open
Abstract
Movement of individuals through events, such as storms or crop transportation, may affect survival and distribution of insect pests, as well as population genetic structure at a regional scale. Understanding what factors contribute to gene flow in pest populations remains very important for sustainable pest management. The diamondback moth (Plutella xylostella) is an insect pest well known for its capacity of moving over short to long distances. Here, we used newly isolated microsatellite markers to analyze the genetic structure of nine populations across the Taiwan Strait of China (Taiwan and Fujian). A total of 12,152 simple sequence repeats (SSRs) were initially identified from the P. xylostella transcriptome (~94 Mb), with an average of 129 SSRs per Mb. Nine SSRs were validated to be polymorphic markers, and eight were used for this population genetic study. Our results showed that the P. xylostella populations could be divided into distinct two clusters, which is likely due to the year-round airflows in this region. A pattern of isolation by distance among the local populations within Fujian was found, and may be related to vegetable transportation. Considering the complexity of the P. xylostella population genetic structure from local and regional to global levels, we propose that developing ecologically sound strategies for managing this pest will require knowledge of the link between behavioral and population ecology and its genetic structure.
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Affiliation(s)
- Fushi Ke
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Fujian‐Taiwan Joint Innovative Centre for Ecological Control of Crop PestsFujian Agriculture and Forestry UniversityFuzhou350002China
- Key Laboratory of Integrated Pest Management for Fujian‐Taiwan CropsMinistry of AgricultureFuzhou350002China
| | - Shijun You
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Department of BotanyUniversity of British Columbia#3529‐6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
| | - Weiyi He
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Fujian‐Taiwan Joint Innovative Centre for Ecological Control of Crop PestsFujian Agriculture and Forestry UniversityFuzhou350002China
- Key Laboratory of Integrated Pest Management for Fujian‐Taiwan CropsMinistry of AgricultureFuzhou350002China
| | - Tiansheng Liu
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Fujian‐Taiwan Joint Innovative Centre for Ecological Control of Crop PestsFujian Agriculture and Forestry UniversityFuzhou350002China
- Key Laboratory of Integrated Pest Management for Fujian‐Taiwan CropsMinistry of AgricultureFuzhou350002China
| | - Liette Vasseur
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Department of Biological SciencesBrock University500 Glenridge AvenueSt. CatharinesOntarioL2S 3A1Canada
| | - Carl J. Douglas
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Department of BotanyUniversity of British Columbia#3529‐6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
| | - Minsheng You
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Fujian‐Taiwan Joint Innovative Centre for Ecological Control of Crop PestsFujian Agriculture and Forestry UniversityFuzhou350002China
- Key Laboratory of Integrated Pest Management for Fujian‐Taiwan CropsMinistry of AgricultureFuzhou350002China
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Sequence variation of Bemisia tabaci Chemosensory Protein 2 in cryptic species B and Q: New DNA markers for whitefly recognition. Gene 2015; 576:284-91. [PMID: 26481237 DOI: 10.1016/j.gene.2015.10.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 12/22/2022]
Abstract
Bemisia tabaci Gennadius biotypes B and Q are two of the most important worldwide agricultural insect pests. Genomic sequences of Type-2 B. tabaci chemosensory protein (BtabCSP2) were cloned and sequenced in B and Q biotypes, revealing key biotype-specific variations in the intron sequence. A Q260 sequence was found specifically in Q-BtabCSP2 and Cucumis melo LN692399, suggesting ancestral horizontal transfer of gene between the insect and the plant through bacteria. A cleaved amplified polymorphic sequences (CAPS) method was then developed to differentiate B and Q based on the sequence variation in exon of BtabCSP2 gene. The performances of CSP2-based CAPS for whitefly recognition were assessed using B. tabaci field collections from Shandong Province (P.R. China). Our SacII based CAPS method led to the same result compared to mitochondrial cytochrome oxidase-based CAPS method in the field collections. We therefore propose an explanation for CSP origin and a new rapid simple molecular method based on genomic DNA and chemosensory gene to differentiate accurately the B and Q whiteflies of the Bemisia complex around the world.
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Du L, Li W, Fan Z, Shen F, Yang M, Wang Z, Jian Z, Hou R, Yue B, Zhang X. First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics. Mol Ecol Resour 2015; 15:1001-13. [DOI: 10.1111/1755-0998.12367] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Lianming Du
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Wujiao Li
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife; Chengdu Research Base of Giant Panda Breeding; Chengdu Sichuan 610081 China
| | - Mingyu Yang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zili Wang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zuoyi Jian
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife; Chengdu Research Base of Giant Panda Breeding; Chengdu Sichuan 610081 China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
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