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Othman SN, Shin Y, Kim HT, Chuang MF, Bae Y, Hoti J, Zhang Y, Jang Y, Borzée A. Evaluating the efficiency of popular species identification analytical methods, and integrative workflow using morphometry and barcoding bioinformatics for taxonomy and origin of traded cryptic brown frogs. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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Trujillo-Argueta S, del Castillo RF, Velasco-Murguía A. Testing the effectiveness of rbcLa DNA-barcoding for species discrimination in tropical montane cloud forest vascular plants (Oaxaca, Mexico) using BLAST, genetic distance, and tree-based methods. PeerJ 2022; 10:e13771. [PMID: 35990900 PMCID: PMC9390329 DOI: 10.7717/peerj.13771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
DNA-barcoding is a species identification tool that uses a short section of the genome that provides a genetic signature of the species. The main advantage of this novel technique is that it requires a small sample of tissue from the tested organism. In most animal groups, this technique is very effective. However, in plants, the recommended standard markers, such as rbcLa, may not always work, and their efficacy remains to be tested in many plant groups, particularly from the Neotropical region. We examined the discriminating power of rbcLa in 55 tropical cloud forest vascular plant species from 38 families (Oaxaca, Mexico). We followed the CBOL criteria using BLASTn, genetic distance, and monophyly tree-based analyses (neighbor-joining, NJ, maximum likelihood, ML, and Bayesian inference, BI). rbcLa universal primers amplified 69.0% of the samples and yielded 91.3% bi-directional sequences. Sixty-three new rbcLa sequences were established. BLAST discriminates 80.8% of the genus but only 15.4% of the species. There was nil minimum interspecific genetic distances in Quercus, Oreopanax, and Daphnopsis. Contrastingly, Ericaceae (5.6%), Euphorbiaceae (4.6%), and Asteraceae (3.3%) species displayed the highest within-family genetic distances. According to the most recent angiosperm classification, NJ and ML trees successfully resolved (100%) monophyletic species. ML trees showed the highest mean branch support value (87.3%). Only NJ and ML trees could successfully discriminate Quercus species belonging to different subsections: Quercus martinezii (white oaks) from Q. callophylla and Q. laurina (red oaks). The ML topology could distinguish species in the Solanaceae clade with similar BLAST matches. Also, the BI topology showed a polytomy in this clade, and the NJ tree displayed low-support values. We do not recommend genetic-distance approaches for species discrimination. Severe shortages of rbcLa sequences in public databases of neotropical species hindered effective BLAST comparisons. Instead, ML tree-based analysis displays the highest species discrimination among the tree-based analyses. With the ML topology in selected genera, rbcLa helped distinguish infra-generic taxonomic categories, such as subsections, grouping affine species within the same genus, and discriminating species. Since the ML phylogenetic tree could discriminate 48 species out of our 55 studied species, we recommend this approach to resolve tropical montane cloud forest species using rbcLa, as an initial step and improve DNA amplification methods.
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Zhou C, Feng M, Tang Y, Yang C, Meng X, Nie G. Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene. Ecol Evol 2021; 11:10502-10514. [PMID: 34367592 PMCID: PMC8328406 DOI: 10.1002/ece3.7855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 01/02/2023] Open
Abstract
Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree-based methods (NJ, ML, and bPTP) and distance-based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p-distances had similar results. Mean K2P distances and p-distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.
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Affiliation(s)
- Chuan‐jiang Zhou
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Meng‐xia Feng
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Yong‐tao Tang
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Chang‐xing Yang
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Xiao‐lin Meng
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
| | - Guo‐xing Nie
- College of FisheriesEngineering Technology Research Center of Henan Province for Aquatic Animal CultivationEngineering Lab of Henan Province for Aquatic Animal Disease ControlHenan Normal UniversityXinxiangChina
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Bonatto CC, Silva LP. A MALDI-TOF mass spectrometry-based approach for molecular profiling of leaves from pasture and feed forages species. BIOCHEM SYST ECOL 2021. [DOI: 10.1016/j.bse.2020.104215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gunnels T, Creswell M, McFerrin J, Whittall JB. The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements. PLoS One 2020; 15:e0236774. [PMID: 33180770 PMCID: PMC7660467 DOI: 10.1371/journal.pone.0236774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/28/2020] [Indexed: 11/18/2022] Open
Abstract
The dietary supplement industry is rapidly growing yet, a recent study revealed that up to 60% of supplements may have substituted ingredients, some of which can be harmful contaminants or additives. When ingredients cannot be verified morphologically or biochemically, DNA barcoding complemented with a molecular phylogenetic analysis can be a powerful method for species authentication. We employed a molecular phylogenetic analysis for species authentication of the commonly used fungal supplement, reishi (Ganoderma lingzhi), by amplifying and sequencing the nuclear ribosomal internal transcribed spacer regions (ITS) with genus-specific primers. PCR of six powdered samples and one dried sample all sold as G. lucidum representing independent suppliers produced single, strong amplification products in the expected size-range for Ganoderma. Both best-hit BLAST and molecular phylogenetic analyses clearly identified the presence of G. lingzhi DNA in all seven herbal supplements. We detected variation in the ITS sequences among our samples, but all herbal supplement samples fall within a large clade of G. lingzhi ITS sequences. ITS-based phylogenetic analysis is a successful and cost-effective method for DNA-based species authentication that could be used in the herbal supplement industry for this and other fungal and plant species that are otherwise difficult to identify.
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Affiliation(s)
- Tess Gunnels
- Department of Biology, Santa Clara University, Santa Clara, California, United States of America
- Oregon’s Wild Harvest, Redmond, Oregon, United States of America
| | - Matthew Creswell
- Oregon’s Wild Harvest, Redmond, Oregon, United States of America
| | - Janis McFerrin
- Oregon’s Wild Harvest, Redmond, Oregon, United States of America
| | - Justen B. Whittall
- Department of Biology, Santa Clara University, Santa Clara, California, United States of America
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Gostel MR, Zúñiga JD, Kress WJ, Funk VA, Puente-Lelievre C. Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding. Sci Rep 2020; 10:8701. [PMID: 32457375 PMCID: PMC7250904 DOI: 10.1038/s41598-020-64919-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/20/2020] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding is a valuable tool to support species identification with broad applications from traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidic Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high-throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (producing up to 23,040 PCR products) during a single thermal cycling protocol. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array and Illumina MiSeq. We tested 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS. This workflow was used to build a reference library for 78 families and 96 genera from all major plant lineages - many currently lacking in public databases. Our results show that this technique is an efficient alternative to traditional PCR and Sanger sequencing to generate large amounts of plant DNA barcodes and build more comprehensive barcode databases.
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Affiliation(s)
- Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, Texas, 76107-3400, USA.
| | - Jose D Zúñiga
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, 20892, USA
| | - W John Kress
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
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Elucidating genetic variability and population structure in Venturia inaequalis associated with apple scab diseaseusing SSR markers. PLoS One 2019; 14:e0224300. [PMID: 31693681 PMCID: PMC6834240 DOI: 10.1371/journal.pone.0224300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/09/2019] [Indexed: 01/20/2023] Open
Abstract
Apple scab caused by Venturia inaequalis Cooke (Wint.) is one the important diseases of trade and industrial significance in apple. In present study variability studies in pathogen isolates were studied, which is one of the most important factors for devising management studies of scab disease in apple. Genetic diversity of 30 Venturia inaequalis isolates from 12 districts of two geographical distinct regions of Jammu and Kashmir was calculated based on the allele frequencies of 28 SSR markers and the internal transcribed spacer (ITS) region of the ribosomal DNA. The ITS based characterized sequences were submitted to NCBI GenBank and accession numbers were sanctioned. Dendrogram showed that all the accessions formed 2 main clusters with various degree of sub clustering within the clusters. Analysis based on SSR study reveals that the heterozygosity ranged from 0.0 and 0.5, with an average value of 0.39. The expected heterozygosis or gene diversity (He) ranged from 0.0 to 0.50 with an average of 0.40. The Fst value ranges from 0 to 0.6 with an average of 0.194. Diversity within each population (HS) values ranging from 0.26 to 0.33. Average differentiation among populations (GST) was 0.11 and populations were isolated by significant distance (r 2 = 0.50, P < 0.01). From the AMOVA analysis, 25% of variation was observed among population, 9% among individuals and 66% within individuals observed in the population. Structure analysis grouped isolates into two populations. Principle coordinate analysis explained variation of 36.6% in population 1, 14.30% in population 2 and 13.10% in population 3(Admixture) with 64.07% as overall cumulative percentage of variation. This indicates that extensive short-distance gene flow occurs in Kashmir region that dispersal over longer distances also appears to occur frequently enough to prevent differentiation due to genetic drift. Also it is evident that Jammu and Kashmir most likely has V. inaequalis subpopulations linked to diverse climatic conditions of the Jammu region compared to the mountainous inland Kashmir region. The results of present study would help to understand the genetic diversity of V. inaequalis from Jammu and Kashmir that would lead in the development of more effective management strategies and development of new resistant cultivars through marker-assisted selection.
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Liu L, Guo Z, Zhong C, Shi S. DNA barcoding reveals insect diversity in the mangrove ecosystems of Hainan Island, China. Genome 2018; 61:797-806. [PMID: 30398899 DOI: 10.1139/gen-2018-0062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Insect diversity is an indicator of environmental conditions. Frequent outbreaks of mangrove pests have threatened the fragile mangrove ecosystem in China and the sustainable utilization of mangrove resources. The understanding of mangrove pests, as well as a fundamental knowledge of insect diversity, in mangrove forests in China has been hindered by the difficulty of morphological species delimitation because captured insect specimens are either larvae or incompletely preserved adults. DNA barcoding technology uses only a small amount of DNA to conduct species identification. Taking advantage of this, we investigated the entomofauna of mangrove forests on Hainan Island by using a barcode combining cytochrome c oxidase subunit I (COI) and cytochrome-b (Cytb). We collected 627 specimens at six localities around the island, which were identified as 219 insect species belonging to 11 orders and 72 families. Lepidoptera, Coleoptera, and Hymenoptera are the most species-rich and abundant taxa. We also identified 13 mangrove pests, 5 parasitoids, and 12 species of predators.
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Affiliation(s)
- Lu Liu
- a State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zixiao Guo
- a State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Cairong Zhong
- b Hainan Dongzhai Harbor National Nature Reserve, Haikou, Hainan, China
| | - Suhua Shi
- a State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Dormontt EE, van Dijk KJ, Bell KL, Biffin E, Breed MF, Byrne M, Caddy-Retalic S, Encinas-Viso F, Nevill PG, Shapcott A, Young JM, Waycott M, Lowe AJ. Advancing DNA Barcoding and Metabarcoding Applications for Plants Requires Systematic Analysis of Herbarium Collections—An Australian Perspective. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00134] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Song C, Lin XL, Wang Q, Wang XH. DNA barcodes successfully delimit morphospecies in a superdiverse insect genus. ZOOL SCR 2018. [DOI: 10.1111/zsc.12284] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Chao Song
- College of Life Sciences; Nankai University; Tianjin China
| | - Xiao-Long Lin
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
| | - Qian Wang
- Tianjin key Laboratory of Aqua-Ecology & Aquaculture; Fisheries of College; Tianjin Agricultural University; Tianjin China
| | - Xin-Hua Wang
- College of Life Sciences; Nankai University; Tianjin China
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