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Bassouya M, Chedadi M, Zahra JF, Kara M, Assouguem A, Ullah R, Ibrahim MA, Bari A, Fidan H, Soufyane L, Alami A, Bari A. A comparative analysis of dendrometric, macromorphological, and micromorphological characteristics of Pistacia atlantica subsp. atlantica and Pistacia terebinthus in the middle Atlas region of Morocco. Open Life Sci 2024; 19:20220941. [PMID: 39310810 PMCID: PMC11416073 DOI: 10.1515/biol-2022-0941] [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: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 09/25/2024] Open
Abstract
The genus Pistacia, with its species having notable ecological, economic, and medicinal implications, demonstrates remarkable environmental adaptability. The central objective of the study is to analyze interspecific variations between Pistacia atlantica subsp. atlantica and Pistacia terebinthus across three distinct bioclimatic zones in the Middle Atlas region of Morocco. The methodology includes collecting dendrometric measurements and conducting macromorphological examinations on these two taxa, with a detailed analysis of 27 qualitative and quantitative variables. A micro-morphological analysis of leaves, using scanning electron microscopy (SEM), is employed to explore specific features such as size and stomatal density, as well as qualitative aspects like epidermal cell shape and trichomes. Dendrometric measurements have revealed that the canopy surface and the number of trunks per tree can serve as distinctive features between the two species. Regarding the sex ratio of Pistacia atlantica subsp. atlantica, 59% of the examined trees are males, primarily associated with the jujube tree in arid zones and the dwarf palm in humid areas. In contrast, female Pistacia terebinthus exhibit a similar percentage, predominantly associated with oak groves and cade juniper in their distribution areas. Principal component analysis of biometric measurements emphasized a significant disparity between the two species, representing 60.25% of the total variance. The use of SEM unveiled new features facilitating the identification of the two species. By leveraging the macromorphological and micromorphological variability of pistachio trees, we can qualify those best suited to diverse bioclimates. In this regard, we suggest incorporating them into reforestation and rehabilitation programs aimed at restoring our declining ecosystems.
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Affiliation(s)
- Mohammed Bassouya
- Laboratory of Biotechnology, Environment Agrifood and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohamed Chedadi
- Laboratory of Biotechnology, Environment Agrifood and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Jawhari Fatima Zahra
- Laboratory of Biotechnology, Environment Agrifood and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Kara
- Laboratory of Biotechnology, Conservation and Valorisation of Naturals Resources (LBCVNR), Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, B.P. 1796 Atlas, Fez, 30000, Morocco
| | - Amine Assouguem
- National School of Agriculture of Meknes, Department of Plant Protection and Environment, Meknes, Morocco
- Laboratory of Functional Ecology and Environment, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, Imouzzer Street, P.O. Box 2202, Fez, Morocco
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohamed A. Ibrahim
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Hafize Fidan
- Department of Tourism and Culinary Management, Faculty of Economics, University of Food Technologies, 4000, Plovdiv, Bulgaria
| | - Lafraxo Soufyane
- Laboratory of Biotechnology, Environment Agrifood and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Abdellatif Alami
- Laboratory of Applied Organic Chemistry, Faculty of Sciences and Technology of Fez, Sidi Mohamed Ben Abdellah University, Route d’Immouzer, Fez, Morocco
| | - Amina Bari
- Laboratory of Biotechnology, Environment Agrifood and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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Kafkas S, Ma X, Zhang X, Topçu H, Navajas-Pérez R, Wai CM, Tang H, Xu X, Khodaeiaminjan M, Güney M, Paizila A, Karcı H, Zhang X, Lin J, Lin H, Herrán RDL, Rejón CR, García-Zea JA, Robles F, Muñoz CDV, Hotz-Wagenblatt A, Min XJ, Özkan H, Motalebipour EZ, Gozel H, Çoban N, Kafkas NE, Kilian A, Huang H, Lv X, Liu K, Hu Q, Jacygrad E, Palmer W, Michelmore R, Ming R. Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution. PLANT COMMUNICATIONS 2023; 4:100497. [PMID: 36435969 DOI: 10.1016/j.xplc.2022.100497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 10/01/2022] [Accepted: 11/23/2022] [Indexed: 05/11/2023]
Abstract
Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.
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Affiliation(s)
- Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hayat Topçu
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Haibao Tang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuming Xu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Mortaza Khodaeiaminjan
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Murat Güney
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Aibibula Paizila
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Harun Karcı
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Xiaodan Zhang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jing Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Han Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Carmelo Ruiz Rejón
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | | | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Coral Del Val Muñoz
- Department of Computer Science, University of Granada, Granada, Spain; Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), 18014 Granada, Spain
| | - Agnes Hotz-Wagenblatt
- German Cancer Research Center, Omics IT and Data Management Core Facility, Heidelberg, Germany
| | - Xiangjia Jack Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | | | - Hatice Gozel
- Pistachio Research Institute, Şahinbey, Gaziantep 27060, Turkey
| | - Nergiz Çoban
- Pistachio Research Institute, Şahinbey, Gaziantep 27060, Turkey
| | - Nesibe Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Andrej Kilian
- Diversity Arrays Technology, University of Canberra, Canberra, ACT, Australia
| | - HuaXing Huang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuanrui Lv
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kunpeng Liu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qilin Hu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ewelina Jacygrad
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - William Palmer
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Richard Michelmore
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Nezami E, Gallego PP. History, Phylogeny, Biodiversity, and New Computer-Based Tools for Efficient Micropropagation and Conservation of Pistachio ( Pistacia spp.) Germplasm. PLANTS (BASEL, SWITZERLAND) 2023; 12:323. [PMID: 36679036 PMCID: PMC9864209 DOI: 10.3390/plants12020323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The word "pstk" [pistag], used in the ancient Persian language, is the linguistic root from which the current name "pistachio", used worldwide, derives. The word pistachio is generally used to designate the plants and fruits of a single species: Pistacia vera L. Both the plant and its fruits have been used by mankind for thousands of years, specifically the consumption of its fruits by Neanderthals has been dated to about 300,000 years ago. Native to southern Central Asia (including northern Afghanistan and northeastern Iran), its domestication and cultivation occurred about 3000 years ago in this region, spreading to the rest of the Mediterranean basin during the Middle Ages and finally being exported to America and Australia at the end of the 19th century. The edible pistachio is an excellent source of unsaturated fatty acids, carbohydrates, proteins, dietary fiber, vitamins, minerals and bioactive phenolic compounds that help promote human health through their antioxidant capacity and biological activities. The distribution and genetic diversity of wild and domesticated pistachios have been declining due to increasing population pressure and climatic changes, which have destroyed natural pistachio habitats, and the monoculture of selected cultivars. As a result, the current world pistachio industry relies mainly on a very small number of commercial cultivars and rootstocks. In this review we discuss and summarize the current status of: etymology, origin, domestication, taxonomy and phylogeny by molecular analysis (RAPID, RFLP, AFLP, SSR, ISSR, IRAP, eSSR), main characteristics and world production, germplasm biodiversity, main cultivars and rootstocks, current conservation strategies of both conventional propagation (seeds, cutting, and grafting), and non-conventional propagation methods (cryopreservation, slow growth storage, synthetic seed techniques and micropropagation) and the application of computational tools (Design of Experiments (DoE) and Machine Learning: Artificial Neural Networks, Fuzzy logic and Genetic Algorithms) to design efficient micropropagation protocols for the genus Pistacia.
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Affiliation(s)
- Esmaeil Nezami
- Department of Plant Breeding, Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj P.O. Box 31485-498, Iran
| | - Pedro P. Gallego
- Department of Plant Biology and Soil Science, Faculty of Biology, University of Vigo, 36310 Vigo, Spain
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Han B, Zhang MJ, Xian Y, Xu H, Cui CC, Liu D, Wang L, Li DZ, Li WQ, Xie XM. Variations in genetic diversity in cultivated Pistacia chinensis. FRONTIERS IN PLANT SCIENCE 2022; 13:1030647. [PMID: 36438104 PMCID: PMC9691265 DOI: 10.3389/fpls.2022.1030647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.
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Affiliation(s)
- Biao Han
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Ming-Jia Zhang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yang Xian
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Hui Xu
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Cheng-Cheng Cui
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Dan Liu
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Lei Wang
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen-Qing Li
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Xiao-Man Xie
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
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Tajabadi A, Esmailizadeh A. Whole genome resequencing data sets of different species from Pistacia genus. BMC Res Notes 2021; 14:290. [PMID: 34315525 PMCID: PMC8314588 DOI: 10.1186/s13104-021-05702-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/18/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Pistacia genus belongs to the flowering plants in the cashew family and contains at least 11 species. The whole-genome resequencing data of different species from Pistacia genus are described herein. The data reported here will be useful for better understand the adaptive evolution, demographic history, genetic diversity, population structure, and domestication of pistachio. DATA DESCRIPTION Genomic DNA was isolated from fresh leaves and used to construct libraries with insert size of 350 bp. Sequence libraries were made and sequenced on the Illumina Hiseq 4000 platform to produce 150 bp paired-end reads. A total number of 4,851,118,730 billion reads (ranging from 33,305,900 to 34,990,618 reads per sample) were created across all samples. We produced a total of 727.67 Gbp data which have been deposited in the Genome Sequence Archive (GSA) database with the Accession of CRA000978. All of the data are also available as the sequence read archive (SRA) format in the National Center for Biotechnology Information (NCBI) with identifier of SRP189222, mirroring our deposited data in GSA.
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Affiliation(s)
- Ali Tajabadi
- Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
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Benmahieddine A, Belyagoubi-Benhammou N, Belyagoubi L, El Zerey-Belaskri A, Gismondi A, Di Marco G, Canini A, Bechlaghem N, Atik Bekkara F, Djebli N. Influence of plant and environment parameters on phytochemical composition and biological properties of Pistacia atlantica Desf. BIOCHEM SYST ECOL 2021. [DOI: 10.1016/j.bse.2021.104231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Karcι H, Paizila A, Topçu H, Ilikçioğlu E, Kafkas S. Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. Front Genet 2020; 11:1021. [PMID: 33033493 PMCID: PMC7509152 DOI: 10.3389/fgene.2020.01021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/10/2020] [Indexed: 01/28/2023] Open
Abstract
In this study, we aimed to develop novel genic simple sequence repeat (eSSR) markers and to study phylogenetic relationship among Pistacia species. Transcriptome sequencing was performed in different tissues of Siirt and Atl cultivars of pistachio (Pistacia vera). A total of 37.5-Gb data were used in the assembly. The number of total contigs and unigenes was calculated as 98,831, and the length of N50 was 1,333 bp after assembly. A total of 14,308 dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide SSR motifs (4–17) were detected, and the most abundant SSR repeat types were trinucleotide (29.54%), dinucleotide (24.06%), hexanucleotide (20.67%), pentanucleotide (18.88%), and tetranucleotide (6.85%), respectively. Overall 250 primer pairs were designed randomly and tested in eight Pistacia species for amplification. Of them, 233 were generated polymerase chain reaction products in at least one of the Pistacia species. A total of 55 primer pairs that had amplifications in all tested Pistacia species were used to characterize 11 P. vera cultivars and 78 wild Pistacia genotypes belonging to nine Pistacia species (P. khinjuk, P. eurycarpa, P. atlantica, P. mutica, P. integerrima, P. chinensis, P. terebinthus, P. palaestina, and P. lentiscus). A total of 434 alleles were generated from 55 polymorphic eSSR loci with an average of 7.89 alleles per locus. The mean number of effective allele was 3.40 per locus. Polymorphism information content was 0.61, whereas observed (Ho) and expected heterozygosity (He) values were 0.39 and 0.65, respectively. UPGMA (unweighted pair-group method with arithmetic averages) and STRUCTURE analysis divided 89 Pistacia genotypes into seven populations. The closest species to P. vera was P. khinjuk. P. eurycarpa was closer P. atlantica than P. khinjuk. P. atlantica–P. mutica and P. terebinthus–P. palaestina pairs of species were not clearly separated from each other, and they were suggested as the same species. The present study demonstrated that eSSR markers can be used in the characterization and phylogenetic analysis of Pistacia species and cultivars, as well as genetic linkage mapping and QTL (quantitative trait locus) analysis.
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Affiliation(s)
- Harun Karcι
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Aibibula Paizila
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Hayat Topçu
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | | | - Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
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Depa Ł, Kaszyca‐Taszakowska N, Taszakowski A, Kanturski M. Ant‐induced evolutionary patterns in aphids. Biol Rev Camb Philos Soc 2020; 95:1574-1589. [DOI: 10.1111/brv.12629] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 01/02/2023]
Affiliation(s)
- Łukasz Depa
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences University of Silesia in Katowice Bankowa 9 40‐007 Katowice Poland
| | - Natalia Kaszyca‐Taszakowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences University of Silesia in Katowice Bankowa 9 40‐007 Katowice Poland
| | - Artur Taszakowski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences University of Silesia in Katowice Bankowa 9 40‐007 Katowice Poland
| | - Mariusz Kanturski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences University of Silesia in Katowice Bankowa 9 40‐007 Katowice Poland
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Qualitative and quantitative analyses of phenolic compounds by HPLC–DAD–ESI/MS in Tunisian Pistacia vera L. Leaves unveiled a rich source of phenolic compounds with a significant antioxidant potential. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2019. [DOI: 10.1007/s11694-019-00165-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Zeng L, Tu XL, Dai H, Han FM, Lu BS, Wang MS, Nanaei HA, Tajabadipour A, Mansouri M, Li XL, Ji LL, Irwin DM, Zhou H, Liu M, Zheng HK, Esmailizadeh A, Wu DD. Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Genome Biol 2019; 20:79. [PMID: 30999938 PMCID: PMC6474056 DOI: 10.1186/s13059-019-1686-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 04/01/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses. RESULTS Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild P. vera genomes and 35 closely related wild Pistacia genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild Pistacia species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection. CONCLUSIONS Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The Pistacia genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops.
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Affiliation(s)
- Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xiao-Long Tu
- Allwegene Technologies Inc., Beijing, 102209, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | | | - Bing-She Lu
- College of Landscape Architecture and Tourism, Agricultural University of Hebei, Baoding, 071000, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Ali Tajabadipour
- Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Xiao-Long Li
- Biomarker Technologies Corporation, Beijing, China
| | - Li-Li Ji
- Allwegene Technologies Inc., Beijing, 102209, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Hong Zhou
- Chinese Academy of Forestry Sciences, Beijing, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | | | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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11
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Mannino G, Gentile C, Maffei ME. Chemical partitioning and DNA fingerprinting of some pistachio (Pistacia vera L.) varieties of different geographical origin. PHYTOCHEMISTRY 2019; 160:40-47. [PMID: 30690343 DOI: 10.1016/j.phytochem.2019.01.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 05/20/2023]
Abstract
The genus Pistacia (Anacardiaceae family) is represented by several species, of which only P. vera L. produces edible seeds (pistachio). Despite the different flavor and taste, a correct identification of pistachio varieties based on the sole phenotypic character is sometimes hard to achieve. Here we used a combination of chemical partitioning and molecular fingerprinting for the unequivocal identification of commercial pistachio seed varieties (Bronte, Kern, Kerman, Larnaka, Mateur and Mawardi) of different geographical origin. The total phenolic content was higher in the variety Bronte followed by Larnaka and Mawardi cultivars. The total anthocyanin content was higher in Bronte and Larnaka varieties, whereas the total proanthocyanidin content was higher in Bronte, followed by Mawardi and Larnaka varieties. HPLC-DAD-ESI-MS/MS analyses revealed significant (P < 0.05) higher amounts of cyanidin-3-glucoside, idein, eryodictol-7-galactoside, quercetin-3-glucoside, luteolin-glucoside and marein in the variety Bronte, whereas higher amounts of peonidin-3-glucoside, okanin 4'-galactoside, hyperoside and quercetin-4'-glucoside were found in the variety Larnaka. The highest content of catechin was found in the Mawardi variety. A significantly (P < 0.05) higher total amount of fatty acids was found in the varieties Mateur, Kern and Bronte, followed by the varieties Larnaka and Mawardi, whereas the variety Kerman showed the lowest total fatty acid content. GC-FID and GC-MS analyses revealed the presence of several polyunsaturated fatty acids. Kern and Mateur varieties showed a significantly (P < 0.05) higher amount of linoleic acid, whereas the variety Bronte showed the highest amount of oleic acid. Molecular fingerprinting was achieved by ITS DNA PCR-RFLP analysis. Three different restriction enzymes (RsaI, TaqαI and PstI) were used to selectively cleave the resulting amplicons. A TaqαI site could be selectively found in the varieties Kerman, Larnaka and Mateur, whereas the digestion of the PCR products by RsaI gave specific patters exclusively on Bronte and Mawardi. Digestion by PstI gave specific patters exclusively on the Kern variety. The results showed that the Mediterranean varieties (Mateur, Bronte and Larnaka) show similar chemical patterns and (particularly for Mateur and Larnaka) a close phylogenetic relationship, allowing a chemical and molecular partitioning with respect to the other varieties.
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Affiliation(s)
- Giuseppe Mannino
- Plant Physiology Unit, Dept. Life Sciences and Systems Biology. University of Turin, Via Quarello 15/a, 10135, Turin, Italy
| | - Carla Gentile
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Massimo E Maffei
- Plant Physiology Unit, Dept. Life Sciences and Systems Biology. University of Turin, Via Quarello 15/a, 10135, Turin, Italy.
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12
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Khadivi A, Esmaeili A, Mardani N. Genetic diversity of cultivated pistachio as revealed by microsatellite molecular markers. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1442745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Ali Khadivi
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - Akbar Esmaeili
- Department of Horticultural Crops Research, Agriculture Ministry, Ilam, Iran
| | - Neda Mardani
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
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13
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Patel S, Rauf A, Khan H. The relevance of folkloric usage of plant galls as medicines: Finding the scientific rationale. Biomed Pharmacother 2018; 97:240-247. [PMID: 29091872 DOI: 10.1016/j.biopha.2017.10.111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 10/18/2022] Open
Abstract
Galls, the abnormal growths in plants, induced by virus, bacteria, fungi, nematodes, arthropods, or even other plants, are akin to cancers in fauna. The galls which occur in a myriad of forms are phytochemically-distinct from the normal plant tissues, for these are the sites of tug-of-war, just like the granuloma in animals. To counter the stressors, in the form of the effector proteins of the invaders, the host plants elaborate a large repertoire of metabolites, which they normally will not produce. Perturbation of the jasmonic acid pathway, and the overexpression of auxin, and cytokinin, promote the tissue proliferation and the resultant galls. Though the plant family characteristics and the attackers determine the gall biochemistry, most of the galls are rich in bioactive phytochemicals such as phenolic acids, anthocyanins, purpurogallin, flavonoids, tannins, steroids, triterpenes, alkaloids, lipophilic components (tanshinone) etc. Throughout the long trajectory of evolution, humans have learned to use the galls as therapeutics, much like other plant parts. In diverse cultures, the evidence of folkloric usage of galls abound. Among others, galls from the plant genus like Rhus, Pistacia, Quercus, Terminalia etc. are popular as ethnomedicine. This review mines the literature on galling agents, and the medicinal relevance of galls.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, 92182, USA.
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, 23561, K.P.K, Pakistan
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan, 23200, Pakistan
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14
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Rauf A, Patel S, Uddin G, Siddiqui BS, Ahmad B, Muhammad N, Mabkhot YN, Hadda TB. Phytochemical, ethnomedicinal uses and pharmacological profile of genus Pistacia. Biomed Pharmacother 2017; 86:393-404. [PMID: 28012394 DOI: 10.1016/j.biopha.2016.12.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/02/2016] [Accepted: 12/07/2016] [Indexed: 12/19/2022] Open
Abstract
Pistacia genus belong to family Anacardiaceae and it is versatile in that its member species have food (P. vera), medicinal (P. lentiscus) and ornamental (P. chinensis) values. Various species of this genus have folkloric uses with credible mention in diverse pharmacopeia. As a trove of phenolic compounds, terpenoids, monoterpenes, flavonoids, alkaloids, saponins, fatty acids, and sterols, this genus has garnered pharmaceutical attention in recent times. With adequate clinical studies, this genus might be exploited for therapy of a multitude of inflammatory diseases, as promised by preliminary studies. In this regard, the ethnomedicinal, phytochemistry, biological potencies, risks, and scopes of Pistacia genus have been reviewed here.
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Affiliation(s)
- Abdur Rauf
- Department of chemistry, University of Swabi Anbar-23430, Khyber Pakhtunkhwa, Pakistan.
| | - Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego-92182, USA.
| | - Ghias Uddin
- Institute of Chemical Sciences, University of Peshawar, Peshawar-25120, Pakistan
| | - Bina S Siddiqui
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Bashir Ahmad
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar-KPK-25120, KPK, Pakistan
| | - Naveed Muhammad
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan-23200, Pakistan
| | - Yahia N Mabkhot
- Department of Chemistry, Faculty of Science, King Saud University, Riyadh-11451, Saudi Arabia
| | - Taibi Ben Hadda
- Laboratoire Chimie Matériaux, FSO, Université Mohammed Ier, Oujda-60000, Morocco
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15
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Ziya Motalebipour E, Kafkas S, Khodaeiaminjan M, Çoban N, Gözel H. Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species. BMC Genomics 2016; 17:998. [PMID: 27923352 PMCID: PMC5142174 DOI: 10.1186/s12864-016-3359-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species. RESULTS To explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. CONCLUSIONS The results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.
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Affiliation(s)
- Elmira Ziya Motalebipour
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, 01330, Adana, Turkey
| | - Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, 01330, Adana, Turkey.
| | - Mortaza Khodaeiaminjan
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, 01330, Adana, Turkey
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Talebi M, Akbari M, Zamani M, Sayed-Tabatabaei BE. Molecular polymorphism in Pistacia vera L. using non-coding regions of chloroplast DNA. J Genet Eng Biotechnol 2016; 14:31-37. [PMID: 30647594 PMCID: PMC6299891 DOI: 10.1016/j.jgeb.2016.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/23/2016] [Accepted: 04/21/2016] [Indexed: 10/31/2022]
Abstract
The present study describes plastid DNA polymorphism and reports a comparative analysis of two non-coding cpDNA regions (trnC-trnD and atpB-rbcL) in pistachio. Seventeen different genotypes of domestic and wild pistachio from Iran, Syria, Turkey and America were sampled. Total genomic DNA was extracted and amplified with trnC-trnD and atpB-rbcL specific primers and then were sequenced. Phylogenetic relationships and depiction of phylogenetic trees were conducted. Cultivated genotypes of Pistacia vera were classified in a group regardless of their geographic location. P. vera was isolated from Sarakhs but they placed in the two close groups. Among cultivated genotypes, Jalab was separated from other cultivated genotypes. Pistacia Khinjuk was classified with Pistacia atlantica subsp. mutica. The findings confirm the common splitting hypothesis for commercial pistachio genotypes of the P. vera wild-type and also indicated the direct impact of Iranian genotypes in the evolutionary process of cultivated pistachios in other parts of the world. In conclusion it can be inferred that cultivated varieties of pistachio and P. vera var. sarakhs have the same origin, moreover genomic chloroplast could appropriately identify the interspecies relationships of pistachios.
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Affiliation(s)
- Majid Talebi
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Mohammad Akbari
- Department of Horticultural Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Maryam Zamani
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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17
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Molecular Evaluation of Genetic Diversity in Wild-Type Mastic Tree (Pistacia lentiscus L.). Biochem Genet 2016; 54:619-35. [DOI: 10.1007/s10528-016-9742-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
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18
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Aliakbarkhani ST, Akbari M, Hassankhah A, Talaie A, Moghadam MF. Phenotypic and genotypic variation in Iranian Pistachios. J Genet Eng Biotechnol 2015; 13:235-241. [PMID: 30647589 PMCID: PMC6299885 DOI: 10.1016/j.jgeb.2015.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/06/2015] [Accepted: 05/24/2015] [Indexed: 11/19/2022]
Abstract
As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD) markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z) regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp) of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.
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Affiliation(s)
| | - Mohammad Akbari
- Department of Horticultural Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Amin Hassankhah
- Department of Horticulture, College of Abouraihan, University of Tehran, Tehran, Iran
| | - Alireza Talaie
- Department of Horticultural Sciences, Faculty of Agriculture, University of Tehran, Karaj, Iran
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Xie L, Yang ZY, Wen J, Li DZ, Yi TS. Biogeographic history of Pistacia (Anacardiaceae), emphasizing the evolution of the Madrean-Tethyan and the eastern Asian-Tethyan disjunctions. Mol Phylogenet Evol 2014; 77:136-46. [PMID: 24747126 DOI: 10.1016/j.ympev.2014.04.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 03/27/2014] [Accepted: 04/03/2014] [Indexed: 11/19/2022]
Abstract
Pistacia L. exhibits a disjunct distribution in Mediterranean Eurasia and adjacent North Africa, eastern Asia, and North to Central America. The spatio-temporal diversification history of Pistacia was assessed to test hypotheses on the Madrean-Tethyan and the Eurasian Tethyan disjunctions through phylogenetic and biogeographic analyses. Maximum parsimony and Bayesian methods were employed to analyze sequences of multiple nuclear and plastid loci of Pistacia species. Bayesian dating analysis was conducted to estimate the divergence times of clades. The likelihood method LAGRANGE was used to infer ancestral areas. The New World species of Pistacia formed a clade sister to the Old World clade in all phylogenetic analyses. The eastern Asian Pistacia weinmannifolia-P. cucphuongensis clade was sister to a clade of the remaining Old World species, which were further resolved into three subclades. Pistacia was estimated to have originated at 37.60 mya (with 95% highest posterior density interval (HPD): 25.42-48.51 mya). A vicariance event in the early Miocene (19.79 mya with 95% HPD: 10.88-30.36 mya) was inferred to account for the intercontinental disjunction between the New World and the Old World species, which is consistent with the Madrean-Tethyan hypothesis. The two Old World eastern Asian-Tethyan disjunctions are best explained by one vicariance event in the early Miocene (15.87 mya with 95% HPD: 8.36-24.36 mya) and one dispersal event in late Miocene (5.89 mya with 95% HPD: 2.68-9.16 mya). The diversification of the Old World Pistacia species was significantly affected by extensive geological and climatic changes in the Qinghai-Tibetan plateau (QTP) and in the Mediterranean region.
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Affiliation(s)
- Lei Xie
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, PR China; College of Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Zhi-Yun Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, PR China
| | - Jun Wen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, PR China; Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, PR China
| | - Ting-Shuang Yi
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, PR China.
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20
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Traditional Uses of Pistacia lentiscus in Veterinary and Human Medicine. MEDICINAL AND AROMATIC PLANTS OF THE WORLD 2014. [DOI: 10.1007/978-94-017-9276-9_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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21
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Crous PW, Quaedvlieg W, Sarpkaya K, Can C, Erkılıç A. Septoria-like pathogens causing leaf and fruit spot of pistachio. IMA Fungus 2013; 4:187-99. [PMID: 24563831 PMCID: PMC3905937 DOI: 10.5598/imafungus.2013.04.02.04] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/15/2013] [Indexed: 11/10/2022] Open
Abstract
Several species of Septoria are associated with leaf and fruit spot of pistachio (Pistacia vera), though their identity has always been confused, making identification problematic. The present study elucidates the taxonomy of the Septoria spp. associated with pistachio, and distinguishes four species associated with this host genus. Partial nucleotide sequence data for five gene loci, ITS, LSU, EF-1α, RPB2 and Btub were generated for a subset of isolates. Cylindroseptoria pistaciae, which is associated with leaf spots of Pistacia lentiscus in Spain, is characterised by pycnidial conidiomata that give rise to cylindrical, aseptate conidia. Two species of Septoria s. str. are also recognised on pistachio, S. pistaciarum, and S. pistaciae. The latter is part of the S. protearum species complex, and appears to be a wide host range pathogen occurring on hosts in several different plant families. Septoria pistacina, a major pathogen of pistachio in Turkey, is shown to belong to Pseudocercospora, and not Septoria as earlier suspected. Other than for its pycnidial conidiomata, it is a typical species of Pseudocercospora based on its smooth, pigmented conidiogenous cells and septate conidia. This phenomenon has also been observed in Pallidocercospora, and seriously questions the value of conidiomatal structure at generic level, which has traditionally been used to separate hyphomycetous from coelomycetous ascomycetes. Other than DNA barcodes to facilitate the molecular identification of these taxa occurring on pistachio, a key is also provided to distinguish species based on morphology.
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Affiliation(s)
- Pedro W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - William Quaedvlieg
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Kamil Sarpkaya
- Pistachio Research Station, Üniversite Bulvari 27060 Şahinbey/Gaziantep, Turkey
| | - Canan Can
- Gaziantep University, Faculty of Art and Science, Department of Biology, Gaziantep, Turkey
| | - Ali Erkılıç
- Cukurova University, Faculty of Agriculture, Department of Plant Protection, Adana, Turkey
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22
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Talebi M, Kazemi M, Sayed-Tabatabaei BE. Molecular diversity and phylogenetic relationships of Pistacia vera, Pistacia atlantica subsp. mutica and Pistacia khinjuk using SRAP markers. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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AL-Saghir MG, Porter DM. Taxonomic Revision of the Genus <i>Pistacia</i> L. (Anacardiaceae). ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ajps.2012.31002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Al-Saghir MG. Perspective on Chromosome Numbers in the Genus Pistacia L. (Anacardiaceae). ACTA ACUST UNITED AC 2010. [DOI: 10.3923/ijpbg.2010.153.157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Ozden-Tokatli Y, Akdemir H, Tilkat E, Onay A. Current status and conservation of Pistacia germplasm. Biotechnol Adv 2010; 28:130-41. [DOI: 10.1016/j.biotechadv.2009.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 10/26/2009] [Accepted: 10/29/2009] [Indexed: 10/20/2022]
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26
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AL-Saghir MG. Phylogenetic Analysis of the Genus Pistacia L. (Anacardiaceae) Based
on Morphological Data. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/ajps.2010.28.35] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Affiliation(s)
- Emine Ayaz
- a Faculty of Science and Art, Department of Biology , The University of Dicle , Diyarbakir, Turkey
| | - Süreyya Namli
- a Faculty of Science and Art, Department of Biology , The University of Dicle , Diyarbakir, Turkey
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28
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Benhassaini H, Bendeddouche FZ, Mehdadi Z, Romane A. GC/MS Analysis of the Essential Oil from the Oleoresin of Pistacia Atlantica Desf. subsp. Atlantica from Algeria. Nat Prod Commun 2008. [DOI: 10.1177/1934578x0800300621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The oleoresin of Pistacia atlantica Desf. ssp. atlantica, growing wild in different arid and semi-arid regions of Algeria, is a popular naturally-occurring chewing gum and has been used traditionally in the treatment of peptic ulcer. GC/MS analysis of the essential oil obtained from solvent distillation of the fresh oleoresin has led to the identification of many terpenoids: α-pinene (39.4%), β-pinene (12.9%), carvacrol (11.8%), pinocarvone (5.5%), limonene (5.1%), germacrene-D (2.4%), trans-pinocarveol (2.1%), camphenol (2%), borneol (2%), α-terpene (1.8%), p-cymene (1.7%), terpinolene (1.4%), terpinene-4-ol (1.4%), isopinocarveol (1.1%) and verbenene (1.0%). Other minor constituents were also identified.
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Affiliation(s)
- Hachemi Benhassaini
- Department of Environmental Science, Faculty of Science, University of Sidi Bel-Abbès, BP 89 Hai Larbi BenMhidi, Algeria
| | - Fatima Z. Bendeddouche
- Department of Environmental Science, Faculty of Science, University of Sidi Bel-Abbès, BP 89 Hai Larbi BenMhidi, Algeria
| | - Zoheir Mehdadi
- Department of Environmental Science, Faculty of Science, University of Sidi Bel-Abbès, BP 89 Hai Larbi BenMhidi, Algeria
| | - Abderrahmane Romane
- Laboratoire de chimie organique appliqué, Faculté des sciences Semlalia, Université Cadi Ayyad, Marrakech, Morocco
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30
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Yi T, Wen J, Golan-Goldhirsh A, Parfitt DE. Phylogenetics and reticulate evolution in Pistacia (Anacardiaceae). AMERICAN JOURNAL OF BOTANY 2008; 95:241-251. [PMID: 21632348 DOI: 10.3732/ajb.95.2.241] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The systematic position and intrageneric relationships of the economically important Pistacia species (Anacardiaceae) are controversial. The phylogeny of Pistacia was assessed using five data sets: sequences of nuclear ribosomal ITS, the third intron of the nuclear nitrate reductase gene (NIA-i3), and the plastid ndhF, trnL-F and trnC-trnD. Significant discordance was detected among ITS, NIA-i3, and the combined plastid DNA data sets. ITS, NIA-i3, and the combined plastid data sets were analyzed separately using Bayesian and parsimony methods. Both the ITS and the NIA-i3 data sets resolved the relationships among Pistacia species well; however, these two data sets had significant discordance. The ITS phylogeny best reflects the evolutionary relationships among Pistacia species. Lineage sorting of the NIA-i3 alleles may explain the conflicts between the NIA-i3 and the ITS data sets. The combined analysis of three plastid DNA data sets resolved Pistacia species into three major clades, within which only a few subclades were supported. Pistacia was shown to be monophyletic in all three analyses. The previous intrageneric classification was largely inconsistent with the molecular data. Some Pistacia species appear not to be genealogical species, and evidence for reticulate evolution is presented. Pistacia saportae was shown to be a hybrid with P. lentiscus (maternal) and P. terebinthus (paternal) as the parental taxa.
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Affiliation(s)
- Tingshuang Yi
- Key Laboratory of Plant Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204 China
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31
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The chemical composition of fruits of Pistacia atlantica desf. subsp. atlantica from Algeria. Chem Nat Compd 2007. [DOI: 10.1007/s10600-007-0059-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Zhang T, . HL, . XZ, . XY, . DZ. Molecular Cloning and Sequence Analysis of Prion Protein Gene of Dezhou Donkey in China. ACTA ACUST UNITED AC 2005. [DOI: 10.3923/ajava.2006.23.32] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Wool D. Differential colonization of host trees by galling aphids: Selection of hosts or selection by hosts? Basic Appl Ecol 2005. [DOI: 10.1016/j.baae.2005.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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Stehlik I, Blattner FR, Holderegger R, Bachmann K. Nunatak survival of the high Alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages. Mol Ecol 2002; 11:2027-36. [PMID: 12296946 DOI: 10.1046/j.1365-294x.2002.01595.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) and sequence analysis of noncoding regions of chloroplast DNA were used to investigate 37 populations of Eritrichium nanum covering its total distribution area, the European Alps. There was no haplotypic variation within the populations, and most haplotypes were restricted to single sites or to neighbouring populations, suggesting low levels of long distance gene flow via seeds. The present geographical distribution of haplotypes probably reflects an ancient geographical pattern within two regions in the intensely glaciated western and eastern central Alps identified as genetic hotspot areas. These two regions contained seven of the total of 11 haplotypes, including many of the most derived ones. The divergent haplotypes formed closely related groups, which supported a separate evolution of these haplotypes in these two regions and, more importantly, gave strong evidence for the in situ survival of these populations on nunataks within the western and eastern central Alps during Pleistocene glaciation. This result is in concordance with a previous study on E. nanum using nuclear markers. Only one haplotype was common and widespread throughout the distributional range of E. nanum. At the same time, it was the evolutionarily basal-most and all other haplotypes were best described as its descendants. This haplotype is hypothesized to be genetically identical to a Tertiary Alpine colonizing ancestor, whose distribution was secondarily fragmented and infiltrated by derived haplotypes originating through local mutations.
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Affiliation(s)
- I Stehlik
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland.
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35
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Hershkovitz MA, Zimmer EA. Ribosomal DNA evidence and disjunctions of western American Portulacaceae. Mol Phylogenet Evol 2000; 15:419-39. [PMID: 10860651 DOI: 10.1006/mpev.1999.0720] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phylogenetic analysis of ribosomal DNA internal transcribed spacer sequences from 35 members of western American Portulacaceae plus seven Portulacaceae outgroups generally supports morphologically based interpretations of multiple intercontinental disjunctions. The data neither support nor refute monophyly of the western American group but strongly support a group comprising the western American taxa plus Phemeranthus, the only strictly American genus of the morphology-based eastern American/African group of Portulacaceae, along with the Australian genus Parakeelya. Support is strong for the monophyly of Calandrinia, Montiopsis, Lewisia, Claytonia, and Montia, along with a sister relationship of the last two. The data neither strongly support nor refute the morphologically based diagnosis of Cistanthe, but they strongly support a clade including the North American Cistanthe section Calyptridium and the South American Cistanthe sections Amarantoideae and Philippiamra. The internal transcribed spacer data fail to resolve the phylogenetic relationships among most of the western American lineages, suggesting either rapid radiation or, alternatively, erratic evolution of the internal transcribed spacer. The internal transcribed spacer and morphological evidence together suggest that in this group there have been 8-13 dispersal and colonization events across >2000 km (1 for every 15-26 extant species in this group). The internal transcribed spacer data document complex molecular evolutionary patterns, including strong substitution biases, among-site rate heterogeneity, positional bias for deamination-type substitutions, nonstationarity, and variable rates of insertion/deletion. Our phylogenetic conclusions, however, do not appear to be sensitive to these patterns.
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Affiliation(s)
- M A Hershkovitz
- Laboratory of Molecular Systematics, Smithsonian Institution, DC, Washington, 20560, USA
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36
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Yonemori K, Kanzaki S, Parfitt DE, Utsunomiya N, Subhadrabandhu S, Sugiura A. Phylogenetic relationship of Diospyros kaki (persimmon) to Diospyros spp. (Ebenaceae) of Thailand and four temperate zone Diospyros spp. from an analysis of RFLP variation in amplified cpDNA. Genome 1998. [DOI: 10.1139/g97-106] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The relationships among 17 Diospyros species from Thailand, with particular emphasis on the relationship of these species to temperate Diospyros species, including Diospyros kaki, were studied, using 81 cpDNA restriction site mutations detected in the 3.2- and 2.1-kb regions of amplified cpDNA and six different length mutations detected in the 2.1-kb region of amplified cpDNA. Parsimony and neighbor-joining analyses were conducted to identify relationships among species. Three temperate zone species, D. kaki, Diospyros lotus, and Diospyros virginiana, were monophyletic with one subtropical species, Diospyros ehretioides, suggesting a close evolutionary relationship among them. An immediate common progenitor for D. kaki and D. virginiana is suggested from cpDNA homology and the polyploidized karyotypes of both species. Our results did not support Ng's hypothesis that Diospyros glandulosa (synonym Diospyros roxburghii) is the progenitor of D. kaki. Two species, Diospyros rhodocalyx and Diospyros confertiflora, were so distant from the remaining species that additional study is needed to determine whether they should be placed in the same genus.Key words: cpDNA, Diospyros, PCR, phylogeny, persimmon, RFLP, taxonomy.
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