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Lin Y, Xiang Y, Wei S, Zhang Q, Liu Y, Zhang Z, Tang S. Genetic diversity and population structure of an insect-pollinated and bird-dispersed dioecious tree Magnolia kwangsiensis in a fragmented karst forest landscape. Ecol Evol 2024; 14:e70094. [PMID: 39091326 PMCID: PMC11291554 DOI: 10.1002/ece3.70094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024] Open
Abstract
This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units.
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Affiliation(s)
- Yanfang Lin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
- Wuzhou No. 18 Middle SchoolWuzhouChina
| | - Yingying Xiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Sujian Wei
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Yanhua Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Zhiyong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
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Sun Y, Nan H, Zhang C, Yang X, Zhao Y, Feng G, Ma L. Genetic characteristics of Blastocystis sp. in cattle from Hebei Province, China. Microb Pathog 2024; 190:106629. [PMID: 38522492 DOI: 10.1016/j.micpath.2024.106629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Blastocystis sp. is a protozoan parasite that infects the intestines of humans and animals, causing chronic diseases such as skin rashes, abdominal pain, and irritable bowel syndrome. A survey was conducted to determine the prevalence and genetic diversity of Blastocystis sp. infection in cattle, in Hebei Province, China. 2746 cattle fecal samples were collected from 11 cities in Hebei Province and analyzed using polymerase chain reaction targeting the Blastocystis sp. barcoding gene. MEGA, PhyloSuite, and PopART were used to analyze the subtype, sequence signature, pairwise genetic distance, and genetic diversity indices. The results showed that the Blastocystis sp. detection rate was 12.60% (346/2746). The infection rate in different herds was affected by region, age, breeding mode, and variety; that is, the infection rates in areas of southern Hebei, cattle under one year old, intensive raising, and dairy cattle were higher than the infection rates in northern Hebei, cattle over one year old, scatter feeding, and beef cattle. Seven Blastocystis subtypes were identified, namely, ST1, ST2, ST5, ST10, ST14, ST21, and ST26; ST10 was the dominant subtype, and ST14 was the second most common subtype. A total of 374 polymorphic and conserved sites were obtained, including 273 invariable (monomorphic) sites and 101 variable (polymorphic) sites, accounting for 27.01% of all nucleotides. The nucleotide diversity index (Pi) was 0.07749, and the haplotype (gene) diversity index (Hd) was 0.946. This study provides the first comprehensive information on the epidemiological situation of Blastocystis sp. infection in cattle from Hebei Province, China, and revealed rich genetic diversity of Blastocystis sp.
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Affiliation(s)
- Yuxin Sun
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Huizhu Nan
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Chao Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xin Yang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Gang Feng
- Tangshan Municipal Administration Center of Zoo, Tangshan, 063000, China
| | - Lei Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
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Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae. Genes (Basel) 2022; 13:genes13122291. [PMID: 36553558 PMCID: PMC9778145 DOI: 10.3390/genes13122291] [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: 10/19/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Physalis angulata var. villosa, rich in withanolides, has been used as a traditional Chinese medicine for many years. To date, few extensive molecular studies of this plant have been conducted. In the present study, the plastome of P. angulata var. villosa was sequenced, characterized and compared with that of other Physalis species, and a phylogenetic analysis was conducted in the family Solanaceae. The plastome of P. angulata var. villosa was 156,898 bp in length with a GC content of 37.52%, and exhibited a quadripartite structure typical of land plants, consisting of a large single-copy (LSC, 87,108 bp) region, a small single-copy (SSC, 18,462 bp) region and a pair of inverted repeats (IR: IRA and IRB, 25,664 bp each). The plastome contained 131 genes, of which 114 were unique and 17 were duplicated in IR regions. The genome consisted of 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. A total of 38 long, repeat sequences of three types were identified in the plastome, of which forward repeats had the highest frequency. Simple sequence repeats (SSRs) analysis revealed a total of 57 SSRs, of which the T mononucleotide constituted the majority, with most of SSRs being located in the intergenic spacer regions. Comparative genomic analysis among nine Physalis species revealed that the single-copy regions were less conserved than the pair of inverted repeats, with most of the variation being found in the intergenic spacer regions rather than in the coding regions. Phylogenetic analysis indicated a close relationship between Physalis and Withania. In addition, Iochroma, Dunalia, Saracha and Eriolarynx were paraphyletic, and clustered together in the phylogenetic tree. Our study published the first sequence and assembly of the plastome of P. angulata var. villosa, reported its basic resources for evolutionary studies and provided an important tool for evaluating the phylogenetic relationship within the family Solanaceae.
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Genetic diversity, genetic structure, and demographic history of Cinnamomum chago, a plant species with extremely small populations in China. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Bourguiba H, Batnini MA, Naccache C, Zitouna N, Trifi-Farah N, Audergon JM, Krichen L. Chloroplastic and nuclear diversity of endemic Prunus armeniaca L. species in the oasis agroecosystems. Genetica 2021; 149:239-251. [PMID: 34231081 DOI: 10.1007/s10709-021-00127-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/28/2021] [Indexed: 11/26/2022]
Abstract
Tunisia is characterized by the presence of specific seed-propagated apricot (Prunus armeniaca L.) material which is found in the oasis agroecosystems. In order to highlight the genetic diversity, population structure, and demographic history of this germplasm, 33 apricot accessions collected from six different oasis regions in southwestern Tunisia were genotyped using 24 microsatellite markers. A total number of 111 alleles was detected with an average of 4.62 alleles per locus. Bayesian model-based clustering analysis indicated four subdivisions within the collection sampled that corresponded mainly to the geographic origin of the material. The analysis of the 33 accessions using chloroplast markers allowed the identification of 32 haplotypes. Overall, the present study highlighted the high Tunisian apricot's diversity in the traditional oasis agroecosystems with low genetic differentiation. Understanding the structure of seed-propagated apricot collection is crucial for managing collections in regard to adaptive traits for Arid and Saharan climates as well as for identifying interesting genotypes that can be integrated into international coordinated actions of breeding programs.
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Affiliation(s)
- Hedia Bourguiba
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia.
| | - Mohamed-Amine Batnini
- Department of Plant Pathology, OARDC/OSU, 120 Selby, 1680 Madison Ave, Wooster, OH, 44691, USA
| | - Chahnez Naccache
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Biochimie et Biotechnology (LR01ES05), Tunis, Tunisia
| | - Nadia Zitouna
- LR16IPT05, Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Neila Trifi-Farah
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia
| | - Jean-Marc Audergon
- INRAe Centre PACA, UR 1052 GAFL, Domaine St Maurice, 67, allée des chênes, CS60094, 84143, Montfavet Cedex, France
| | - Lamia Krichen
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia
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Li WW, Liu LQ, Zhang QP, Zhou WQ, Fan GQ, Liao K. Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences. Sci Rep 2021; 11:13623. [PMID: 34211010 PMCID: PMC8249649 DOI: 10.1038/s41598-021-93050-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/15/2021] [Indexed: 11/18/2022] Open
Abstract
To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.
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Affiliation(s)
- Wen-Wen Li
- College of Horticulture and Forestry, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Li-Qiang Liu
- College of Horticulture and Forestry, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Qiu-Ping Zhang
- Xiongyue National Germplasm Resources Garden of the Liaoning Institute of Pomology, Xiongyue, Shenyang, China
| | - Wei-Quan Zhou
- College of Horticulture and Forestry, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Guo-Quan Fan
- Luntai National Fruit Germplasm Resources Garden of Xinjiang Academy of Agricultural Sciences, Luntai, Xinjiang, China
| | - Kang Liao
- College of Horticulture and Forestry, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Sánchez-Del Pino I, Alfaro A, Andueza-Noh RH, Mora-Olivo A, Chávez-Pesqueira M, Ibarra-Morales A, Moore MJ, Flores-Olvera H. High phylogeographic and genetic diversity of Tidestromia lanuginosa supports full-glacial refugia for arid-adapted plants in southern and central Coahuila, Mexico. AMERICAN JOURNAL OF BOTANY 2020; 107:1296-1308. [PMID: 33001458 DOI: 10.1002/ajb2.1536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Recent phylogeographic work suggests the existence of latitudinal gradients in genetic diversity in northern Mexican plants, but very few studies have examined plants of the Chihuahuan Desert. Tidestromia lanuginosa is a morphologically variable annual species whose distribution includes the Chihuahuan Desert Region. Here we undertook phylogeographic analyses of chloroplast loci in this species to test whether genetic diversity and differentiation of Mexican populations of T. lanuginosa change along a latitudinal gradient and whether diversity is higher in Coahuila, consistent with ideas of lower plant community turnover during the Pleistocene. METHODS Haplotype network, maximum likelihood tree, and Bayesian phylogenetic haplotype were reconstructed, and genetic diversity was assessed among 26 populations. Barrier analysis was used to explore barriers to gene flow. RESULTS Four major population groups were identified, corresponding with physiographic provinces in Mexico. Each population group displayed high levels of genetic structure, haplotype, and nucleotide diversity. Diversity was highest in southern populations across the species as a whole and among the Chihuahuan Desert populations. CONCLUSIONS Tidestromia lanuginosa provides an important example of high phylogeographic and genetic diversity in plants of northern Mexico. Barriers to gene flow among the major population groups have most likely been due to a combination of orographic, climatic, and edaphic variables. The high genetic diversity of T. lanuginosa in southern and central Coahuila is consistent with the hypothesis of full-glacial refugia for arid-adapted plants in this area, and highlights the importance of this region as a center of diversity for the Chihuahuan Desert flora.
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Affiliation(s)
- Ivonne Sánchez-Del Pino
- Centro de Investigación Científica de Yucatán, A.C. Calle 43 No 130 x 32 y 34, Col. Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97205, México
| | - Alejandra Alfaro
- Centro de Investigación Científica de Yucatán, A.C. Calle 43 No 130 x 32 y 34, Col. Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97205, México
| | - Rubén H Andueza-Noh
- CONACYT-Instituto Tecnológico de Conkal, Avenida Tecnológico s/n Conkal, Yucatán, Mérida, Yucatán, C.P. 97345, México
| | - Arturo Mora-Olivo
- Instituto de Ecología Aplicada, Universidad Autónoma de Tamaulipas, Ciudad Victoria, Tamaulipas, México
| | - Mariana Chávez-Pesqueira
- Centro de Investigación Científica de Yucatán, A.C. Calle 43 No 130 x 32 y 34, Col. Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97205, México
| | - Ariadna Ibarra-Morales
- Centro de Investigación Científica de Yucatán, A.C. Calle 43 No 130 x 32 y 34, Col. Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97205, México
| | | | - Hilda Flores-Olvera
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apdo. Postal 70-367, Ciudad de México, C.P. 04510, Mexico
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Zhang X, Liu YH, Wang YH, Shen SK. Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences. PLANTS (BASEL, SWITZERLAND) 2020; 9:E338. [PMID: 32156013 PMCID: PMC7154904 DOI: 10.3390/plants9030338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 01/05/2023]
Abstract
Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000-100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.
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Affiliation(s)
- Xue Zhang
- School of Life Sciences, Yunnan University, Kunming 650091, China
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming 650091, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming 650091, China
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Key Laboratory for Restoration and Reconstruction of Degraded Ecosystem in Northwest China of Ministry of Education, Ningxia University, Yinchuan 750021, China
| | - Yuan-Huan Liu
- School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yue-Hua Wang
- School of Life Sciences, Yunnan University, Kunming 650091, China
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming 650091, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming 650091, China
| | - Shi-Kang Shen
- School of Life Sciences, Yunnan University, Kunming 650091, China
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming 650091, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming 650091, China
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The complete chloroplast genome of Magnolia polytepala: Comparative analyses offer implication for genetics and phylogeny of Yulania. Gene 2020; 736:144410. [PMID: 32007581 DOI: 10.1016/j.gene.2020.144410] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 11/22/2022]
Abstract
Magnoliaceae is a primitive taxon in the angiosperms, comprising approximately 240 species in 2-17 genera. Many of them have been widely cultivated due to their horticultural and medicinal value. However, there are uncertainties and controversies about the delimitation of the genera except Liriodendron L. in this family. The Yulania taxa is also the focus of dispute at the genus and section levels. In this study, we compared ten Yulania plastomes, including the newly sequenced M. polytepala. The plastome-wide comparative analysis demonstrated that 1) Yulania cp genomes were highly conserved, and the majority differences existed in IR regions with the loss/retention of trnV-GAC or ycf15 gene, 2) mutational hotspots with high levels of nucleotide diversity (Pi > 0.02) existed in both coding (rpoA, and ycf1) and no-coding (ccsA-ndhD, ndhE-ndhG, ndhF-rpl32, petA-psbJ, rpl32-trnL, rps3-rps19, and trnH-psbA) regions among the genus Yulania. Combined with other data from Magnoliaceae plastomes, our reconstructed molecular phylogenetic tree revealed that Yulania is monophyletic, separated from the genus Magnolia L. (=Magnolia subg. Magnolia L.), but seems a sister of Michelia L. Moreover, M. polytepala which belongs to the genus Yulania is most closely related to M. liliiflora. All these results indicated that plastome data may contribute to investigating taxonomy, population genetics and phylogeny of Yulania.
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Xu X, Zhang J, Zheng W. The complete chloroplast genome of threatened Magnolia laevifolia, a rare ornamental shrub with strong aromatic flowers. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0819-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Genetic diversity of Spanish Prunus domestica L. germplasm reveals a complex genetic structure underlying. PLoS One 2018; 13:e0195591. [PMID: 29630655 PMCID: PMC5891032 DOI: 10.1371/journal.pone.0195591] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/25/2018] [Indexed: 12/17/2022] Open
Abstract
European plum (Prunus domestica L.) is an ancient domesticated species cultivated in temperate areas worldwide whose genetic structure has been scarcely analyzed to date. In this study, a broad representation of Spanish European plum germplasm collected in Northeastern Spain and a representative set of reference cultivars were compared using nuclear and chloroplast markers. The number of alleles per locus detected with the SSR markers ranged from 8 to 39, with an average of 23.4 alleles, and 8 haplotypes were identified. Bayesian model-based clustering, minimum spanning networks, and the analysis of molecular variance showed the existence of a hierarchical structure. At the first level, two genetic groups were found, one containing 'Reine Claude' type reference cultivars altogether with ca. 25% of local genotypes, and a second one much more diverse. This latter group split in two groups, one containing most (ca. 70%) local genotypes and some old Spanish and French reference cultivars, whereas the other included 24 reference cultivars and only six local genotypes. A third partition level allowed a significant finer delineation into five groups. As a whole, the genetic structure of European plum from Northeastern Spain was shown to be complex and conditioned by a geographical proximity factor. This study not only contributes to genetic conservation and breeding for this species at the national level, but also supports the relevance of undertaking similar tasks of collection and characterization in other unexplored areas. Moreover, this kind of research could lead to future coordinated actions for the examination of the whole European plum diversity, to define conservation strategies, and could be used to better understand the genetic control of traits of horticultural interest through association mapping.
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