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Zhang H, Zhao D, Hu C, Duan W, Chu H, Chu Z. The complete mitogenome of Paratanakia chii (Cypriniformes; Cyprinidae). Mitochondrial DNA B Resour 2023; 8:515-517. [PMID: 37091580 PMCID: PMC10114962 DOI: 10.1080/23802359.2023.2171692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Paratanakia chii is a bitterling fish of the genus Paratanakia, subfamily Acheilognathinae and family Cyprinidae. The mitochondrial DNA sequence of P. chii is reported in this paper. The complete mitochondrial genome of P. chii is 16,575 bp in length, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 displacement loop (D-loop). The genome sequence is consistent with those of most other carp. The majority of PCGs have AT- (Met) start codons and TA- end codons. The A + T contents of the genome, PCGs, transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs) are 56.92%, 58.07%, 56.34%, and 54.21%, respectively. Phylogenetic analysis showed that P. chii is most closely related to Tanankia himantegus. These data will benefit relative ecological and phylogenetic studies.
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Affiliation(s)
- Haixia Zhang
- College of Fisheries, Zhejiang Ocean University, Zhoushan, China
| | - Dan Zhao
- College of Fisheries, Zhejiang Ocean University, Zhoushan, China
| | - Chang Hu
- College of Fisheries, Zhejiang Ocean University, Zhoushan, China
| | - Wenli Duan
- College of Fisheries, Zhejiang Ocean University, Zhoushan, China
| | - Hang Chu
- College of Fisheries, Zhejiang Ocean University, Zhoushan, China
| | - Zhangjie Chu
- College of Fisheries, Zhejiang Ocean University, Zhoushan, China
- CONTACT Zhangjie Chu College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
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Wang J, Yan Z, Zhong P, Shen Z, Yang G, Ma L. Screening of universal DNA barcodes for identifying grass species of Gramineae. FRONTIERS IN PLANT SCIENCE 2022; 13:998863. [PMID: 36161013 PMCID: PMC9490308 DOI: 10.3389/fpls.2022.998863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
There is currently international interest in applying DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of four candidate plant DNA barcoding regions [rbcL, matK, trnL-F, and internal transcribed spacer (ITS)] in seven genera of Gramineae including Agropyron, Bromus, Elymus, Elytrigia, Festuca, Leymus, and Lolium. Fourteen accessions were analyzed, and matK and ITS showed the highest species, subspecies, and variety discriminatory power, each resolving 11 accessions. Species discrimination using rbcL and trnL-F was lower, resolving 7 and 8 accessions, respectively. Subspecies and variety discrimination using rbcL and trnL-F could not identify 4 accessions of Agropyron. A technical system can be established using the proposed DNA barcode to rapidly and reliably identify the seven genera of Gramineae. This study serves as a "useful reference" for identifying the genetic diversity of grass germplasm resources. DNA barcoding can be utilized to uncover the relatives of different species within the same family or between different families. It can also be used to determine the related groups of important herbage, turfgrass, and crops and provide crucial background information for discovering excellent genes and improving existing crop varieties.
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Affiliation(s)
- Jianli Wang
- Pratacultural Science Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhenfei Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Peng Zhong
- Branch of Animal Husbandry and Veterinary, Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Zhongbao Shen
- Pratacultural Science Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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3
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Li P, Li D, Hong Y, Chen M, Zhang X, Hu L, Liu C. Combining DNA Mini-Barcoding and Species-Specific Primers PCR Technology for Identification of Heosemys grandis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.822871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Heosemys grandis, a species of Asian water turtle, that has a wide range of applications in the food and pharmaceutical industries. Since some processed products cannot be identified exclusively by morphological and microscopic identification, a reliable and quick approach to guarantee authenticity is critical. Thus, we fostered an effective and stable molecular identification system to identify Heosemys grandis based on DNA mini-barcoding and species-specific primers PCR technology. A total of 48 turtle samples from 16 different species were collected. To distinguish Heosemys grandis from its counterfeits, DNA mini-barcoding and a pair of species-specific primers were designed and verified by PCR after analyzing the COI sequences of samples. The results showed that only Heosemys grandis samples could generate a single clear band following amplification using species-specific primers. Employing DNA mini-barcoding to amplify samples can verify authenticity by sequence alignment. These findings indicated that species-specific primers PCR technology combined with DNA mini-barcoding could accurately detect the authenticity of Heosemys grandis. This technology broadens the application of molecular biology techniques in the food and pharmaceutical industries. It provides a reliable and convenient method for identifying raw materials to standardize the market and protect customers’ rights and interests.
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Kim C, Kim DK, Sun H, Kim JH. Phylogenetic relationship, biogeography, and conservation genetics of endangered Fraxinus chiisanensis (Oleaceae), endemic to South Korea. PLANT DIVERSITY 2022; 44:170-180. [PMID: 35505990 PMCID: PMC9043305 DOI: 10.1016/j.pld.2021.06.004] [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: 01/24/2021] [Revised: 06/03/2021] [Accepted: 06/13/2021] [Indexed: 06/14/2023]
Abstract
Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.
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Affiliation(s)
- Changkyun Kim
- Plant Research Division, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
| | - Dong-Kap Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon 11186, Republic of Korea
| | - Hang Sun
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, Yunnan, PR China
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea
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Hinsinger DD, Strijk JS. Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PHYTOKEYS 2019; 132:75-89. [PMID: 31607787 PMCID: PMC6783484 DOI: 10.3897/phytokeys.132.36365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/28/2019] [Indexed: 06/01/2023]
Abstract
The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada and compared its sequence with those available from other main taxonomic groups in Quercus. We quantify genomic divergence amongst oaks and performed a sliding window analysis to detect the most variable regions amongst members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs amongst oaks species and sections and stress the need for a large global assessment of genetic diversity in this economically and ecologically important genus.
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Affiliation(s)
- Damien Daniel Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi 530005, China
| | - Joeri Sergej Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi 530005, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Lao PDR
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Fitzek E, Delcamp A, Guichoux E, Hahn M, Lobdell M, Hipp AL. A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting. Ecol Evol 2018; 8:5837-5851. [PMID: 29938097 PMCID: PMC6010771 DOI: 10.1002/ece3.4122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 11/16/2022] Open
Abstract
DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite-associated DNA sequencing (RAD-seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof-of-concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD-seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.
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Affiliation(s)
- Elisabeth Fitzek
- HerbariumThe Morton ArboretumLisleIllinois
- Present address:
Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinois
| | - Adline Delcamp
- Site de Pierroton, Platforme Genome TranscriptomeINRACESTASFrance
- UMR1202 Biodiversité Gènes and CommunautésUniversity of BordeauxCESTASFrance
| | - Erwan Guichoux
- Site de Pierroton, Platforme Genome TranscriptomeINRACESTASFrance
- UMR1202 Biodiversité Gènes and CommunautésUniversity of BordeauxCESTASFrance
| | | | | | - Andrew L. Hipp
- HerbariumThe Morton ArboretumLisleIllinois
- Department of BotanyThe Field MuseumChicagoIllinois
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Pham KK, Hipp AL, Manos PS, Cronn RC. A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny. Genome 2017; 60:720-732. [DOI: 10.1139/gen-2016-0191] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%–21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%–41% of plastome variation, geography 3%–41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.
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Affiliation(s)
- Kasey K. Pham
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA
| | - Andrew L. Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Paul S. Manos
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Richard C. Cronn
- Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331-4401, USA
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Hinsinger DD, Strijk JS. Toward phylogenomics of Lauraceae: The complete chloroplast genome sequence of Litsea glutinosa (Lauraceae), an invasive tree species on Indian and Pacific Ocean islands. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Hassold S, Lowry PP, Bauert MR, Razafintsalama A, Ramamonjisoa L, Widmer A. DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species. PLoS One 2016; 11:e0157881. [PMID: 27362258 PMCID: PMC4928830 DOI: 10.1371/journal.pone.0157881] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/05/2016] [Indexed: 12/01/2022] Open
Abstract
Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world’s most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods.
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Affiliation(s)
- Sonja Hassold
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, Missouri, United States of America
- ISYEB (UMR 7205), Département Systématique et Evolution, Muséum National d’Histoire Naturelle, Paris, France
| | | | | | | | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- * E-mail:
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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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Huang XC, Ci XQ, Conran JG, Li J. Application of DNA Barcodes in Asian Tropical Trees--A Case Study from Xishuangbanna Nature Reserve, Southwest China. PLoS One 2015; 10:e0129295. [PMID: 26121045 PMCID: PMC4509572 DOI: 10.1371/journal.pone.0129295] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/27/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world. METHODOLOGY AND PRINCIPAL FINDINGS A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH-psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH-psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6-58.1%) and genus (72.8-76.2%) identification. With trnH-psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7-28.5% and 31.6-35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas. CONCLUSIONS/SIGNIFICANCE Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH-psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.
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Affiliation(s)
- Xiao-cui Huang
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiu-qin Ci
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - John G. Conran
- Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, Benham Bldg DX, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Jie Li
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
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Zedane L, Hong-Wa C, Murienne J, Jeziorski C, Baldwin BG, Besnard G. Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12509] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Loubab Zedane
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Cynthia Hong-Wa
- Missouri Botanical Garden; PO Box 299 St. Louis MO 63166-0299 USA
| | - Jérôme Murienne
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Céline Jeziorski
- INRA; UAR1209; département de Génétique Animale; INRA Auzeville 31326; Castanet-Tolosan France
- GeT-PlaGe; Genotoul; INRA Auzeville 31326; Castanet-Tolosan France
| | - Bruce G. Baldwin
- Jepson Herbarium and Department of Integrative Biology; University of California; Berkeley CA 94720-2465 USA
| | - Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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Nithaniyal S, Newmaster SG, Ragupathy S, Krishnamoorthy D, Vassou SL, Parani M. DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India. PLoS One 2014; 9:e107669. [PMID: 25259794 PMCID: PMC4178033 DOI: 10.1371/journal.pone.0107669] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/22/2014] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF) barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group. METHODOLOGY/PRINCIPAL FINDINGS We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF) species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK) correctly identified 136 out of 143 species (95%). This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method. CONCLUSIONS We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.
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Affiliation(s)
- Stalin Nithaniyal
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
- Interdisciplinary School of Indian System of Medicine, SRM University, Chennai, India
| | - Steven G. Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Sophie Lorraine Vassou
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
| | - Madasamy Parani
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
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14
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Heinze B, Koziel-Monte A, Jahn D. Analysis of variation in chloroplast DNA sequences. Methods Mol Biol 2014; 1115:85-120. [PMID: 24415471 DOI: 10.1007/978-1-62703-767-9_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This chapter introduces and reviews methods for analyzing variation in chloroplast DNA, mainly by polymerase chain reaction (PCR) and subsequent revelation of polymorphisms. Sources for chloroplast primers are discussed, as well as methods such as Sanger sequencing, PCR followed by restriction fragment length polymorphism (RFLP), gel electrophoresis, fragment analysis on automated DNA sequencers, denaturing high-performance liquid chromatography (dHPLC), and next-generation sequencing (NGS). A special section deals with peculiarities of chloroplast DNA variation, such as tandem repeats and mini- and microsatellites.
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MESH Headings
- Base Sequence
- Chromatography, High Pressure Liquid
- DNA Primers/genetics
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Chloroplast/isolation & purification
- Databases, Genetic
- Electrophoresis, Agar Gel
- Electrophoresis, Polyacrylamide Gel
- Genetic Techniques
- Genetic Variation
- High-Throughput Nucleotide Sequencing
- Nucleic Acid Denaturation
- Polymerase Chain Reaction
- Polymorphism, Genetic
- Polymorphism, Restriction Fragment Length
- Sequence Analysis, DNA
- Tandem Repeat Sequences/genetics
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Affiliation(s)
- Berthold Heinze
- Department of Genetics, Federal Research Centre for Forests, Vienna, Austria
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15
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Ojeda DI, Santos-Guerra A, Oliva-Tejera F, Jaen-Molina R, Caujapé-Castells J, Marrero-Rodríguez A, Cronk Q. DNA barcodes successfully identified Macaronesian Lotus (Leguminosae) species within early diverged lineages of Cape Verde and mainland Africa. AOB PLANTS 2014; 6:plu050. [PMID: 25147310 PMCID: PMC4168286 DOI: 10.1093/aobpla/plu050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Plant DNA barcoding currently relies on the application of a two-locus combination, matK + rbcL. Despite the universality of these two gene regions across plants, it is suspected that this combination might not have sufficient variation to discriminate closely related species. In this study, we tested the performance of this two-locus plant barcode along with the additional plastid regions trnH-psbA, rpoC1 and rpoB and the nuclear region internal transcribed spacer (nrITS) in a group of 38 species of Lotus from the Macaronesian region. The group has radiated into the five archipelagos within this region from mid-Miocene to early Pleistocene, and thus provides both early divergent and recent radiations that pose a particularly difficult challenge for barcoding. The group also has 10 species considered under different levels of conservation concern. We found different levels of species discrimination depending on the age of the lineages. We obtained 100 % of the species identification from mainland Africa and Cape Verde when all six regions were combined. These lineages radiated >4.5 Mya; however, in the most recent radiations from the end of the Pliocene to the mid-Pleistocene (3.5-1.5 Mya), only 30 % of the species were identified. Of the regions examined, the intergenic region trnH-psbA was the most variable and had the greatest discriminatory power (18 %) of the plastid regions when analysed alone. The nrITS region was the best region when analysed alone with a discriminatory power of 26 % of the species. Overall, we identified 52 % of the species and 30 % of the endangered or threatened species within this group when all six regions were combined. Our results are consistent with those of other studies that indicate that additional approaches to barcoding will be needed in recently evolved groups, such as the inclusion of faster evolving regions from the nuclear genome.
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Affiliation(s)
- Dario I Ojeda
- The Biodiversity Research Centre, Department of Botany, University of British Columbia, 6804 SW Marine Drive, Vancouver V6T 1Z4, Canada
| | | | - Felicia Oliva-Tejera
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Ruth Jaen-Molina
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Juli Caujapé-Castells
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Aguedo Marrero-Rodríguez
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Quentin Cronk
- The Biodiversity Research Centre, Department of Botany, University of British Columbia, 6804 SW Marine Drive, Vancouver V6T 1Z4, Canada
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16
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Percy DM, Argus GW, Cronk QC, Fazekas AJ, Kesanakurti PR, Burgess KS, Husband BC, Newmaster SG, Barrett SC, Graham SW. Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep? Mol Ecol 2014; 23:4737-56. [DOI: 10.1111/mec.12837] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 05/29/2014] [Accepted: 06/04/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Diana M. Percy
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - George W. Argus
- Canadian Museum of Nature; PO Box 3443 Stn “D” Ottawa ON Canada K1P 6P4
| | - Quentin C. Cronk
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - Aron J. Fazekas
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | | | - Kevin S. Burgess
- Department of Biology; Columbus State University; Columbus GA 31907-5645 USA
| | - Brian C. Husband
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Steven G. Newmaster
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Spencer C.H. Barrett
- Department of Ecology & Evolutionary Biology; University of Toronto; 25 Willcocks Street Toronto ON Canada M5S 3B2
| | - Sean W. Graham
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
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17
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Hinsinger DD, Gaudeul M, Couloux A, Bousquet J, Frascaria-Lacoste N. The phylogeography of Eurasian Fraxinus species reveals ancient transcontinental reticulation. Mol Phylogenet Evol 2014; 77:223-37. [PMID: 24795215 DOI: 10.1016/j.ympev.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/14/2014] [Accepted: 04/18/2014] [Indexed: 01/16/2023]
Abstract
To investigate the biogeographical history of ashes species of the Eurasian section Fraxinus and to test the hypothesis of ancient reticulations, we sequenced nuclear DNA (nETS and nITS, 1075 bp) for 533 samples and scored AFLP for 63 samples of Eurasian ashes within the section Fraxinus. The nITS phylogeny retrieved the classical view of the evolution of the section, whereas nETS phylogeny indicated an unexpected separation of F. angustifolia in two paraphyletic groups, respectively found in southeastern Europe and in the other parts of the Mediterranean basin. In the nETS phylogeny, the former group was closely related to F. excelsior, whereas the later was closely related to F. mandshurica, a species which is restricted nowadays to northeastern Asia. This topological incongruence between the two loci indicated the occurrence of an ancient reticulation between European and Asian ash species. Several other ancient reticulation events between the two European species and the other species of the section were supported by the posterior predictive checking method. Some of these reticulation events would have occurred during the Miocene, when climatic variations may have lead these species to expand their distribution range and come into contact. The recurrent reticulations observed among Eurasian ash species indicate that they should be considered as conspecific taxa, with subspecific status for some groups. Altogether, the results of the present study provide a rare documented evidence for the occurrence of multiple ancient reticulations within a group of temperate tree taxa with modern disjunct distributions in Eurasia. These ancient reticulation events indicate that the speciation process is slow in ashes, necessitating long periods of geographical isolation. The implications for speciation processes in temperate trees with similar life history and reproductive biology are discussed.
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Affiliation(s)
- Damien D Hinsinger
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France; Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Myriam Gaudeul
- Muséum National d'Histoire Naturelle, UMR CNRS 7205 'Origine, Structure et Evolution de la Biodiversité', 16 rue Buffon, CP 39, F-75005 Paris, France.
| | - Arnaud Couloux
- Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, F-91057 Evry Cedex, France.
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Nathalie Frascaria-Lacoste
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France.
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18
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Gere J, Yessoufou K, Daru BH, Mankga LT, Maurin O, van der Bank M. Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae. Zookeys 2013; 365:129-47. [PMID: 24453555 PMCID: PMC3890675 DOI: 10.3897/zookeys.365.5728] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 09/13/2013] [Indexed: 11/19/2022] Open
Abstract
Recent studies indicate that the discriminatory power of the core DNA barcodes (rbcLa + matK) for land plants may have been overestimated since their performance have been tested only on few closely related species. In this study we focused mainly on how the addition of complementary barcodes (nrITS and trnH-psbA) to the core barcodes will affect the performance of the core barcodes in discriminating closely related species from family to section levels. In general, we found that the core barcodes performed poorly compared to the various combinations tested. Using multiple criteria, we finally advocated for the use of the core + trnH-psbA as potential DNA barcode for the family Combretaceae at least in southern Africa. Our results also indicate that the success of DNA barcoding in discriminating closely related species may be related to evolutionary and possibly the biogeographic histories of the taxonomic group tested.
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Affiliation(s)
- Jephris Gere
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
| | - Kowiyou Yessoufou
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
- C4 EcoSolutions, 9 Mohr Road Tokai, Cape Town, South Africa 7945
| | - Barnabas H. Daru
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
| | - Ledile T. Mankga
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
| | - Olivier Maurin
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
| | - Michelle van der Bank
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
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19
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Laiou A, Mandolini LA, Piredda R, Bellarosa R, Simeone MC. DNA barcoding as a complementary tool for conservation and valorisation of forest resources. Zookeys 2013; 365:197-213. [PMID: 24453558 PMCID: PMC3890678 DOI: 10.3897/zookeys.365.5670] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 12/06/2013] [Indexed: 11/17/2022] Open
Abstract
Since the pre-historic era, humans have been using forests as a food, drugs and handcraft reservoir. Today, the use of botanical raw material to produce pharmaceuticals, herbal remedies, teas, spirits, cosmetics, sweets, dietary supplements, special industrial compounds and crude materials constitute an important global resource in terms of healthcare and economy. In recent years, DNA barcoding has been suggested as a useful molecular technique to complement traditional taxonomic expertise for fast species identification and biodiversity inventories. In this study, in situ application of DNA barcodes was tested on a selected group of forest tree species with the aim of contributing to the identification, conservation and trade control of these valuable plant resources. The "core barcode" for land plants (rbcL, matK, and trnH-psbA) was tested on 68 tree specimens (24 taxa). Universality of the method, ease of data retrieval and correct species assignment using sequence character states, presence of DNA barcoding gaps and GenBank discrimination assessment were evaluated. The markers showed different prospects of reliable applicability. RbcL and trnH-psbA displayed 100% amplification and sequencing success, while matK did not amplify in some plant groups. The majority of species had a single haplotype. The trnH-psbA region showed the highest genetic variability, but in most cases the high intraspecific sequence divergence revealed the absence of a clear DNA barcoding gap. We also faced an important limitation because the taxonomic coverage of the public reference database is incomplete. Overall, species identification success was 66.7%. This work illustrates current limitations in the applicability of DNA barcoding to taxonomic forest surveys. These difficulties urge for an improvement of technical protocols and an increase of the number of sequences and taxa in public databases.
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Affiliation(s)
- Angeliki Laiou
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
| | - Luca Aconiti Mandolini
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
| | - Roberta Piredda
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
| | - Rosanna Bellarosa
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
| | - Marco Cosimo Simeone
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
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20
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Hinsinger DD, Basak J, Gaudeul M, Cruaud C, Bertolino P, Frascaria-Lacoste N, Bousquet J. The phylogeny and biogeographic history of ashes (fraxinus, oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees. PLoS One 2013; 8:e80431. [PMID: 24278282 PMCID: PMC3837005 DOI: 10.1371/journal.pone.0080431] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022] Open
Abstract
The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.
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Affiliation(s)
- Damien Daniel Hinsinger
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Jolly Basak
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Myriam Gaudeul
- Unité mixte de recherche 7205 ‘Origine, Structure et Evolution de la Biodiversité’, Muséum National d'Histoire Naturelle, Paris, France
| | | | - Paola Bertolino
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Nathalie Frascaria-Lacoste
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, Canada
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21
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Saarela JM, Sokoloff PC, Gillespie LJ, Consaul LL, Bull RD. DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. PLoS One 2013; 8:e77982. [PMID: 24348895 PMCID: PMC3865322 DOI: 10.1371/journal.pone.0077982] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/08/2013] [Indexed: 01/16/2023] Open
Abstract
Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.
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Affiliation(s)
- Jeffery M. Saarela
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Paul C. Sokoloff
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Lynn J. Gillespie
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Laurie L. Consaul
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Roger D. Bull
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
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22
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Tripathi AM, Tyagi A, Kumar A, Singh A, Singh S, Chaudhary LB, Roy S. The internal transcribed spacer (ITS) region and trnH-psbA [corrected] are suitable candidate loci for DNA barcoding of tropical tree species of India. PLoS One 2013; 8:e57934. [PMID: 23460915 PMCID: PMC3584017 DOI: 10.1371/journal.pone.0057934] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 01/29/2013] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND DNA barcoding as a tool for species identification has been successful in animals and other organisms, including certain groups of plants. The exploration of this new tool for species identification, particularly in tree species, is very scanty from biodiversity-rich countries like India. rbcL and matK are standard barcode loci while ITS, and trnH-psbA are considered as supplementary loci for plants. METHODOLOGY AND PRINCIPAL FINDINGS Plant barcode loci, namely, rbcL, matK, ITS, trnH-psbA, and the recently proposed ITS2, were tested for their efficacy as barcode loci using 300 accessions of tropical tree species. We tested these loci for PCR, sequencing success, and species discrimination ability using three methods. rbcL was the best locus as far as PCR and sequencing success rate were concerned, but not for the species discrimination ability of tropical tree species. ITS and trnH-psbA were the second best loci in PCR and sequencing success, respectively. The species discrimination ability of ITS ranged from 24.4 percent to 74.3 percent and that of trnH-psbA was 25.6 percent to 67.7 percent, depending upon the data set and the method used. matK provided the least PCR success, followed by ITS2 (59. 0%). Species resolution by ITS2 and rbcL ranged from 9.0 percent to 48.7 percent and 13.2 percent to 43.6 percent, respectively. Further, we observed that the NCBI nucleotide database is poorly represented by the sequences of barcode loci studied here for tree species. CONCLUSION Although a conservative approach of a success rate of 60-70 percent by both ITS and trnH-psbA may not be considered as highly successful but would certainly help in large-scale biodiversity inventorization, particularly for tropical tree species, considering the standard success rate of plant DNA barcode program reported so far. The recommended matK and rbcL primers combination may not work in tropical tree species as barcode markers.
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Affiliation(s)
- Abhinandan Mani Tripathi
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Antariksh Tyagi
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Anoop Kumar
- Plant Diversity, Systematic and Herbarium Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Akanksha Singh
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Shivani Singh
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Lal Babu Chaudhary
- Plant Diversity, Systematic and Herbarium Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Sribash Roy
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
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Pillon Y, Johansen J, Sakishima T, Chamala S, Barbazuk WB, Roalson EH, Price DK, Stacy EA. Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations. BMC Evol Biol 2013; 13:35. [PMID: 23394592 PMCID: PMC3605094 DOI: 10.1186/1471-2148-13-35] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 01/25/2013] [Indexed: 11/17/2022] Open
Abstract
Background DNA barcoding of land plants has relied traditionally on a small number of markers from the plastid genome. In contrast, low-copy nuclear genes have received little attention as DNA barcodes because of the absence of universal primers for PCR amplification. Results From pooled-species 454 transcriptome data we identified two variable intron-less nuclear loci for each of two species-rich genera of the Hawaiian flora: Clermontia (Campanulaceae) and Cyrtandra (Gesneriaceae) and compared their utility as DNA barcodes with that of plastid genes. We found that nuclear genes showed an overall greater variability, but also displayed a high level of heterozygosity, intraspecific variation, and retention of ancient alleles. Thus, nuclear genes displayed fewer species-diagnostic haplotypes compared to plastid genes and no interspecies gaps. Conclusions The apparently greater coalescence times of nuclear genes are likely to limit their utility as barcodes, as only a small proportion of their alleles were fixed and unique to individual species. In both groups, species-diagnostic markers from either genome were scarce on the youngest island; a minimum age of ca. two million years may be needed for a species flock to be barcoded. For young plant groups, nuclear genes may not be a superior alternative to slowly evolving plastid genes.
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Affiliation(s)
- Yohan Pillon
- Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, HI 96720, USA.
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López-Alvarez D, López-Herranz ML, Betekhtin A, Catalán P. A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae). PLoS One 2012; 7:e51058. [PMID: 23240000 PMCID: PMC3519806 DOI: 10.1371/journal.pone.0051058] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/29/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30). METHODOLOGY/PRINCIPAL FINDINGS We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid. CONCLUSION/SIGNIFICANCE Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents.
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Affiliation(s)
- Diana López-Alvarez
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
| | | | - Alexander Betekhtin
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Pilar Catalán
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
- * E-mail:
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