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Zhang D, Ren J, Jiang H, Wanga VO, Dong X, Hu G. Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae). Sci Rep 2023; 13:7237. [PMID: 37142659 PMCID: PMC10160070 DOI: 10.1038/s41598-023-34083-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots of several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported the size and gene contents of the plastomes, with little information on the comparative analysis of the plastid genomes of this genus. Additionally, there are still some species whose chloroplast genome information has not been reported. In this study, the complete plastomes of six Polygonatum were sequenced and assembled, among them, the chloroplast genome of P. campanulatum was reported for the first time. Comparative and phylogenetic analyses were then conducted with the published plastomes of three related species. Results indicated that the whole plastome length of the Polygonatum species ranged from 154,564 bp (P. multiflorum) to 156,028 bp (P. stenophyllum) having a quadripartite structure of LSC and SSC separated by two IR regions. A total of 113 unique genes were detected in each of the species. Comparative analysis revealed that gene content and total GC content in these species were highly identical. No significant contraction or expansion was observed in the IR boundaries among all the species except P. sibiricum1, in which the rps19 gene was pseudogenized owing to incomplete duplication. Abundant long dispersed repeats and SSRs were detected in each genome. There were five remarkably variable regions and 14 positively selected genes were identified among Polygonatum and Heteropolygonatum. Phylogenetic results based on chloroplast genome strongly supported the placement of P. campanulatum with alternate leaves in sect. Verticillata, a group characterized by whorled leaves. Moreover, P. verticillatum and P. cyrtonema were displayed as paraphyletic. This study revealed that the characters of plastomes in Polygonatum and Heteropolygonatum maintained a high degree of similarity. Five highly variable regions were found to be potential specific DNA barcodes in Polygonatum. Phylogenetic results suggested that leaf arrangement was not suitable as a basis for delimitation of subgeneric groups in Polygonatum and the definitions of P. cyrtonema and P. verticillatum require further study.
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Affiliation(s)
- Dongjuan Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Ren
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Hui Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Essono Mintsa M, Kumulungui BS, Obiang CS, Dussert E, Choque E, Herfurth D, Ravallec R, Ondo JP, Mesnard F. Cytotoxicity and Identification of Antibacterial Compounds from Baillonella toxisperma Bark Using a LC-MS/MS and Molecular Networking Approach. Metabolites 2023; 13:metabo13050599. [PMID: 37233640 DOI: 10.3390/metabo13050599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/20/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
Baillonella toxisperma is a medicinal plant used in northern Gabon to treat microbial diseases. It is a plant well-known by local populations, but very few studies have focused on the molecules responsible for the antibacterial activities of B. toxisperma. This study proposes a dereplication strategy based on molecular networking generated from HPLC-ESI-Q/TOF data, allowing investigation of the molecules responsible for the antibacterial activity of B. toxisperma. From this strategy, eighteen compounds were putatively identified. All of these compounds belonged mainly to five families of natural compounds, including phenylpropanolamines, stilbenes, flavonoids, lignans and phenolic glycosides. The chemical study carried out from the bark of B. toxisperma allowed us to identify, for the first time, compounds such as resveratrol and derivatives, epicatechin, epigallocatechin and epigallocatechin gallate. In addition, antibacterial activity (diffusion method and microdilution) and cytotoxicity (Cell Counting Kit-8 (CCK-8 Assay)) in vitro were evaluated. The crude ethanolic extract, as well as the fractions of B. toxisperma, showed significant antibacterial activity. However, the ethanolic fractions F2 and F4 presented high antibacterial activity compared to the crude extract. Cytotoxicity studies on colon-cancer cells (Caco-2) and human keratinocyte cells (HaCaT) showed moderate cytotoxicity in both cell types. This study clearly shows the therapeutic potential of the ethanolic extract of the bark of B. toxisperma and provides information on the phytochemical composition and bioactive compounds of the plant.
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Affiliation(s)
- Morel Essono Mintsa
- UMRt BioEcoAgro 1158-INRAE, BIOPI, Université de Picardie Jules Verne, 1 Rue des Louvels, 80000 Amiens, France
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville P.O. Box 769, Gabon
- Laboratoire Innovation Matériau Bois Habitat (LIMBHA), Ecole Supérieure du Bois, 7 Rue Christian Pauc, 44306 Nantes, France
| | - Brice Serge Kumulungui
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville P.O. Box 769, Gabon
| | - Cédric Sima Obiang
- Laboratoire de Recherches en Biochimie (LAREBIO), Université des Sciences et Techniques de Masuku, Franceville P.O. Box 943, Gabon
| | - Elodie Dussert
- UMRt BioEcoAgro 1158-INRAE, Institut Charles Violette, Université de Lille, 59655 Lille, France
| | - Elodie Choque
- UMRt BioEcoAgro 1158-INRAE, BIOPI, Université de Picardie Jules Verne, 1 Rue des Louvels, 80000 Amiens, France
| | - Damien Herfurth
- UMRt BioEcoAgro 1158-INRAE, BIOPI, Université de Picardie Jules Verne, 1 Rue des Louvels, 80000 Amiens, France
| | - Rozenn Ravallec
- UMRt BioEcoAgro 1158-INRAE, Institut Charles Violette, Université de Lille, 59655 Lille, France
| | - Joseph-Privat Ondo
- Laboratoire de Recherches en Biochimie (LAREBIO), Université des Sciences et Techniques de Masuku, Franceville P.O. Box 943, Gabon
| | - François Mesnard
- UMRt BioEcoAgro 1158-INRAE, BIOPI, Université de Picardie Jules Verne, 1 Rue des Louvels, 80000 Amiens, France
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Tchokponhoué DA, Achigan-Dako EG, Sognigbé N, Nyadanu D, Hale I, Odindo AO, Sibiya J. Genome-wide diversity analysis suggests divergence among Upper Guinea and the Dahomey Gap populations of the Sisrè berry (Syn: miracle fruit) plant (Synsepalum dulcificum [Schumach. & Thonn.] Daniell) in West Africa. THE PLANT GENOME 2023; 16:e20299. [PMID: 36661287 DOI: 10.1002/tpg2.20299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 11/20/2022] [Indexed: 05/10/2023]
Abstract
Although Synsepalum dulcificum is viewed as one of the most economically promising orphan tree crops worldwide, its genetic improvement and sustainable conservation are hindered by a lack of understanding of its evolutionary history and current population structure. Here, we report for the first time the application of genome-wide single nucleotide polymorphism genotyping to a diverse panel of S. dulcificum accessions to depict the genetic diversity and population structure of the species in the Dahomey Gap (DG) and Upper Guinea (UG) regions to infer its evolutionary history. Our findings suggest low overall genetic diversity but strong population divergence within the species. Neighbor-joining analysis detected two genetic groups in the UG and DG regions, while STRUCTURE distinguished three genetic groups, corresponding to the UG, Western DG, and Central DG regions. Application of Monmonier's algorithm revealed the existence of a barrier disrupting connectivity between the UG and DG groups. The Western DG group consistently exhibited the highest levels of nucleotide and haplotype diversities, while that of the Central DG exhibited the lowest. Analyses of Tajima's D, Fu's Fs, and Achaz Y* statistics suggest that while both UG and Central DG groups likely experienced recent expansions, the Western DG group is at equilibrium. These findings suggest a geographical structuring of genetic variation which supports the conclusion of differential evolutionary histories among West African groups of S. dulcificum. These results provide foundational insights to guide informed breeding population development and design sustainable conservation strategies for this species.
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Affiliation(s)
- Dèdéou A Tchokponhoué
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - Enoch G Achigan-Dako
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - N'Danikou Sognigbé
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
- Ecole d'Horticulture et d'Aménagement des Espaces Verts, Université Nationale d'Agriculture, Kétou, Republic of Benin
- World Vegetable Center, East and Southern Africa, Arusha, Tanzania
| | - Daniel Nyadanu
- Cocoa Research Institute of Ghana (CRIG), Akim Tafo, Ghana
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - Alfred O Odindo
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Julia Sibiya
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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BuscoPhylo: a webserver for Busco-based phylogenomic analysis for non-specialists. Sci Rep 2022; 12:17352. [PMID: 36253435 PMCID: PMC9576783 DOI: 10.1038/s41598-022-22461-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/14/2022] [Indexed: 01/10/2023] Open
Abstract
Here we present the BuscoPhylo tool that enables both students and established scientists to easily perform Busco-based phylogenomic analysis starting from a set of genomes sequences. BuscoPhylo is an efficient and user-friendly web server freely accessible at https://buscophylo.inra.org.ma/ . The source code, along with documentation, is freely available under an MIT license at https://github.com/alaesahbou/BuscoPhylo .
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Peng JY, Zhang XS, Zhang DG, Wang Y, Deng T, Huang XH, Kuang TH, Zhou Q. Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu & Q. E. Yang and comparative analyses with other Sinosenecio species. BMC Genomics 2022; 23:639. [PMID: 36076168 PMCID: PMC9454173 DOI: 10.1186/s12864-022-08872-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sinosenecio B. Nordenstam (Asteraceae) currently comprises 44 species. To investigate the interspecific relationship, several chloroplast markers, including ndhC-trnV, rpl32-trnL, matK, and rbcL, are used to analyze the phylogeny of Sinosenecio. However, the chloroplast genomes of this genus have not been thoroughly investigated. We sequenced and assembled the Sinosenecio albonervius chloroplast genome for the first time. A detailed comparative analysis was performed in this study using the previously reported chloroplast genomes of three Sinosenecio species. Results The results showed that the chloroplast genomes of four Sinosenecio species exhibit a typical quadripartite structure. There are equal numbers of total genes, protein-coding genes and RNA genes among the annotated genomes. Per genome, 49–56 simple sequence repeats and 99 repeat sequences were identified. Thirty codons were identified as RSCU values greater than 1 in the chloroplast genome of S. albonervius based on 54 protein-coding genes, indicating that they showed biased usage. Among 18 protein-coding genes, 46 potential RNA editing sites were discovered. By comparing these chloroplast genomes' structures, inverted repeat regions and coding regions were more conserved than single-copy and non-coding regions. The junctions among inverted repeat and single-copy regions showed slight difference. Several hot spots of genomic divergence were detected, which can be used as new DNA barcodes for species identification. Phylogenetic analysis of the whole chloroplast genome showed that the four Sinosenecio species have close interspecific relationships. Conclusions The complete chloroplast genome of Sinosenecio albonervius was revealed in this study, which included a comparison of Sinosenecio chloroplast genome structure, variation, and phylogenetic analysis for related species. These will help future research on Sinosenecio taxonomy, identification, origin, and evolution to some extent. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08872-3.
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Affiliation(s)
- Jing-Yi Peng
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China
| | - Xiao-Shuang Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Dai-Gui Zhang
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China.,Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, College of Hunan Province, Jishou, 416000, Hunan, China
| | - Yi Wang
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Xian-Han Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Tian-Hui Kuang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Qiang Zhou
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China. .,Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, College of Hunan Province, Jishou, 416000, Hunan, China.
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Wei R, Li Q. The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications. Genes (Basel) 2022; 13:genes13081361. [PMID: 36011272 PMCID: PMC9407434 DOI: 10.3390/genes13081361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Stemona parviflora is an endangered species, narrowly endemic to Hainan and Southwest Guangdong. The taxonomic classification of S. parviflora remains controversial. Moreover, studying endangered species is helpful for current management and conservation. In this study, the first complete chloroplast genome of S. parviflora was assembled and compared with other Stemona species. The chloroplast genome size of S. parviflora was 154,552 bp, consisting of 87 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and one pseudogene. The ψycf1 gene was lost in the cp genome of S. sessilifolia, but it was detected in four other species of Stemona. The inverted repeats (IR) regions have a relatively lower length variation compared with the large single copy (LSC) and small single copy (SSC) regions. Long repeat sequences and simple sequence repeat (SSR) were detected, and most SSR were distributed in the LSC region. Codon usage bias analyses revealed that the RSCU value of the genus Stemona has almost no difference. As with most angiosperm chloroplast genomes, protein-coding regions were more conservative than the inter-gene spacer. Seven genes (atpI, ccsA, cemA, matK, ndhA, petA, and rpoC1) were detected under positive selection in different Stemona species, which may result from adaptive evolution to different habitats. Phylogenetic analyses show the Stemona cluster in two main groups; S. parviflora were closest to S. tuberosa. A highly suitable region of S. parviflora was simulated by Maxent in this study; it is worth noting that the whole territory of Taiwan has changed to a low fitness area and below in the 2050 s, which may not be suitable for the introduction and cultivation of S. parviflora. In addition, limited by the dispersal capacity of S. parviflora, it is necessary to carry out artificial grafts to expand the survival areas of S. parviflora. Our results provide valuable information on characteristics of the chloroplast genome, phylogenetic relationships, and potential distribution range of the endangered species S. parviflora.
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Affiliation(s)
- Ran Wei
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
| | - Qiang Li
- Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Correspondence:
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Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2194021. [PMID: 35937412 PMCID: PMC9348943 DOI: 10.1155/2022/2194021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022]
Abstract
Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.
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Mutinda ES, Mkala EM, Dong X, Yang JX, Waswa EN, Nanjala C, Odago WO, Hu GW, Wang QF. Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia. PLANTS 2022; 11:231. [DOI: https:/doi.org/10.3390/plants11020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.
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Mutinda ES, Mkala EM, Dong X, Yang JX, Waswa EN, Nanjala C, Odago WO, Hu GW, Wang QF. Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia. PLANTS 2022; 11:plants11020231. [PMID: 35050119 PMCID: PMC8781850 DOI: 10.3390/plants11020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/29/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.
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Affiliation(s)
- Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- East African Herbarium, National Museums of Kenya, Nairobi 451660-0100, Kenya
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Emmanuel Nyongesa Waswa
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Consolata Nanjala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wyclif Ochieng Odago
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- East African Herbarium, National Museums of Kenya, Nairobi 451660-0100, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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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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11
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Yang J, Hu G, Hu G. Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales. BMC Genomics 2022; 23:27. [PMID: 34991482 PMCID: PMC8734052 DOI: 10.1186/s12864-021-08259-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. RESULTS The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. CONCLUSION This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.
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Affiliation(s)
- Jiaxin Yang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Guoxiong Hu
- College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Guangwan Hu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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Yang Z, Liu Z, Xu H, Chen Y, Du P, Li P, Lai W, Hu H, Luo J, Ding Y. The Chromosome-Level Genome of Miracle Fruit ( Synsepalum dulcificum) Provides New Insights Into the Evolution and Function of Miraculin. FRONTIERS IN PLANT SCIENCE 2022; 12:804662. [PMID: 35046985 PMCID: PMC8763355 DOI: 10.3389/fpls.2021.804662] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/29/2021] [Indexed: 05/25/2023]
Abstract
Miracle fruit (Synsepalum dulcificum) is a rare valuable tropical plant famous for a miraculous sweetening glycoprotein, miraculin, which can modify sour flavors to sweet flavors tasted by humans. Here, we present a chromosome-level high-quality genome of S. dulcificum with an assembly genome size of ∼550 Mb, contig N50 of ∼14.14 Mb, and 37,911 annotated protein-coding genes. Phylogenetic analysis revealed that S. dulcificum was most closely related to Camellia sinensis and Diospyros oleifera, and that S. dulcificum diverged from the Diospyros genus ∼75.8 million years ago (MYA), and that C. sinensis diverged from Synsepalum ∼63.5 MYA. Ks assessment and collinearity analysis with S. dulcificum and other species suggested that a whole-genome duplication (WGD) event occurred in S. dulcificum and that there was good collinearity between S. dulcificum and Vitis vinifera. On the other hand, transcriptome and metabolism analysis with six tissues containing three developmental stages of fleshes and seeds of miracle fruit revealed that Gene Ontology (GO) terms and metabolic pathways of "cellular response to chitin," "plant-pathogen interaction," and "plant hormone signal transduction" were significantly enriched during fruit development. Interestingly, the expression of miraculin (Chr10G0299340) progressively increased from vegetative organs to reproductive organs and reached an incredible level in mature fruit flesh, with an fragments per kilobase of transcript per million (FPKM) value of ∼113,515, which was the most highly expressed gene among all detected genes. Combining the unique signal peptide and the presence of the histidine-30 residue together composed the main potential factors impacting miraculin's unique properties in S. dulcificum. Furthermore, integrated analysis of weighted gene coexpression network analysis (WGCNA), enrichment and metabolite correlation suggested that miraculin plays potential roles in regulating plant growth, seed germination and maturation, resisting pathogen infection, and environmental pressure. In summary, valuable genomic, transcriptomic, and metabolic resources provided in this study will promote the utilization of S. dulcificum and in-depth research on species in the Sapotaceae family.
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Affiliation(s)
- Zhuang Yang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Zhenhuan Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Hang Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yayu Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Pengmeng Du
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Ping Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Wenjie Lai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Haiyan Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yuanhao Ding
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
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Yang JX, Peng S, Wang JJ, Ding SX, Wang Y, Tian J, Yang H, Hu GW, Wang QF. Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China. PLANT DIVERSITY 2021; 43:409-419. [PMID: 34816066 PMCID: PMC8591143 DOI: 10.1016/j.pld.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/02/2021] [Accepted: 01/07/2021] [Indexed: 06/13/2023]
Abstract
Corallorhiza sinensis, a new species of mycoheterotrophic orchid from western Sichuan, China, is described and illustrated based on molecular and morphological evidence. It is morphologically similar to Corallorhiza trifida, but can be distinguished by bigger flowers, both sepals and petals with 3 veins, and longer lateral lobes of lip. To distinguish the new Corallorhiza species and explore its phylogenetic position within subtribe Calypsoinae, this study employed sequences of the nuclear ribosomal DNA (nrDNA) and whole plastome assembled from the genome skimming approach. The plastome is 148,124 bp in length, including a pair of inverted repeats (IRs) of 26,165 bp, a large single-copy region (LSC) of 82,207 bp, and a small single-copy region (SSC) of 13,587 bp. Further, phylogenetic analyses were performed using nrDNA sequence and 79 coding sequences (CDSs) from 26 complete plastomes of subtribe Calypsoinae. The phylogenetic tree based on nrDNA sequence suggested that Corallorhiza is a monophyletic group, and strongly support C. sinensis as sister to the rest species of Corallorhiza. The plastid tree showed that 10 Corallorhiza species grouped into two clades and C. sinensis is most closely related to the North American C. striata and C. bentleyi instead of Oreorchis foliosa and O . angustata in the same clade. The plastid tree and nrDNA tree indicate Oreorchis is a paraphyletic. Although the topological conflicts are displayed between plastome and nrDNA phylogenies of C. sinensis, it is still the most closely related to Corallorhiza. Comparative analysis showed that C. sinensis populations are characteristic of the intermediate morphological traits between Corallorhiza and Oreorchis. The finding of this new species from China shed new light on the phylogeny of Oreorchis and Corallorhiza.
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Affiliation(s)
- Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Peng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Jie Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shi-Xiong Ding
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yan Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Tian
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Han Yang
- Administration of Siguniang Mountains National Nature Reserve, Xiaojin, 624206, China
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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Turudić A, Liber Z, Grdiša M, Jakše J, Varga F, Šatović Z. Towards the Well-Tempered Chloroplast DNA Sequences. PLANTS 2021; 10:plants10071360. [PMID: 34371563 PMCID: PMC8309291 DOI: 10.3390/plants10071360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
With the development of next-generation sequencing technology and bioinformatics tools, the process of assembling DNA sequences has become cheaper and easier, especially in the case of much shorter organelle genomes. The number of available DNA sequences of complete chloroplast genomes in public genetic databases is constantly increasing and the data are widely used in plant phylogenetic and biotechnological research. In this work, we investigated possible inconsistencies in the stored form of publicly available chloroplast genome sequence data. The impact of these inconsistencies on the results of the phylogenetic analysis was investigated and the bioinformatic solution to identify and correct inconsistencies was implemented. The whole procedure was demonstrated using five plant families (Apiaceae, Asteraceae, Campanulaceae, Lamiaceae and Rosaceae) as examples.
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Affiliation(s)
- Ante Turudić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia; (M.G.); (F.V.); (Z.Š.)
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-91-3141592
| | - Zlatko Liber
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
- Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia
| | - Martina Grdiša
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia; (M.G.); (F.V.); (Z.Š.)
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
| | - Jernej Jakše
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia;
| | - Filip Varga
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia; (M.G.); (F.V.); (Z.Š.)
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
| | - Zlatko Šatović
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia; (M.G.); (F.V.); (Z.Š.)
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
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Wanga VO, Dong X, Oulo MA, Mkala EM, Yang JX, Onjalalaina GE, Gichua MK, Kirika PM, Gituru RW, Hu GW, Wang QF. Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement. FRONTIERS IN PLANT SCIENCE 2021; 12:691833. [PMID: 34194461 PMCID: PMC8238049 DOI: 10.3389/fpls.2021.691833] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/19/2021] [Indexed: 05/15/2023]
Abstract
Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas Xerophyta Juss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.
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Affiliation(s)
- Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Guy Eric Onjalalaina
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Moses Kirega Gichua
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | - Robert Wahiti Gituru
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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