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Chen W, Zhao G, Lei M, Zhu R. The complete chloroplast genome sequence of Nostolachma jenkinsii (Hook.f.) Deb & J.Lahiri, an endangered coffeeae plant. Mitochondrial DNA B Resour 2024; 9:907-910. [PMID: 39055530 PMCID: PMC11271133 DOI: 10.1080/23802359.2024.2342936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/09/2024] [Indexed: 07/27/2024] Open
Abstract
Nostolachma jenkinsii (Hook.f.) Deb & J.Lahiri, a member of the Rubiaceae family, is an endangered wild plant species with potential economic value. In this research, the complete chloroplast genome of N. jenkinsii was sequenced to gain insight into its genome feature and better understand the phylogenetic relationships among the Rubiaceae species. The chloroplast genome, with a total length of 155,036 bp, comprises two inverted repeats (IR) regions spanning 25,692 bp each, a large single-copy (LSC) region measuring 85,437 bp, and a short single-copy (SSC) region measuring 18,215 bp. There is an overall 37% GC content in the chloroplast genome. By annotation analysis,. 54 tRNA genes, 10 rRNA genes, and 107 protein-coding genes were all annotated in N. jenkinsii. Furthermore, we applied phylogenetic analysis that revealed a close relationship between N. jenkinsii, D. fruticosa and D. dubia, placing them together within the Rubiaceae family.
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Affiliation(s)
| | - Guanfei Zhao
- Institute of Vegetable Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Xizang, China
| | - Ming Lei
- Tibet Plateau Institute of Biology, Xizang, China
| | - Rongjie Zhu
- Institute of Vegetable Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Xizang, China
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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. PLoS One 2024; 19:e0302365. [PMID: 38768140 PMCID: PMC11104678 DOI: 10.1371/journal.pone.0302365] [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: 06/15/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
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Ciborowski K, Szczecińska M, Maździarz M, Sawicki J, Paukszto Ł. Decoding Evolution of Rubioideae: Plastomes Reveal Sweet Secrets of Codon Usage, Diagnostides, and Superbarcoding. Genes (Basel) 2024; 15:562. [PMID: 38790191 PMCID: PMC11121115 DOI: 10.3390/genes15050562] [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: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Galium genus belongs to the Rubiaceae family, which consists of approximately 14,000 species. In comparison to its well-known relatives, the plastomes of the Galium genus have not been explored so far. The plastomes of this genus have a typical, quadripartite structure, but differ in gene content, since the infA gene is missing in Galium palustre and Galium trfidum. An evaluation of the effectiveness of using entire chloroplast genome sequences as superbarcodes for accurate plant species identification revealed the high potential of this method for molecular delimitation within the genus and tribe. The trnE-UUC-psbD region showed the biggest number of diagnostides (diagnostic nucleotides) which might be new potential barcodes, not only in Galium, but also in other closely related genera. Relative synonymous codon usage (RSCU) appeared to be connected with the phylogeny of the Rubiaceae family, showing that during evolution, plants started preferring specific codons over others.
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Affiliation(s)
| | | | | | - Jakub Sawicki
- Department of Botany and Evolutionary Ecology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland; (K.C.); (M.S.); (M.M.); (Ł.P.)
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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae). Ecol Evol 2024; 14:e10868. [PMID: 38274863 PMCID: PMC10809029 DOI: 10.1002/ece3.10868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
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Guerra-Guimarães L, Pinheiro C, Oliveira ASF, Mira-Jover A, Valverde J, Guedes FADF, Azevedo H, Várzea V, Muñoz Pajares AJ. The chloroplast protein HCF164 is predicted to be associated with Coffea S H9 resistance factor against Hemileia vastatrix. Sci Rep 2023; 13:16019. [PMID: 37749157 PMCID: PMC10520047 DOI: 10.1038/s41598-023-41950-4] [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: 04/18/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid "Híbrido de Timor". Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.
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Affiliation(s)
- Leonor Guerra-Guimarães
- CIFC - Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal.
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal.
| | - Carla Pinheiro
- UCIBIO Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- Associate Laboratory i4HB Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Ana Sofia F Oliveira
- Center for Computational Chemistry, School of Chemistry, University of Bristol, University Walk, Bristol, BS8 1TS, UK
| | - Andrea Mira-Jover
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
- Área de Ecología, Departamento de Biología Aplicada, Universidad Miguel Hernández, Elche, Spain
| | - Javier Valverde
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | - Fernanda A de F Guedes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade Do Porto, 4099-002, Porto, Portugal
| | - Vitor Várzea
- CIFC - Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
| | - Antonio Jesús Muñoz Pajares
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- Research Unit Modeling Nature, Universidad de Granada, 18071, Granada, Spain.
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Verstraete B, Janssens S, De Block P, Asselman P, Méndez G, Ly S, Hamon P, Guyot R. Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes. PeerJ 2023; 11:e15778. [PMID: 37554339 PMCID: PMC10405798 DOI: 10.7717/peerj.15778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/29/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity. METHODS Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts. RESULTS All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.
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Affiliation(s)
| | - Steven Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - Gabriela Méndez
- Grupo de Investigación (BIOARN), Universidad Politécnica Salesiana, Quito, Ecuador
- Facultad de ingenieria, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Serigne Ly
- DIADE, Université de Montpellier, Montpellier, France
| | - Perla Hamon
- DIADE, Université de Montpellier, Montpellier, France
| | - Romain Guyot
- DIADE, Université de Montpellier, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
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Zhao SY, Muchuku JK, Liang HY, Wang QF. A complete chloroplast genome of a traditional Chinese medicine herb, Rubia podantha, and phylogenomics of Rubiaceae. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:843-853. [PMID: 37520807 PMCID: PMC10382452 DOI: 10.1007/s12298-023-01302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 08/01/2023]
Abstract
Rubia podantha Diels is endemic to southwestern China and belongs to the family Rubiaceae. It is used in traditional Chinese medicines. To enrich the genetic data and resolve Rubiaceae's phylogeny, we assembled a complete chloroplast (cp) genome of R. podantha using Illumina HiSeq reads. The whole length of the cp genome was 154,866 bp. Annotation using PGA software found 113 genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The large single-copy region was 84,717 bp, the inverted repeat B (IRa) region was 26,516 bp, the small single copy was 17,117 bp, and the inverted repeats B (IRb) region was 26,516 bp. Moreover, 64 SSRs were identified. Phylogenomic analysis using cp genomes of 109 Rubiaceae species found that R. podantha is closely related to R. cordifola. Rubiaceae was separated into three subfamilies: Ixoroideae, Cinchonoideae, and Rubiodeae. The genus Saprosma was not imbedded within the Spermacoceae alliance as reported in previous studies. Instead, it was imbedded within the Psychotrieae alliance. Divergence time estimation indicated that R. podantha split from its relative R. cordifolia around 1.25 million years ago. The assembled chloroplast genome in this study provided useful molecular information about the evolution of R. podantha and was a basis for phylogenetic analyses of Rubiaceae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01302-y.
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Affiliation(s)
- Shu-Ying Zhao
- School of Environment and Ecology, Jiangsu Open University, Nanjing, 210036 China
| | - John K. Muchuku
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200 Kenya
| | - Hai-Ying Liang
- School of Environment and Ecology, Jiangsu Open University, Nanjing, 210036 China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
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Castro AA, Nunes R, Carvalho LR, Targueta CP, Dos Santos Braga-Ferreira R, de Melo-Ximenes AA, Corvalán LCJ, Bertoni BW, Pereira AMS, de Campos Telles MP. Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily. Sci Rep 2023; 13:8390. [PMID: 37225737 DOI: 10.1038/s41598-023-34334-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.
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Affiliation(s)
- Andrezza Arantes Castro
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Rhewter Nunes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil.
- Instituto Federal de Goiás - Campus Cidade de Goiás (IFG), Goiás, GO, 74600-000, Brazil.
| | - Larissa Resende Carvalho
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Ramilla Dos Santos Braga-Ferreira
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Amanda Alves de Melo-Ximenes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Leonardo Carlos Jeronimo Corvalán
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | | | | | - Mariana Pires de Campos Telles
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás (PUC - GO), Goiânia, GO, 74605-050, Brazil
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Pham MH, Tran TH, Le TD, Le TL, Hoang H, Chu HH. The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships. Genes (Basel) 2023; 14:genes14010227. [PMID: 36672968 PMCID: PMC9859165 DOI: 10.3390/genes14010227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/19/2022] [Accepted: 01/07/2023] [Indexed: 01/18/2023] Open
Abstract
Ophiorrhiza baviensis Drake, a flowering medical plant in the Rubiaceae, exists uncertainly within the Ophiorrhiza genus' evolutionary relationships. For the first time, the whole chloroplast (cp) genome of an O. baviensis Drake species was sequenced and annotated. Our findings demonstrate that the complete cp genome of O. baviensis is 154,770 bp in size, encoding a total of 128 genes, including 87 protein-coding genes, 8 rRNAs, and 33 tRNAs. A total of 59 SSRs were screened in the studied cp genome, along with six highly variable loci, which can be applied to generate significant molecular markers for the Ophiorrhiza genus. The comparative analysis of the O. baviensis cp genome with two published others of the Ophiorrhiza genus revealed a high similarity; however, there were some notable gene rearrangements in the O. densa plastome. The maximum likelihood phylogenetic trees were constructed based on the concatenation of the rps16 gene and the trnL-trnF intergenic spacer sequence, indicating a close relationship between the studied O. baviensis and other Ophiorrhiza. This study will provide a theoretical molecular basis for identifying O. baviensis Drake, as well as species of the Ophiorrhiza genus, and contribute to shedding light on the chloroplast genome evolution of Rubiaceae.
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Affiliation(s)
- Mai Huong Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Thu Hoai Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Thi Dung Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Tung Lam Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Ha Hoang
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, VAST, Hanoi 100000, Vietnam
- Correspondence:
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Amenu SG, Wei N, Wu L, Oyebanji O, Hu G, Zhou Y, Wang Q. Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution. BMC PLANT BIOLOGY 2022; 22:88. [PMID: 35219317 PMCID: PMC8881883 DOI: 10.1186/s12870-022-03480-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/15/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices. RESULTS All plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1, rps16-trnQ-UUG, and psbM-trnD. These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance. CONCLUSIONS Plastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.
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Affiliation(s)
- Sara Getachew Amenu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Lei Wu
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China
| | - Oyetola Oyebanji
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, People's Republic of China
- Department of Botany, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Guangwan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
| | - Yadong Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
| | - Qingfeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
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11
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Saldaña CL, Rodriguez-Grados P, Chávez-Galarza JC, Feijoo S, Guerrero-Abad JC, Vásquez HV, Maicelo JL, Jhoncon JH, Arbizu CI. Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona ( Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species. Genes (Basel) 2022; 13:genes13010113. [PMID: 35052453 PMCID: PMC8774758 DOI: 10.3390/genes13010113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022] Open
Abstract
Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.
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Affiliation(s)
- Carla L. Saldaña
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Pedro Rodriguez-Grados
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
- Facultad de Ciencias, Universidad Nacional José Faustino Sánchez Carrión, Av. Mercedes Indacochea Nro. 609, Huacho 15136, Peru
| | - Julio C. Chávez-Galarza
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Shefferson Feijoo
- Estación Experimental Agraria San Bernardo, Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Carretera Cusco, Puerto Maldonado, Tambopata, Madre de Dios 17000, Peru;
| | - Juan Carlos Guerrero-Abad
- Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru;
| | - Héctor V. Vásquez
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Jorge L. Maicelo
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Jorge H. Jhoncon
- Centro de Investigación de Plantas Andinas y Nativas, Facultad de Ciencias, Universidad Nacional de Educación Enrique Guzmán y Valle, Av. Enrique Guzmán y Valle s/n, Lima 15472, Peru;
- Unidad de Investigación, Perú Maca SAC, Panamericana Sur KM. 37.2 Mz. D1. Lote 03A, Lima 15823, Peru
| | - Carlos I. Arbizu
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
- Correspondence:
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12
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Bian A, Lu L. The complete chloroplast genome of Ixora chinensis and phylogenetic relationships. Mitochondrial DNA B Resour 2021; 6:3217-3221. [PMID: 34676293 PMCID: PMC8526029 DOI: 10.1080/23802359.2021.1989336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this study, the complete chloroplast (cp) genome of Ixora chinensis was sequenced by next-generation sequencing for the first time. The complete cp genome is 154,787 in length and contained 131 genes, consisting of 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The phylogenetic position based on chloroplast genomes suggests that I. chinensis was closely related to I. chinensis (MN850660.1) within the Ixora clade, which may provide useful information for further understanding the evolution of I. chinensis.
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Affiliation(s)
- Ana Bian
- Key Laboratory of Landscape Plants with Fujian and Taiwan Characteristics of Fujian Colleges and Universities, Department of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, Fujian, China
| | - Luanmei Lu
- Key Laboratory of Landscape Plants with Fujian and Taiwan Characteristics of Fujian Colleges and Universities, Department of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, Fujian, China
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13
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Raharimalala N, Rombauts S, McCarthy A, Garavito A, Orozco-Arias S, Bellanger L, Morales-Correa AY, Froger S, Michaux S, Berry V, Metairon S, Fournier C, Lepelley M, Mueller L, Couturon E, Hamon P, Rakotomalala JJ, Descombes P, Guyot R, Crouzillat D. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago. Sci Rep 2021; 11:8119. [PMID: 33854089 PMCID: PMC8046976 DOI: 10.1038/s41598-021-87419-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/23/2021] [Indexed: 02/02/2023] Open
Abstract
Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.
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Affiliation(s)
- Nathalie Raharimalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Stephane Rombauts
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Andrew McCarthy
- grid.418923.50000 0004 0638 528XEuropean Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Andréa Garavito
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia ,Centro de Bioinformática y biología computacional de Colombia – BIOS, Ecoparque los Yarumos, Manizales, Caldas, Colombia
| | - Simon Orozco-Arias
- grid.7779.e0000 0001 2290 6370Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia ,grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia
| | - Laurence Bellanger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Alexa Yadira Morales-Correa
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Solène Froger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Stéphane Michaux
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Victoria Berry
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Sylviane Metairon
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Coralie Fournier
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland ,grid.8591.50000 0001 2322 4988Present Address: University of Geneva, CMU-Décanat, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Maud Lepelley
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Lukas Mueller
- grid.5386.8000000041936877XBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - Emmanuel Couturon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Perla Hamon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Jean-Jacques Rakotomalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Patrick Descombes
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Romain Guyot
- grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia ,grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Dominique Crouzillat
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
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14
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Charr JC, Garavito A, Guyeux C, Crouzillat D, Descombes P, Fournier C, Ly SN, Raharimalala EN, Rakotomalala JJ, Stoffelen P, Janssens S, Hamon P, Guyot R. Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee). Mol Phylogenet Evol 2020; 151:106906. [PMID: 32653553 DOI: 10.1016/j.ympev.2020.106906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022]
Abstract
For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017-based on 28,800 nuclear SNPs-indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid full-genome sequences highlighted an incongruous placement of Coffea canephora (Robusta coffee) between maternal and nuclear trees. In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed. In agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates Psilanthus from Coffea (with exception to C. rhamnifolia, closer to Psilanthus than to Coffea). In contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both Psilanthus and Coffea species, and two with either Psilanthus or Coffea species. Interestingly, Coffea and Psilanthus taxa sampled in West and Central Africa are members of the same group. Several mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for C. arabica) are involved in the evolutionary history of the coffee species. While sharing similar morphological characteristics, the genetic relationships within C. canephora have shown that some populations are well differentiated and genetically isolated. Given the position of its closely-related species, we may also consider C. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.
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Affiliation(s)
- Jean-Claude Charr
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, France.
| | - Andrea Garavito
- Departamento de Ciencias biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Christophe Guyeux
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, France.
| | | | | | | | - Serigne N Ly
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France.
| | | | | | - Piet Stoffelen
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.
| | - Steven Janssens
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.
| | - Perla Hamon
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France.
| | - Romain Guyot
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France; Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia.
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