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Diouf M, Zoclanclounon YAB, Mboup PA, Diouf D, Malédon E, Rivallan R, Chair H, Dossa K. Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD. Plant Genome 2024:e20428. [PMID: 38234122 DOI: 10.1002/tpg2.20428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 12/04/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.
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Affiliation(s)
- Moussa Diouf
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | | | - Pape Adama Mboup
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Erick Malédon
- UMR AGAP Institut, CIRAD, Petit Bourg, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Ronan Rivallan
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Hâna Chair
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Komivi Dossa
- UMR AGAP Institut, CIRAD, Petit Bourg, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Sharaf A, Ndiribe CC, Omotoriogun TC, Abueg L, Badaoui B, Badiane Markey FJ, Beedessee G, Diouf D, Duru VC, Ebuzome C, Eziuzor SC, Jaufeerally Fakim Y, Formenti G, Ghanmi N, Guerfali FZ, Houaga I, Ideozu JE, Katee SM, Khayi S, Kuja JO, Kwon-Ndung EH, Marks RA, Moila AM, Mungloo-Dilmohamud Z, Muzemil S, Nigussie H, Osuji JO, Ras V, Tchiechoua YH, Zoclanclounon YAB, Tolley KA, Ziyomo C, Mapholi N, Muigai AWT, Djikeng A, Ebenezer TE. Bridging the gap in African biodiversity genomics and bioinformatics. Nat Biotechnol 2023; 41:1348-1354. [PMID: 37699986 DOI: 10.1038/s41587-023-01933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Affiliation(s)
- Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Charlotte C Ndiribe
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | - Taiwo Crossby Omotoriogun
- Biotechnology Unit, Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
- A.P. Leventis Ornithological Research Institute, University of Jos, Jos, Nigeria
| | - Linelle Abueg
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Bouabid Badaoui
- Mohammed V University in Rabat, Rabat, Morocco
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laâyoune, Morocco
| | | | - Girish Beedessee
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Vincent C Duru
- Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Nigeria
| | | | - Samuel C Eziuzor
- Department of Isotope Biogeochemistry, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
| | | | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Nidhal Ghanmi
- Bioinformatics Lab, Pasteur Institute of Tunis, Tunis, Tunisia
| | - Fatma Zahra Guerfali
- Laboratory of Transmission, Control and Immunobiology of Infections, Pasteur Institute of Tunis, Tunis, Tunisia
- University of Tunis El Manar, University Campus Farhat Hached, Tunis, Tunisia
| | - Isidore Houaga
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Slimane Khayi
- Biotechnology Research Unit, CRRA-Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Josiah O Kuja
- Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | | | - Rose A Marks
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | | | - Sadik Muzemil
- School of Life Science, University of Warwick, Coventry, UK
| | - Helen Nigussie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Verena Ras
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, South Africa
| | - Yves H Tchiechoua
- Pan African University Institute for Basic Sciences Technology and Innovation, Nairobi, Kenya
| | | | - Krystal A Tolley
- South African National Biodiversity Institute, Claremont, Cape Town, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | | | - Ntanganedzeni Mapholi
- Department of Agriculture and Animal Health, University of South Africa, Florida, South Africa
| | - Anne W T Muigai
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
- National Defense University-Kenya, Nakuru, Kenya.
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Edinburgh, UK.
- International Livestock Research Institute, Nairobi, Kenya.
- Department of Agriculture and Animal Health, University of South Africa, Florida, South Africa.
| | - ThankGod Echezona Ebenezer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- Early Cancer Institute, Department of Oncology, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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Zoclanclounon YAB, Thamilarasan SK, Mo Y, Ahn BO, Kim JG, Lee K. Insights into chloroplast genome structure and phylogenetic relationships within the Sesamum species complex (Pedaliaceae). Front Genet 2023; 14:1207306. [PMID: 37323670 PMCID: PMC10267711 DOI: 10.3389/fgene.2023.1207306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Background: In the Sesamum species complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships. Results: In the present study, we generated complete chloroplast genomes of six wild relatives (Sesamum alatum, Sesamum angolense, Sesamum pedaloides, Ceratotheca sesamoides (syn. Sesamum sesamoides), Ceratotheca triloba (syn. Sesamum trilobum), and Sesamum radiatum) and a Korean cultivar, Sesamum indicum cv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863-153, 338 bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, including ndhA, ndhE, ndhF, ycf1, and psaC-ndhD. Concordant tree topologies suggest ndhF as a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate that S. radiatum (2n = 64) occurred concomitantly with the sister species C. sesamoides (2n = 32) approximately 0.05 million years ago (Mya). In addition, S. alatum was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others. Conclusion: Altogether, we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum, respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in the Sesamum species complex.
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Affiliation(s)
- Yedomon Ange Bovys Zoclanclounon
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Senthil Kumar Thamilarasan
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Youngjun Mo
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Byoung-Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Jeong-Gu Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Keunpyo Lee
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
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Sohn SI, Pandian S, Rakkammal K, Largia MJV, Thamilarasan SK, Balaji S, Zoclanclounon YAB, Shilpha J, Ramesh M. Jasmonates in plant growth and development and elicitation of secondary metabolites: An updated overview. Front Plant Sci 2022; 13:942789. [PMID: 36035665 PMCID: PMC9407636 DOI: 10.3389/fpls.2022.942789] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Secondary metabolites are incontestably key specialized molecules with proven health-promoting effects on human beings. Naturally synthesized secondary metabolites are considered an important source of pharmaceuticals, food additives, cosmetics, flavors, etc., Therefore, enhancing the biosynthesis of these relevant metabolites by maintaining natural authenticity is getting more attention. The application of exogenous jasmonates (JAs) is well recognized for its ability to trigger plant growth and development. JAs have a large spectrum of action that covers seed germination, hypocotyl growth regulation, root elongation, petal expansion, and apical hook growth. This hormone is considered as one of the key regulators of the plant's growth and development when the plant is under biotic or abiotic stress. The JAs regulate signal transduction through cross-talking with other genes in plants and thereby deploy an appropriate metabolism in the normal or stressed conditions. It has also been found to be an effective chemical elicitor for the synthesis of naturally occurring secondary metabolites. This review discusses the significance of JAs in the growth and development of plants and the successful outcomes of jasmonate-driven elicitation of secondary metabolites including flavonoids, anthraquinones, anthocyanin, xanthonoid, and more from various plant species. However, as the enhancement of these metabolites is essentially measured via in vitro cell culture or foliar spray, the large-scale production is significantly limited. Recent advancements in the plant cell culture technology lay the possibilities for the large-scale manufacturing of plant-derived secondary metabolites. With the insights about the genetic background of the metabolite biosynthetic pathway, synthetic biology also appears to be a potential avenue for accelerating their production. This review, therefore, also discussed the potential manoeuvres that can be deployed to synthesis plant secondary metabolites at the large-scale using plant cell, tissue, and organ cultures.
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Affiliation(s)
- Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Subramani Pandian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | | | | | - Senthil Kumar Thamilarasan
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | | | - Yedomon Ange Bovys Zoclanclounon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jayabalan Shilpha
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Manikandan Ramesh
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
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Akan OD, Udofia GE, Okeke ES, Mgbechidinma CL, Okoye CO, Zoclanclounon YAB, Atakpa EO, Adebanjo OO. Plastic waste: Status, degradation and microbial management options for Africa. J Environ Manage 2021; 292:112758. [PMID: 34030015 DOI: 10.1016/j.jenvman.2021.112758] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/25/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
This paper presents a review of synthetic polymer (notably plastic) wastes profiles in Africa, their current management status, and better options. Data revealed that of the approximated 86.14 million metric tonnes and 31.5 million metric tonnes of primary polymers and plastics, respectively, and an estimated 230 million metric tonnes of plastic components imported between 1990 and 2017, about 17 million metric tonnes are mismanaged. Leading African nations on the plastic wastes generator table in increasing order are Tunisia (6.9%), Morocco (9.6%), Algeria (11.2%), South Africa (11.6%), Nigeria (16.9%), and the chief is Egypt (18.4%). The volume of plastic wastes generated in Africa directly correlates with her increasing population status, however, the current treatment options have major drawbacks (high energy and technological input, high demand for space, and creation of obnoxious by-products). Ineffective regulations, poor monitoring, and slow adoption of veritable practices by governments are responsible for the steady increase in plastic volume in the African landscapes and environments. In Nigeria, only about 9% and 12% of the total generated wastes are recycled and incinerated. The remainder bulk is either discarded into waste dumps (and a few available landfills) or natural environments. There is a paucity of standard plastic biodegradative work by African scientists, and only a few works show detection of competent synthetic plastic degrading microbes globally. Asides from the ills of possible omission of core degraders, there is a need for researchers to follow standard degradation procedures to arrive at efficient, reproducible, and generally accepted outcomes utilizable on a larger scale. Thus, metagenomic search on the vast African urban and rural plastisphere is the best isolation option.
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Affiliation(s)
- Otobong Donald Akan
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 41004, China; Microbiology Department, Faculty of Biological Science, Akwa-Ibom State University, Ikot Akpaden, Mkpat Enin LGA, Uyo P.M.B., 1167, Akwa-Ibom State, Nigeria.
| | - Godwin Evans Udofia
- Department of Microbiology, Faculty of Science, University of Uyo, Uyo PMB, 1017, Nigeria
| | - Emmanuel Sunday Okeke
- Environmental Chemistry and Toxicology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies University of Nigeria, Nsukka, 410001, Nigeria.
| | - Chiamaka Linda Mgbechidinma
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China; Department of Microbiology, University of Ibadan, Ibadan, Oyo State, 200243, Nigeria
| | - Charles Obinwanne Okoye
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, 410001, Nigeria
| | - Yedomon Ange Bovys Zoclanclounon
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, 54896, South Korea; Department of Management of Environment, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 POB 2009, Cotonou, Benin
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