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Alves RM, de Abreu VAC, Oliveira RP, Almeida JVDA, de Oliveira MDM, Silva SR, Paschoal AR, de Almeida SS, de Souza PAF, Ferro JA, Miranda VFO, Figueira A, Domingues DS, Varani AM. Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation. Gigascience 2024; 13:giae027. [PMID: 38837946 PMCID: PMC11152179 DOI: 10.1093/gigascience/giae027] [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: 12/23/2023] [Revised: 03/21/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family. FINDINGS The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species. CONCLUSIONS The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.
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Affiliation(s)
| | - Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Rafaely Pantoja Oliveira
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - João Victor dos Anjos Almeida
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Mauro de Medeiros de Oliveira
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Saura R Silva
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Alexandre R Paschoal
- Departamento de Ciência da Computação (DACOM), Grupo de e Bioinformática e Reconhecimento de Padrões (bioinfo-cp), Universidade Tecnológica Federal do Paraná (UTFPR), 80230-901 Cornélio Procópio, PR, Brazil
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, OX110QX Didcot, UK
| | - Sintia S de Almeida
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Pedro A F de Souza
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Jesus A Ferro
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Vitor F O Miranda
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, 13416-000 Piracicaba, SP, Brazil
| | - Douglas S Domingues
- Departamento de Genética, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), 13418-900 Piracicaba, SP, Brazil
| | - Alessandro M Varani
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
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Li X, Liu X, Wei J, Li Y, Tigabu M, Zhao X. Development and Transferability of EST-SSR Markers for Pinus koraiensis from Cold-Stressed Transcriptome through Illumina Sequencing. Genes (Basel) 2020; 11:genes11050500. [PMID: 32370137 PMCID: PMC7291311 DOI: 10.3390/genes11050500] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 02/07/2023] Open
Abstract
Pinus koraiensis has significant economic and ecological value in Northeast China. However, due to the lack of suitable molecular markers, only a few available microsatellite markers were developed for further population genetics studies. In this study, for the first time we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers from the cold-stressed transcriptome of P. koraiensis using Illumina Sequencing. We identified a total of 7,235 EST-SSRs from 97,376 sequences, and we tested their transferability among seven related Pinus species. The results showed that trinucleotides were the most abundant type of repeat (1287, 18.74%) excluding mononucleotides, followed by dinucleotides (1284, 18.7%) and tetranucleotides (72, 1.05%). The most dominant dinucleotides and trinucleotide repeat motifs were AT/AT (535, 7.79%) and AAT/ATT (103, 1.5%). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.002 to 0.986 and 0.017 to 0.743, respectively, and the polymorphism information content (PIC) values and number of alleles (Na) varied from 0.029 to 0.794 and 2 to 23, respectively. A total of 8 natural P. koraiensis populations were divided into two main genetic clusters. Furthermore, nine of twenty polymorphic primer pairs were successfully amplified in seven Pinus species, and at least 80% of the successful P. koraiensis EST-SSR primers could be amplified in more than four species (16, 80%). Combined results for the development of EST-SSR markers in P. koraiensis and transferability among related species would contribute to improved studies on the genetic diversity and population structure in P. koraiensis and phylogenetic relationships among Pinus species. They would also provide a significant source for quantitative trait locus analysis.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
| | - Xiaoting Liu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
| | - Jiatong Wei
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
| | - Yan Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
| | - Mulualem Tigabu
- Southern Swedish Forest Research Center, Swedish University of Agricultural Sciences, SE-230 53 Alnarp, Sweden;
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
- Correspondence: ; Tel.: +86-451-8219-2225
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Genome survey and development of 18 microsatellite markers to assess genetic diversity in Spondias tuberosa Arruda Câmara (Anacardiaceae) and cross-amplification in congeneric species. Mol Biol Rep 2019; 46:3511-3517. [PMID: 30915689 DOI: 10.1007/s11033-019-04768-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
Abstract
Spondias tuberosa Arr. Cam belongs to the Anacardiaceae family, an economically important family of plants whose fruits are consumed by humans and animals. The aim of this study was to develop microsatellite markers using sequences from high-throughput sequencing and a magnetic bead enrichment method. The sequences were used to obtain contigs with a minimum of 500 nucleotides using Ray software and the mining of the simple sequence repeats (SSR) was performed with Phobos software, while the primers were designed by Primer3. We developed 18 polymorphic nuclear microsatellite markers and successfully cross-amplified them to three Spondias species. In S. tuberosa, the alleles ranged from 2 to 5 for each locus and Hardy-Weinberg equilibrium was found for 16 loci, with an expected and observed heterozygosity at 0.095-0.755 and 0.1-0.75, respectively. Cross-transferability was obtained for all loci in S. bahiensis, S. dulcis and S. purpurea. We concluded that the microsatellite markers developed in this study are useful in genetic population and conservation studies, as well as for investigating the hybrid origins of Spondias species.
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Singh AK, Chaurasia S, Kumar S, Singh R, Kumari J, Yadav MC, Singh N, Gaba S, Jacob SR. Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat. BMC PLANT BIOLOGY 2018; 18:249. [PMID: 30342465 PMCID: PMC6195990 DOI: 10.1186/s12870-018-1476-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/09/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Salinity severely limits wheat production in many parts of the world. Development of salt tolerant varieties represents the most practical option for enhancing wheat production from these areas. Application of marker assisted selection may assist in fast tracking development of salt tolerant wheat varieties. However, SSR markers available in the public domain are not specifically targeted to functional regions of wheat genome, therefore large numbers of these need to be analysed for identification of markers associated with traits of interest. With the availability of a fully annotated wheat genome assembly, it is possible to develop SSR markers specifically targeted to genic regions. We performed extensive analysis to identify candidate gene based SSRs and assessed their utility in characterizing molecular diversity in a panel of wheat genotypes. RESULTS Our analysis revealed, 161 SSR motifs in 94 salt tolerance candidate genes of wheat. These SSR motifs were nearly equally distributed on the three wheat sub-genomes; 29.8% in A, 35.7% in B and 34.4% in D sub-genome. The maximum number of SSR motifs was present in exons (31.1%) followed by promoters (29.8%), 5'UTRs (21.1%), introns (14.3%) and 3'UTRs (3.7%). Out of the 65 candidate gene based SSR markers selected for validation, 30 were found polymorphic based on initial screening and employed for characterizing genetic diversity in a panel of wheat genotypes including salt tolerant and susceptible lines. These markers generated an average of 2.83 alleles/locus. Phylogenetic analysis revealed four clusters. Salt susceptible genotypes were mainly represented in clusters I and III, whereas high and moderate salt tolerant genotypes were distributed in the remaining two clusters. Population structure analysis revealed two sub-populations, sub-population 1 contained the majority of salt tolerant whereas sub-population 2 contained majority of susceptible genotypes. Moreover, we observed reasonably higher transferability of SSR markers to related wheat species. CONCLUSION We have developed salt responsive gene based SSRs in wheat for the first time. These were highly useful in unravelling functional diversity among wheat genotypes with varying responses to salt stress. The identified gene based SSR markers will be valuable genomic resources for genetic/association mapping of salinity tolerance in wheat.
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Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Shiksha Chaurasia
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Sundeep Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Jyoti Kumari
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Mahesh C. Yadav
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Nidhi Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Sonam Gaba
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, 110012 India
| | - Sherry Rachel Jacob
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
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Edet OU, Kim JS, Okamoto M, Hanada K, Takeda T, Kishii M, Gorafi YSA, Tsujimoto H. Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers. BMC Genet 2018; 19:18. [PMID: 29587653 PMCID: PMC5872505 DOI: 10.1186/s12863-018-0603-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/13/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. RESULTS We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. CONCLUSION The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.
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Affiliation(s)
- Offiong Ukpong Edet
- Arid Land Research Center, Tottori University, Tottori, Japan
- United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074 Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Tomoyuki Takeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Masahiro Kishii
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, Tottori, Japan
- Agricultural Research Corporation (ARC), Wad Madani, Sudan
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Wickramasuriya AM, Dunwell JM. Cacao biotechnology: current status and future prospects. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:4-17. [PMID: 28985014 PMCID: PMC5785363 DOI: 10.1111/pbi.12848] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 05/03/2023]
Abstract
Theobroma cacao-The Food of the Gods, provides the raw material for the multibillion dollar chocolate industry and is also the main source of income for about 6 million smallholders around the world. Additionally, cocoa beans have a number of other nonfood uses in the pharmaceutical and cosmetic industries. Specifically, the potential health benefits of cocoa have received increasing attention as it is rich in polyphenols, particularly flavonoids. At present, the demand for cocoa and cocoa-based products in Asia is growing particularly rapidly and chocolate manufacturers are increasing investment in this region. However, in many Asian countries, cocoa production is hampered due to many reasons including technological, political and socio-economic issues. This review provides an overview of the present status of global cocoa production and recent advances in biotechnological applications for cacao improvement, with special emphasis on genetics/genomics, in vitro embryogenesis and genetic transformation. In addition, in order to obtain an insight into the latest innovations in the commercial sector, a survey was conducted on granted patents relating to T. cacao biotechnology.
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Affiliation(s)
| | - Jim M. Dunwell
- School of Agriculture, Policy and DevelopmentUniversity of ReadingReadingUK
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