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Lin X, Lee SY, Ni J, Zhang X, Hu X, Zou P, Wang W, Liu G. Comparative Analyses of Chloroplast Genome Provide Effective Molecular Markers for Species and Cultivar Identification in Bougainvillea. Int J Mol Sci 2023; 24:15138. [PMID: 37894819 PMCID: PMC10607086 DOI: 10.3390/ijms242015138] [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: 09/04/2023] [Revised: 10/04/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Bougainvillea is popular in ornamental horticulture for its colorful bracts and excellent adaptability, but the complex genetic relationship among this genus is fuzzy due to limited genomic data. To reveal more genomic resources of Bougainvillea, we sequenced and assembled the complete chloroplast (cp) genome sequences of Bougainvillea spectabilis 'Splendens'. The cp genome size was 154,869 bp in length, containing 86 protein-coding genes, 38 tRNAs, and eight rRNAs. Cp genome comparison across 12 Bougainvillea species (B. spectabilis, B. glabra, B. peruviana, B. arborea, B. praecox, B. stipitata, B. campanulata, B. berberidifolia, B. infesta, B. modesta, B. spinosa, and B. pachyphylla) revealed five mutational hotspots. Phylogenetic analysis suggested that B. spectabilis published previously and B. glabra clustered into one subclade as two distinct groups, sister to the subclade of B. spectabilis 'Splendens'. We considered the phylogeny relationships between B. spectabilis and B. glabra to be controversial. Based on two hypervariable regions and three common plastid regions, we developed five molecular markers for species identification in Bougainvillea and applied them to classify 53 ornamental Bougainvillea cultivars. This study provides a valuable genetic resource for Bougainvillea breeding and offers effective molecular markers to distinguish the representative ornamental species of Bougainvillea.
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Affiliation(s)
- Xinggu Lin
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, Nilai 71800, Malaysia;
| | - Jianzhong Ni
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
| | - Xiaomin Zhang
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- College of Forestry, Hainan University, Haikou 570228, China
| | - Xing Hu
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
| | - Peishan Zou
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Faculty of Health and Life Sciences, INTI International University, Nilai 71800, Malaysia;
| | - Wei Wang
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
| | - Guofeng Liu
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
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Ly SN, Garavito A, De Block P, Asselman P, Guyeux C, Charr JC, Janssens S, Mouly A, Hamon P, Guyot R. Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae. PLoS One 2020; 15:e0232295. [PMID: 32353023 PMCID: PMC7192488 DOI: 10.1371/journal.pone.0232295] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/11/2020] [Indexed: 11/19/2022] Open
Abstract
In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.
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Affiliation(s)
- Serigne Ndiawar Ly
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Andrea Garavito
- Departamento Ciencias Biológicas, Universidad de Caldas, Manizales, Colombia
| | | | - Pieter Asselman
- Meise Botanic Garden, Meise, Belgium
- University of Ghent, Ghent, Belgium
| | - Christophe Guyeux
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | - Jean-Claude Charr
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Arnaud Mouly
- Laboratory Chrono-Environment, UMR CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France
- Besançon Botanic Garden, Université de Bourgogne Franche-Comté, Besançon, France
| | - Perla Hamon
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Romain Guyot
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia
- * E-mail:
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