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Tang J, Fan X, Milne RI, Yang H, Tao W, Zhang X, Guo M, Li J, Mao K. Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen ( Populus rotundifolia) in the Hengduan Mountains. PLANT DIVERSITY 2024; 46:321-332. [PMID: 38798733 PMCID: PMC11119543 DOI: 10.1016/j.pld.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/31/2024] [Accepted: 03/31/2024] [Indexed: 05/29/2024]
Abstract
Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia, a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China. Demographic and migration hypotheses were tested using coalescent-based approaches. Limited historical gene flow was observed between the western and eastern groups of P. rotundifolia, but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line, manifesting in clear admixture and high genetic diversity in the central group. Wind-borne pollen and seeds may have facilitated the dispersal of P. rotundifolia following prevalent northwest winds in the spring. We also found that the Hengduan Mountains, where multiple genetic barriers were detected, acted on the whole as a barrier between the western and eastern groups of P. rotundifolia. Ecological niche modeling suggested that P. rotundifolia has undergone range expansion since the last glacial maximum, and demographic reconstruction indicated an earlier population expansion around 600 Ka. The phylogeographic pattern of P. rotundifolia reflects the interplay of biological traits, wind patterns, barriers, niche differentiation, and Quaternary climate history. This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.
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Affiliation(s)
- Jieshi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xiaoyan Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Wenjing Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xinran Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Mengyun Guo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
- School of Ecology and Environment, Tibet University, Lhasa 850000, PR China
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Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z. Phylogenomics reveal Populusgonggaensis as a hybrid between P.lasiocarpa and P.cathayana (Salicaceae). PHYTOKEYS 2024; 237:161-177. [PMID: 38298498 PMCID: PMC10829108 DOI: 10.3897/phytokeys.237.103012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 01/01/2024] [Indexed: 02/02/2024]
Abstract
High levels of intra-specific polymorphism and frequent hybridisation make it difficult to define species and correctly apply their scientific names. Populus L. is a challenging genus with plentiful natural and artificial hybrids. This study is a part of the project 'Flora of Pan-Himalaya' and aims to determine the taxonomic identity of P.gonggaensis N. Chao & J.R. He and to find out whether it is of hybrid origin. Whole-genome sequencing data were obtained from 57 samples. The SNP matrix was developed for phylogenetic reconstruction, ABBA-BABA statistics, PCA and ADMIXTURE analysis. The results indicate that P.gonggaensis is a spontaneous hybrid between P.lasiocarpa and P.cathayana. This study points out the importance of SNP data and comprehensive analyses for discovering the potential interspecific hybridisation and clarifies the usage of the name. In addition, the lectotype of P.gonggaensis was designated.
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Affiliation(s)
- Wenyan Du
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Yachao Wang
- School of Life Science, Fudan University, Shanghai 200433, ChinaFudan UniversityShanghaiChina
| | - Dajun Xie
- Sichuan Academy of Forestry, Chengdu 610000, ChinaSichuan Academy of ForestryChengduChina
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Yuran Bai
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Ce Shang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
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Li M, Song Z, Li Z, Qiao R, Zhang P, Ding C, Xie J, Chen Y, Guo H. Populus root exudates are associated with rhizosphere microbial communities and symbiotic patterns. Front Microbiol 2022; 13:1042944. [PMID: 36619999 PMCID: PMC9812961 DOI: 10.3389/fmicb.2022.1042944] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Microbial communities in the plant rhizosphere are critical for nutrient cycling and ecosystem stability. However, how root exudates and soil physicochemical characteristics affect microbial community composition in Populus rhizosphere is not well understood. Methods This study measured soil physiochemistry properties and root exudates in a representative forest consists of four Populus species. The composition of rhizosphere bacterial and fungal communities was determined by metabolomics and high-throughput sequencing. Results Luvangetin, salicylic acid, gentisic acid, oleuropein, strigol, chrysin, and linoleic acid were the differential root exudates extracted in the rhizosphere of four Populus species, which explained 48.40, 82.80, 48.73, and 59.64% of the variance for the dominant and key bacterial or fungal communities, respectively. Data showed that differential root exudates were the main drivers of the changes in the rhizosphere microbial communities. Nitrosospira, Microvirga, Trichoderma, Cortinarius, and Beauveria were the keystone taxa in the rhizosphere microbial communities, and are thus important for maintaining a stable Populus microbial rhizosphere. The differential root exudates had strong impact on key bacteria than dominant bacteria, key fungi, and dominant fungi. Moreover, strigol had positively effects with bacteria, whereas phenolic compounds and chrysin were negatively correlated with rhizosphere microorganisms. The assembly process of the community structure (keystone taxa and bacterial dominant taxa) was mostly determined by stochastic processes. Discussion This study showed the association of rhizosphere microorganisms (dominant and keystone taxa) with differential root exudates in the rhizosphere of Populus plants, and revealed the assembly process of the dominant and keystone taxa. It provides a theoretical basis for the identification and utilization of beneficial microorganisms in Populus rhizosphere.
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Affiliation(s)
- Mengjie Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhen Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanbiao Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongye Qiao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pingdong Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianbo Xie
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yinglong Chen
- UWA School of Agriculture and Environment, UWA Institute of Agriculture, Perth, WA, Australia
| | - Hui Guo
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China,National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing, China,*Correspondence: Hui Guo,
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Yang J, Feng L, Yue M, He YL, Zhao GF, Li ZH. Species delimitation and interspecific relationships of the endangered herb genus Notopterygium inferred from multilocus variations. Mol Phylogenet Evol 2019; 133:142-151. [PMID: 30639766 DOI: 10.1016/j.ympev.2019.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 01/29/2023]
Abstract
Species identification and discrimination is the basis of biodiversity research. In general, it is considered that numerous nucleotide variations (e.g., whole chloroplast genomes) can identify species with higher resolution than a few loci, e.g., partial chloroplast or nuclear gene fragments. In this study, we tested this hypothesis by sampling population genetics samples of the endangered herb genus Notopterygium. We sequenced the complete plastomes, five nuclear gene regions, three chloroplast DNA fragments, and a nuclear internal transcribed spacer (nrITS) region for 18 populations sampled throughout most of the geographic ranges of all six Notopterygium species. Species identification analysis showed that four DNA barcodes (matK, rbcL, trnS-trnG, and nrITS) and/or combinations of these markers achieved Notopterygium species discrimination at higher resolution than the general plastomes and nuclear gene sequences. In particular, nrITS had the highest discriminatory power among all of the individual markers. Molecular data sets and morphological evidence indicated that all six Notopterygium species could be reclassified unambiguously to four putative species clades. N. oviforme and N. franchetii had the closest relationship. Molecular dating showed that the origin and divergence of Notopterygium species was significantly associated with geological and climatic fluctuations during the middle of the Pliocene. In conclusion, our results suggest that a few nucleotide variations can achieve species discrimination with higher resolution than numerous plastomes and general nuclear gene fragments when discerning related Notopterygium species.
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Affiliation(s)
- Jiao Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan-Ling He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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Wang Y, Huang J, Wang Z, Xu S, Zhang Z. The complete chloroplast genome sequence of Populus pamirica Kom. (Salicaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1566792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yachao Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Huang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zizhao Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shenjian Xu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Nature Conservation, Beijing Forestry University, Beijing, China
- Museum of Beijing Forestry University, Beijing Forestry University, Beijing, China
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Zhou AP, Zong D, Gan PH, Zou XL, Zhang Y, Dan L, He CZ. Analyzing the phylogeny of poplars based on molecular data. PLoS One 2018; 13:e0206998. [PMID: 30412621 PMCID: PMC6226168 DOI: 10.1371/journal.pone.0206998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/23/2018] [Indexed: 01/22/2023] Open
Abstract
Methods for constructing trees using DNA sequences, known as molecular phylogenetics, have been applied to analyses of phylogenetic origin, evolutionary relatedness and taxonomic classification. Combining data sequenced in this study and downloaded from GenBank, we sampled 112 (chloroplast data) / 122 (ITS data) specimens belonging to 49 (chloroplast data) / 46 (ITS data) poplar species or hybrids from six (chloroplast data) / five sections (ITS data). Maximum parsimony and Bayesian inference were used to analyze phylogenetic relationships within the genus Populus based on eight chloroplast combinations and ITS regions. The results suggested that Bayesian inference might be more suitable for the phylogenetic reconstruction of Populus. All Populus species could be divided into two clades: clade 1, including subclades 1 and 2, and clade 2, including subclades 3 and 4. Species within clade 1, involving five sections except for Leuce, clustered coinciding with their two specific main geographical distribution areas: China (subclade 1) and North America (subclade 2). Clustering in subclade 3, section Leuce was confirmed to be of monophyletic origin and independent evolution. Its two subsections, namely Albidae and Trepidae, could be separated by chloroplast data but had frequent gene flow based on ITS data. Phylogeny analysis based on chloroplast data demonstrated once more that section Aigeiros was paraphyletic and further showed that the P. deltoides lineage is restricted in subclade 2 and that P. nigra lineage, located in subclade 3, originated from a hybrid of which an Albidae ancestor species was the material parent. Similarly, section Tacamahaca was found to be paraphyletic and had two lineages: a clade 1 lineage, such as P. cathayana, and a clade 2 lineage, such as P. simonii. Section Leucoides was paraphyletic and closely linked to section Tacamahaca. Their section boundaries were not conclusively delimitated by sequencing information.
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Affiliation(s)
- An-Pei Zhou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Pei-Hua Gan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Xin-Lian Zou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Yao Zhang
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Li Dan
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan, China
| | - Cheng-Zhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China
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Development of 5S rDNA-Based Molecular Markers for the Identification of Populus deltoides Bartr. ex Marshall, Populus nigra L., and Their Hybrids. FORESTS 2018. [DOI: 10.3390/f9100604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Populus L. is a tree genus that includes species with a high ability for interspecies hybridization. This process takes place in nature, and is used in poplar breeding. As а result, species identification in poplar populations and plantations is very difficult. In this study, a molecular marker system was developed for the identification of the most significant poplar species (P. nigra L. and P. deltoids Bartr. ex Marshall). The basis of the system is a polymorphism in non-transcribed spacers (NTSs) of 5S rDNA. The species-specific molecular markers were tested on a number of species and hybrids of poplars. It was shown that the marker system is a powerful tool for species identification, hybrid analysis, parent identification, and poplar breeding.
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Variation of Traits on Seeds and Germination Derived from the Hybridization between the Sections Tacamahaca and Aigeiros of the Genus Populus. FORESTS 2018. [DOI: 10.3390/f9090516] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Poplar is an important research organism, and species in sections Tacamahaca and Aigeiros, have advantages in terms of stress resistance, ease of propagation, and fast growth. Poplar species are widely distributed and well-adapted in the world, presenting a large potential for genetic improvement. Hybridization between different species allows us to generate offspring with a unique combinations of traits. This approach has a huge potential for breeding new poplar varieties that could aid in controlling desertification in the arid and semi-arid zones of the “Three-North” in China. In this study, we carried out a cross test scheme with nine female and thirteen male poplar trees. A total of 105,401 seeds were collected from 117 crosses. Flowering phenology and seed maturation differences of the hybrid progeny were monitored in greenhouses. For male trees, Populus deltoides had the longest flowering time. For female trees, Populus pseudo-simonii showed the longest seed maturity time. The number of carpals and ovules were not the same in different females. Meanwhile, three carpals were found in P. pseudo-simonii. A highly significant positive correlation was found between the seed size and the Thousand Kernel Weight, as well as the seedling cotyledon length. During seed germination, non-radicle and non-hypocotyl seedlings were observed. We also observed a number of cotyledon variants, including single and fused cotyledons, two cotyledons with one cotyledon cracking into two parts, three cotyledons, as well as four cotyledons. These results lay a favorable foundation for combining the research between the sections Tacamahaca and Aigeiros in future work.
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Borkhert EV, Krasnov GS, Bolsheva NL, Kezimana Р, Yurkevich OY, Muravenko OV, Kudryavtseva AV, Melnikova NV. Genetics polymorphism of poplars from Moscow region based on high-throughput sequencing of ITS. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Poplars are widely used in landscaping of Moscow due to the ability to effectively purify the air from harmful impurities and to release a large amount of oxygen. The genusPopulusis characterized by a high level of intraspecies polymorphism, as well as the presence of natural interspecies hybrids. The aim of our work was to evaluate the genetic diversity of poplars, which are growing on the territory of Moscow city by high-throughput sequencing of internal transcribed spacers of 45S rRNA genes (ITS sequences). Sequencing of ITS of 40 poplar plants was performed on Illumina platform (MiSeq) and about 3 000 reads were obtained for each sample in average. Bioinformatics analysis was performed using CLC Genomics Workbench tool. The involved set of poplars had a high level of genetic diversity – the number of single nucleotide polymorphisms (SNPs) detected in each genotype relative to the reference ITS1 and ITS2 sequences ofP. trichocarpavarying from 4 to 44. We showed that even trees which had been planted on the same territory and, probably, at the same time had significant genetic differences. It can be speculated that highly polymorphic plant material was used for planting poplars in Moscow. For some sites with SNPs, several variants of nucleotides were found in the same individual and the ratio of SNPs was different. We assume that close to 50/50 ratio is observed in interspecific hybrids due to genetic differences in the ITS sequences between maternal and paternal genotypes. For SNPs with a predominance of one of the variants, the presence of paralogues among numerous genomic copies of ITS sequences is more likely. The results of our work can provide a framework for molecular genetic markers application with the purpose ofPopulusspecies and interspecific hybrids identification, determination the origin of a number of natural hybrids, and monitoring the diversity of genusPopulusin the Moscow city.
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Zhang L, Wang M, Ma T, Liu J. Taxonomic status of Populuswulianensis and P.ningshanica (Salicaceae). PHYTOKEYS 2018:117-129. [PMID: 30275735 PMCID: PMC6160800 DOI: 10.3897/phytokeys.108.25600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/26/2018] [Indexed: 05/03/2023]
Abstract
Species delimitation in the genus Populus is particularly challenging due to high levels of intraspecific polymorphism as well as frequent interspecific hybridisation and introgression. In this study, we aimed to examine the taxonomic status of Populusningshanica and P.wulianensis using an integrative taxonomy that considers multiple operational criteria. We carried out morphometric analyses of leaf traits and genetic examinations (including sequence variations at five barcoding DNAs and polymorphisms at 14 nuclear microsatellite SSR primers) at the population level between them and two closely related species P.adenopoda and P.davidiana. Results suggest that P.wulianensis belongs to the polymorphic species, P.adenopoda and should be considered as a synonym of the latter. P.ningshanica may have arisen as a result on the hybridisation between P.adenopoda and P.davidiana and therefore should be treated as P.×ningshanica. This study highlights the importance of the integrated evidence in taxonomic decisions of the disputed species.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P. R. ChinaSichuan UniversityChengduChina
| | - Mingcheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P. R. ChinaSichuan UniversityChengduChina
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P. R. ChinaSichuan UniversityChengduChina
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P. R. ChinaSichuan UniversityChengduChina
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Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding. FORESTS 2017. [DOI: 10.3390/f8120492] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Within the genus Populus, about 30 species are classified into six sections, of which some are cross-compatible. Besides naturally occurring hybrids, huge breeding programs have led to a high number of artificially produced hybrids, for which the determination of genetically involved species by morphological characteristics is often difficult. This necessitates the use of molecular markers for the identification of both maternal as well as paternal species, and in the case of complex hybrids, the genealogy. For this reason, we developed new chloroplast and nuclear markers for the differentiation of up to 19 poplar species, with one to 32 individuals per species regularly used in breeding programs based on already known barcoding, other chloroplast regions, and nuclear genes of interest. We developed methods to identify species by either species-specific nucleotide variations or, when no initial information for the species was given, by using a set of markers either in a procedure of exclusion or in a multiplexed marker set. The developed markers can all be used with low-cost equipment, and some can additionally be applied using a genetic analyzer. We combined these markers in multiplexes for a very fast and easy-to-use application for the identification of poplar species and their hybrids.
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Yang J, Yue M, Niu C, Ma XF, Li ZH. Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium. Genes (Basel) 2017; 8:E124. [PMID: 28422071 PMCID: PMC5406871 DOI: 10.3390/genes8040124] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/01/2017] [Accepted: 04/05/2017] [Indexed: 12/14/2022] Open
Abstract
Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete chloroplast (cp) genomes of four Notopterygium species (N. incisum C. C. Ting ex H. T. Chang, N. oviforme R. H. Shan, N. franchetii H. de Boissieu and N. forrestii H. Wolff) were assembled and characterized using next-generation sequencing. We investigated the gene organization, order, size and repeat sequences of the cp genome and constructed the phylogenetic relationships of Notopterygium species based on the chloroplast DNA and nuclear internal transcribed spacer (ITS) sequences. Comparative analysis of plastid genome showed that the cp DNA are the standard double-stranded molecule, ranging from 157,462 bp (N. oviforme) to 159,607 bp (N. forrestii) in length. The circular DNA each contained a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs). The cp DNA of four species contained 85 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes, respectively. We determined the marked conservation of gene content and sequence evolutionary rate in the cp genome of four Notopterygium species. Three genes (psaI, psbI and rpoA) were possibly under positive selection among the four sampled species. Phylogenetic analysis showed that four Notopterygium species formed a monophyletic clade with high bootstrap support. However, the inconsistent interspecific relationships with the genus Notopterygium were identified between the cp DNA and ITS markers. The incomplete lineage sorting, convergence evolution or hybridization, gene infiltration and different sampling strategies among species may have caused the incongruence between the nuclear and cp DNA relationships. The present results suggested that Notopterygium species may have experienced a complex evolutionary history and speciation process.
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Affiliation(s)
- Jiao Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Chuan Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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Zheng H, Fan L, Milne RI, Zhang L, Wang Y, Mao K. Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China. FRONTIERS IN PLANT SCIENCE 2017; 8:375. [PMID: 28377782 PMCID: PMC5359289 DOI: 10.3389/fpls.2017.00375] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/06/2017] [Indexed: 05/13/2023]
Abstract
Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifolia complex. Bayesian clustering, analysis of molecular variance (AMOVA), Principle Coordinate Analysis (PCoA), ecological niche modeling (ENM), and gene flow (migrants per generation), were employed to detect and test genetic clustering, morphological and habitat differentiation, and gene flow between/among putative species. The nSSR data and ENM suggested that there are two separately evolving meta-population lineages that correspond to P. davidiana (pd) and P. rotundifolia (pr). Furthermore, several lines of evidence supported a subdivision of P. davidiana into Northeastern (NEC) and Central-North (CNC) groups, yet they are still functioning as one species. CpDNA data revealed that five haplotype clades formed a pattern of [pdNEC, ((pdCNC, pr), (pdCNC, pr))], but most haplotypes are species-specific. Meanwhile, PCA based on morphology suggested a closer relationship between the CNC group (P. davidiana) and P. rontundifolia. Discrepancy of nSSR and ENM vs. cpDNA and morphology could have reflected a complex lineage divergence and convergence history. P. davidiana and P. rotundifolia can be regarded as a recently diverged species pair that experienced parapatric speciation due to ecological differentiation in the face of gene flow. Our findings highlight the importance of integrative surveys at population level, as we have undertaken, is an important approach to detect the boundary of a group of species that have experienced complex evolutionary history.
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Affiliation(s)
- Honglei Zheng
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Liqiang Fan
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Lei Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Yaling Wang
- Life Science and Engineering College, Northwest University for NationalitiesLanzhou, China
| | - Kangshan Mao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
- *Correspondence: Kangshan Mao ;
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14
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Jiang D, Feng J, Dong M, Wu G, Mao K, Liu J. Genetic origin and composition of a natural hybrid poplar Populus × jrtyschensis from two distantly related species. BMC PLANT BIOLOGY 2016; 16:89. [PMID: 27091174 PMCID: PMC4836070 DOI: 10.1186/s12870-016-0776-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 04/13/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND The factors that contribute to and maintain hybrid zones between distinct species are highly variable, depending on hybrid origins, frequencies and fitness. In this study, we aimed to examine genetic origins, compositions and possible maintenance of Populus × jrtyschensis, an assumed natural hybrid between two distantly related species. This hybrid poplar occurs mainly on the floodplains along the river valleys between the overlapping distributions of the two putative parents. RESULTS We collected 566 individuals from 45 typical populations of P. × jrtyschensis, P. nigra and P. laurifolia. We genotyped them based on the sequence variations of one maternally inherited chloroplast DNA (cpDNA) fragment and genetic polymorphisms at 20 SSR loci. We further sequenced eight nuclear genes for 168 individuals from 31 populations. Two groups of cpDNA haplotypes characteristic of P. nigra and P. laurifolia respectively were both recovered for P. × jrtyschensis. Genetic structures and coalescent tests of two sets of nuclear population genetic data suggested that P. × jrtyschensis originated from hybridizations between the two assumed parental species. All examined populations of P. × jrtyschensis comprise mainly F1 hybrids from interspecific hybridizations between P. nigra and P. laurifolia. In the habitats of P. × jrtyschensis, there are lower concentrations of soil nitrogen than in the habitats occupied by the other two species. CONCLUSIONS Our extensive examination of the genetic composition of P. × jrtyschensis suggested that it is typical of F1-dominated hybrid zones. This finding plus the low concentration of soil nitrogen in the floodplain soils support the F1-dominated bounded hybrid superiority hypothesis of hybrid zone maintenance for this particular hybrid poplar.
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Affiliation(s)
- Dechun Jiang
- />State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu People’s Republic of China
| | - Jianju Feng
- />State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu People’s Republic of China
- />College of Plant Sciences, Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarimu University, Alar, Xinjiang People’s Republic of China
| | - Miao Dong
- />State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu People’s Republic of China
| | - Guili Wu
- />State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu People’s Republic of China
| | - Kangshan Mao
- />State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu People’s Republic of China
| | - Jianquan Liu
- />State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu People’s Republic of China
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15
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Shang C, Du FK, Yin K, Zhang Z. The complete chloroplast genome of Cathay Poplar: Poplus cathayana Rehder. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:86-87. [PMID: 33473418 PMCID: PMC7800142 DOI: 10.1080/23802359.2015.1137835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The complete chloroplast genome of Populus cathayana was determined in this study. The total length of the chloroplast genome size is 155 449 bp, with 36.95% GC content. A pair of inverted repeats of 27 525 bp are separated by a large single-copy region (LSC, 83 911 bp) and a small single-copy region (SSC, 16 488 bp). About 104 unique genes were annotated, including 76 protein coding genes, 24 tRNA genes and 4 rRNA genes.
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Affiliation(s)
- Ce Shang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Fang K Du
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Kangquan Yin
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing, China.,Museum of Beijing Forestry University, Beijing, China
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16
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Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding. PLoS One 2016; 11:e0147209. [PMID: 26800039 PMCID: PMC4723046 DOI: 10.1371/journal.pone.0147209] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/30/2015] [Indexed: 11/28/2022] Open
Abstract
Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.
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17
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Guo YY, Huang LQ, Liu ZJ, Wang XQ. Promise and Challenge of DNA Barcoding in Venus Slipper (Paphiopedilum). PLoS One 2016; 11:e0146880. [PMID: 26752741 PMCID: PMC4713476 DOI: 10.1371/journal.pone.0146880] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/24/2015] [Indexed: 11/19/2022] Open
Abstract
Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation.
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Affiliation(s)
- Yan-Yan Guo
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lai-Qiang Huang
- Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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18
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Han YW, Duan D, Ma XF, Jia Y, Liu ZL, Zhao GF, Li ZH. Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes. FRONTIERS IN PLANT SCIENCE 2016; 7:1707. [PMID: 27899929 PMCID: PMC5110567 DOI: 10.3389/fpls.2016.01707] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/31/2016] [Indexed: 05/20/2023]
Abstract
Aceraceae is a large forest tree family that comprises many economically and ecologically important species. However, because interspecific and/or intraspecific morphological variations result from frequent interspecific hybridization and introgression, it is challenging for non-taxonomists to accurately recognize and identify the tree species in Aceraceae based on a traditional approach. DNA barcoding is a powerful tool that has been proposed to accurately distinguish between species. In this study, we assessed the effectiveness of three core standard markers (matK, rbcL and ITS) plus the chloroplast locus trnS-trnG as Aceraceae barcodes. A total of 231 sequences representing 85 species in this forest family were collected. Of these four barcode markers, the discrimination power was highest for the ITS (I) region (50%) and was progressively reduced in the other three chloroplast barcodes matK (M), trnS-trnG (T) and rbcL (R); the discrimination efficiency of the ITS marker was also greater than any two-locus combination of chloroplast barcodes. However, the combinations of ITS plus single or combined chloroplast barcodes could improve species resolution significantly; T+I (90.5% resolution) and R+M+T+I (90.5% resolution) differentiated the highest portion of species in Aceraceae. Our current results show that the nuclear ITS fragment represents a more promising DNA barcode marker than the maternally inherited chloroplast barcodes. The most efficient and economical method to identify tree species in Aceraceae among single or combined DNA barcodes is the combination of T+I (90.5% resolution).
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Affiliation(s)
- Yu-Wei Han
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Dong Duan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Zhan-Lin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
- *Correspondence: Zhong-Hu Li
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19
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Bolson M, Smidt EDC, Brotto ML, Silva-Pereira V. ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests. PLoS One 2015; 10:e0143049. [PMID: 26630282 PMCID: PMC4704546 DOI: 10.1371/journal.pone.0143049] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023] Open
Abstract
The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the 'best close match' test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.
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Affiliation(s)
- Mônica Bolson
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Eric de Camargo Smidt
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | - Viviane Silva-Pereira
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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20
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Martínez-Garrido J, Serrão EA, Engelen AH, Cox CJ, García-Murillo P, González-Wangüemert M. Multilocus genetic analyses provide insight into speciation and hybridization in aquatic grasses, genusRuppia. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12666] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Jose Martínez-Garrido
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Gambelas Faro 8005-139 Portugal
- Departamento de Ciencias del Mar y Biología Aplicada; Universidad de Alicante (DCMBA, UA); PO Box 99 03080 Alicante Spain
| | - Ester A. Serrão
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Gambelas Faro 8005-139 Portugal
| | - Aschwin H. Engelen
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Gambelas Faro 8005-139 Portugal
| | - Cymon J. Cox
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Gambelas Faro 8005-139 Portugal
| | - Pablo García-Murillo
- Departamento de Biología Vegetal y Ecología; Universidad de Sevilla; C/Profesor García Gonzalez N°2 41012 Sevilla Spain
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21
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Yan HF, Liu YJ, Xie XF, Zhang CY, Hu CM, Hao G, Ge XJ. DNA barcoding evaluation and its taxonomic implications in the species-rich genus Primula L. in China. PLoS One 2015; 10:e0122903. [PMID: 25875620 PMCID: PMC4395239 DOI: 10.1371/journal.pone.0122903] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/24/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Primula is extremely diverse in the east Himalaya-Hengduan Mountains (HHM) in China as a result of rapid radiation. In order to overcome the difficulty of morphological classification of this genus, we surveyed three plastid regions (rbcL, matK, and trnH-psbA) and two nuclear markers (ITS and ITS2) from 227 accessions representing 66 Primula species across 18 sections, to assess their discriminatory power as barcodes. We found that ITS alone or combined with plastid regions showed the best discrimination across different infrageneric ranks and at species level. We suggest rbcL + matK + ITS as the first choice at present to barcode Primula plants. Although the present barcoding combination performed poorly in many closely related species of Primula, it still provided many new insights into current Primula taxonomy, such as the underlying presence of cryptic species, and several potential improper taxonomic treatments. DNA barcoding is one useful technique in the integrative taxonomy of the genus Primula, but it still requires further efforts to improve its effectiveness in some taxonomically challenging groups.
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Affiliation(s)
- Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yun-Jiao Liu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xiu-Feng Xie
- Tropical Agriculture department, Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, China
| | - Cai-Yun Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chi-Ming Hu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- * E-mail: (GH); (XJG)
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (GH); (XJG)
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22
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Porth I, El-Kassaby YA. Using Populus as a lignocellulosic feedstock for bioethanol. Biotechnol J 2015; 10:510-24. [PMID: 25676392 DOI: 10.1002/biot.201400194] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 11/11/2014] [Accepted: 12/30/2014] [Indexed: 11/10/2022]
Abstract
Populus species along with species from the sister genus Salix will provide valuable feedstock resources for advanced second-generation biofuels. Their inherent fast growth characteristics can particularly be exploited for short rotation management, a time and energy saving cultivation alternative for lignocellulosic feedstock supply. Salicaceae possess inherent cell wall characteristics with favorable cellulose to lignin ratios for utilization as bioethanol crop. We review economically important traits relevant for intensively managed biofuel crop plantations, genomic and phenotypic resources available for Populus, breeding strategies for forest trees dedicated to bioenergy provision, and bioprocesses and downstream applications related to opportunities using Salicaceae as a renewable resource. Challenges need to be resolved for every single step of the conversion process chain, i.e., starting from tree domestication for improved performance as a bioenergy crop, bioconversion process, policy development for land use changes associated with advanced biofuels, and harvest and supply logistics associated with industrial-scale biorefinery plants using Populus as feedstock. Significant hurdles towards cost and energy efficiency, environmental friendliness, and yield maximization with regards to biomass pretreatment, saccharification, and fermentation of celluloses and the sustainability of biorefineries as a whole still need to be overcome.
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Affiliation(s)
- Ilga Porth
- Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada.
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