1
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Bolek MG, Detwiler JT, Stigge HA. Selected Wildlife Trematodes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1454:391-440. [PMID: 39008272 DOI: 10.1007/978-3-031-60121-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The trematodes are a species-rich group of parasites, with some estimates suggesting that there are more than 24,000 species. However, the complexities associated with their taxonomic status and nomenclature can hinder explorations of the biology of wildlife trematodes, including fundamental aspects such as host use, life cycle variation, pathology, and disease. In this chapter, we review work on selected trematodes of amphibians, birds, mammals, and their snail intermediate hosts, with the goal of providing a tool kit on how to study trematodes of wildlife. We provide a brief introduction to each group of wildlife trematodes, followed by some examples of the challenges each group of trematodes has relative to the goal of their identification and understanding of the biology and interactions these organisms have with their wildlife hosts.
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Affiliation(s)
- Matthew G Bolek
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA.
| | - Jillian T Detwiler
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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2
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Zou S. Comparative Transcriptome Analysis of Toxic and Non-Toxic Nassarius Communities and Identification of Genes Involved in TTX-Adaptation. Toxins (Basel) 2020; 12:toxins12120761. [PMID: 33276679 PMCID: PMC7761612 DOI: 10.3390/toxins12120761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023] Open
Abstract
Nassarius has caused serious people poisoning and death incident as a popular food due to tetrodotoxin (TTX) accumulation in their body. Understanding the genetic basis of tetrodotoxin (TTX) transformation and resistance in animals could lead to significant insights into adaptive evolution to toxins and toxin poisoning cures in medicine. Here we performed comparative transcriptome analysis for toxic and non-toxic communities in Nassarius succinctus and Nassarius variciferus to reveal their genetic expression and mutation patterns. For both species, the cellular and metabolic process, and binding and catalytic activity accounted for the top classification categories, and the toxic communities generally produced more up-regulated genes than non-toxic communities. Most unigenes and different expression genes were related to disease, e.g., heat shock protein and tissue factor pathway inhibitors, which involve detoxification and coagulation. In mutation levels, the sodium channel gene of N. succinctus had one amino acid mutation "L", which is different from that of other animals. In conclusion, the comparative transcriptome analysis of different species and populations provided an important genetic basis for adaptive evolution to toxins, health and toxin poisoning cure research for TTX in marine gastropoda mollusk. Future studies will focus on the action mechanism of the important functional gene for TTX accumulation and resistance.
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Affiliation(s)
- Shanmei Zou
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, China
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3
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Yang Y, Liu H, Qi L, Kong L, Li Q. Complete Mitochondrial Genomes of Two Toxin-Accumulated Nassariids (Neogastropoda: Nassariidae: Nassarius) and Their Implication for Phylogeny. Int J Mol Sci 2020; 21:ijms21103545. [PMID: 32429583 PMCID: PMC7278921 DOI: 10.3390/ijms21103545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/17/2022] Open
Abstract
The Indo-Pacific nassariids (genus Nassarius) possesses the highest diversity within the family Nassariidae. However, the previous shell or radula-based classification of Nassarius is quite confusing due to the homoplasy of certain morphological characteristics. The toxin accumulators Nassarius glans and Nassarius siquijorensis are widely distributed in the subtidal regions of the Indo-Pacific Ocean. In spite of their biological significance, the phylogenetic positions of N. glans and N. siquijorensis are still undetermined. In the present study, the complete mitochondrial genomes of N. glans and N. siquijorensis were sequenced. The present mitochondrial genomes were 15,296 and 15,337 bp in length, respectively, showing negative AT skews and positive GC skews as well as a bias of AT rich on the heavy strand. They contained 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and several noncoding regions, and their gene order was identical to most caenogastropods. Based on the nucleotide sequences combining 13 protein coding genes and two rRNA genes, a well-supported phylogeny of Nassarius was reconstructed, and several morphological synapomorphies were observed corresponding to the phylogenetic framework. In addition, the sister group relationship between N. variciferus and the remaining toxin-accumulated nassariids was determined, suggesting that the phylogeny might be related to their diet. The divergence time estimation analysis revealed a correlation between speciation events of nassariids and glacial cycles during the Pliocene-Pleistocene epoch.
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Affiliation(s)
- Yi Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Y.Y.); (H.L.); (L.Q.); (L.K.)
| | - Hongyue Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Y.Y.); (H.L.); (L.Q.); (L.K.)
| | - Lu Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Y.Y.); (H.L.); (L.Q.); (L.K.)
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Y.Y.); (H.L.); (L.Q.); (L.K.)
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Y.Y.); (H.L.); (L.Q.); (L.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei Town, Qingdao 266237, China
- Correspondence: ; Tel.: +86-532-8203-2773
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4
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Yang Y, Li Q, Kong L, Yu H. Mitogenomic phylogeny of
Nassarius
(Gastropoda: Neogastropoda). ZOOL SCR 2019. [DOI: 10.1111/zsc.12343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yi Yang
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
- Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
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5
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Gong S, Ding Y, Wang Y, Jiang G, Zhu C. Advances in DNA Barcoding of Toxic Marine Organisms. Int J Mol Sci 2018; 19:E2931. [PMID: 30261656 PMCID: PMC6213214 DOI: 10.3390/ijms19102931] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/28/2018] [Accepted: 09/20/2018] [Indexed: 01/10/2023] Open
Abstract
There are more than 200,000 marine species worldwide. These include many important economic species, such as large yellow croaker, ribbonfish, tuna, and salmon, but also many potentially toxic species, such as blue-green algae, diatoms, cnidarians, ctenophores, Nassarius spp., and pufferfish. However, some edible and toxic species may look similar, and the correct identification of marine species is thus a major issue. The failure of traditional classification methods in certain species has promoted the use of DNA barcoding, which uses short, standard DNA fragments to assist with species identification. In this review, we summarize recent advances in DNA barcoding of toxic marine species such as jellyfish and pufferfish, using genes including cytochrome oxidase I gene (COI), cytochrome b gene (cytb), 16S rDNA, internal transcribed spacer (ITS), and Ribulose-1,5-bisphosphate carboxylase oxygenase gene (rbcL). We also discuss the application of this technique for improving the identification of marine species. The use of DNA barcoding can benefit the studies of biological diversity, biogeography, food safety, and the detection of both invasive and new species. However, the technique has limitations, particularly for the analysis of complex objects and the selection of standard DNA barcodes. The development of high-throughput methods may offer solutions to some of these issues.
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Affiliation(s)
- Shaohua Gong
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Yanfei Ding
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Yi Wang
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Guangze Jiang
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Cheng Zhu
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
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6
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Yang Y, Li Q, Kong L, Yu H. Comparative mitogenomic analysis reveals cryptic species in Reticunassa festiva (Neogastropoda: Nassariidae). Gene 2018; 662:88-96. [DOI: 10.1016/j.gene.2018.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/24/2018] [Accepted: 04/03/2018] [Indexed: 11/29/2022]
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7
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Bioactive Compounds Isolated from Neglected Predatory Marine Gastropods. Mar Drugs 2018; 16:md16040118. [PMID: 29621159 PMCID: PMC5923405 DOI: 10.3390/md16040118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/21/2018] [Accepted: 03/29/2018] [Indexed: 12/19/2022] Open
Abstract
A diverse range of predatory marine gastropods produce toxins, yet most of these molecules remain uncharacterized. Conus species have received the most attention from researchers, leading to several conopeptides reaching clinical trials. This review aims to summarize what is known about bioactive compounds isolated from species of neglected marine gastropods, especially in the Turridae, Terebridae, Babyloniidae, Muricidae, Buccinidae, Colubrariidae, Nassariidae, Cassidae, and Ranellidae families. Multiple species have been reported to contain bioactive compounds with potential toxic activity, but most of these compounds have not been characterized or even clearly identified. The bioactive properties and potential applications of echotoxins and related porins from the Ranellidae family are discussed in more detail. Finally, the review concludes with a call for research on understudied species.
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8
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Pu C, Li H, Zhu A, Chen Y, Zhao Y, Zhan A. Phylogeography in Nassarius mud snails: Complex patterns in congeneric species. PLoS One 2017; 12:e0180728. [PMID: 28704536 PMCID: PMC5507531 DOI: 10.1371/journal.pone.0180728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022] Open
Abstract
One major goal for phylogeographical studies is to elucidate respective roles of multiple evolutionary and ecological forces that shape the current distribution patterns. In marine and coastal ecosystems, it has been generated a common realization that species with enormous population size and pelagic larval stages can disperse across broad geographical scales, leading to weak or even no phylogeographical structure across large geographical scales. However, the violation of such realization has been frequently reported, and it remains largely unexplored on mechanisms responsible for various phylogeographical patterns observed in different species at varied geographical scales. Here, we used a species-rich genus Nassarius to assess and compare phylogeographical patterns in congeneric species, and discuss causes and consequences underlying varied phylogeographical patterns. Interestingly, we observed complex phylogeographical patterns both within single species and across multiple species, and multiple analyses showed varied levels of genetic heterogeneity among sites within and across species. Available evidence suggests that related species with similar biological characteristics may not be necessary to result in consistent phylogeographical patterns. Multiple factors, including larval ecology, interactions between dispersal and natural selection, and human activity-mediated dispersal, can partially explain the complex patterns observed in this study. Deep investigations should be performed on these factors, particularly their respective roles in determining evolutionary/ecological processes to form phylogeographical patterns in species with high dispersal capacities in marine and coastal ecosystems.
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Affiliation(s)
- Chuanliang Pu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Haitao Li
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, Guangdong, China
| | - Aijia Zhu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, Guangdong, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Yan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
- * E-mail:
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9
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Zou S, Fei C, Wang C, Gao Z, Bao Y, He M, Wang C. How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae). Sci Rep 2016; 6:36822. [PMID: 27827440 PMCID: PMC5101840 DOI: 10.1038/srep36822] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/21/2016] [Indexed: 12/17/2022] Open
Abstract
Microalgae identification is extremely difficult. The efficiency of DNA barcoding in microalgae identification involves ideal gene markers and approaches employed, which however, is still under the way. Although Scenedesmus has obtained much research in producing lipids its identification is difficult. Here we present a comprehensive coalescent, distance and character-based DNA barcoding for 118 Scenedesmus strains based on rbcL, tufA, ITS and 16S. The four genes, and their combined data rbcL + tufA + ITS + 16S, rbcL + tufA and ITS + 16S were analyzed by all of GMYC, P ID, PTP, ABGD, and character-based barcoding respectively. It was apparent that the three combined gene data showed a higher proportion of resolution success than the single gene. In comparison, the GMYC and PTP analysis produced more taxonomic lineages. The ABGD generated various resolution in discrimination among the single and combined data. The character-based barcoding was proved to be the most effective approach for species discrimination in both single and combined data which produced consistent species identification. All the integrated results recovered 11 species, five out of which were revealed as potential cryptic species. We suggest that the character-based DNA barcoding together with other approaches based on multiple genes and their combined data could be more effective in microalgae diversity revelation.
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Affiliation(s)
- Shanmei Zou
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Cong Fei
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chun Wang
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhan Gao
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yachao Bao
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Meilin He
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Changhai Wang
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
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10
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Sun S, Li Q, Kong L, Yu H, Zheng X, Yu R, Dai L, Sun Y, Chen J, Liu J, Ni L, Feng Y, Yu Z, Zou S, Lin J. DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs. Sci Rep 2016; 6:33367. [PMID: 27640675 PMCID: PMC5027561 DOI: 10.1038/srep33367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/25/2016] [Indexed: 11/26/2022] Open
Abstract
This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes.
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Affiliation(s)
- Shao’e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ruihai Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lina Dai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yan Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Chen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lehai Ni
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yanwei Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhenzhen Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shanmei Zou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jiping Lin
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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11
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Zou S, Li Q. Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:327-335. [PMID: 26899167 DOI: 10.1007/s10126-016-9692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
With the global biodiversity crisis, DNA barcoding aims for fast species identification and cryptic species diversity revelation. For more than 10 years, large amounts of DNA barcode data have been accumulating in publicly available databases, most of which were conducted by distance or tree-building methods that have often been argued, especially for cryptic species revelation. In this context, overlooked cryptic diversity may exist in the available barcoding data. The character-based DNA barcoding, however, has a good chance for detecting the overlooked cryptic diversity. In this study, marine mollusk was as the ideal case for detecting the overlooked potential cryptic species from existing cytochrome c oxidase I (COI) sequences with character-based DNA barcode. A total of 1081 COI sequences of mollusks, belonging to 176 species of 25 families of Gastropoda, Cephalopoda, and Lamellibranchia, were conducted by character analysis. As a whole, the character-based barcoding results were consistent with previous distance and tree-building analysis for species discrimination. More importantly, quite a number of species analyzed were divided into distinct clades with unique diagnostical characters. Based on the concept of cryptic species revelation of character-based barcoding, these species divided into separate taxonomic groups might be potential cryptic species. The detection of the overlooked potential cryptic diversity proves that the character-based barcoding mode possesses more advantages of revealing cryptic biodiversity. With the development of DNA barcoding, making the best use of barcoding data is worthy of our attention for species conservation.
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Affiliation(s)
- Shanmei Zou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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12
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Zou S, Fei C, Song J, Bao Y, He M, Wang C. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta). PLoS One 2016; 11:e0153833. [PMID: 27092945 PMCID: PMC4841637 DOI: 10.1371/journal.pone.0153833] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/13/2016] [Indexed: 01/19/2023] Open
Abstract
Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.
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Affiliation(s)
- Shanmei Zou
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Cong Fei
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiameng Song
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yachao Bao
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Meilin He
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Changhai Wang
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
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13
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Galindo LA, Puillandre N, Utge J, Lozouet P, Bouchet P. The phylogeny and systematics of the Nassariidae revisited (Gastropoda, Buccinoidea). Mol Phylogenet Evol 2016; 99:337-353. [PMID: 27012605 DOI: 10.1016/j.ympev.2016.03.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/23/2016] [Accepted: 03/15/2016] [Indexed: 01/30/2023]
Abstract
Nassariidae are a group of scavenging, predominantly marine, snails that are diversified on soft bottoms as well as on rocky shores, and are the subject of numerous research papers in ecology, ecotoxicology or paleontology. A weak and/or apparently continuous variation in shell characters has resulted in an intimidating taxonomy, with complex synonymy lists. Over 1320 extant nominal species have been described, of which 442 are currently regarded as valid. Above species level, the state of the art is equally hazy, with four subfamilies and twelve genera currently accepted, and many other names in the graveyard of synonymy. A molecular analysis based on three mitochondrial (COI, 16S, 12S) and two nuclear (28S, H3) markers was conducted. Our dataset includes 218 putative nassariid species, comprising 9 of the 12 valid genera, and 25 nominal genera represented by their type species. The monophyly of the Nassariidae as classically construed is not confirmed. Species of Antillophos, Engoniophos, Phos, Nassaria, Tomlinia and Anentome (formerly considered Buccinidae) are included inside the Nassariidae clade. Within the Nassariinae, the tree unexpectedly demonstrates that species from the Atlantic and the Indo-Pacific form different clades which represent several independent diversification events. Through an integrative approach, the reconstruction of ancestral states was addressed for eight characters supposedly informative for taxonomy. Using numerous fossil calibration points, Nassariidae appear to have originated 120 MYA ago in Atlantic temperate waters during the Lower Cretaceous. Our results have a profound impact on nassariid taxonomy, especially with regard to the validity of subfamily- and genus-level names.
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Affiliation(s)
- Lee Ann Galindo
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 43 Rue Cuvier, F-75231 Paris, France.
| | - Nicolas Puillandre
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 43 Rue Cuvier, F-75231 Paris, France.
| | - José Utge
- UMS 2700, Museum National d'Histoire Naturelle, Département Systématique et Evolution, 43, Rue Cuvier, 75231 Paris, France; Musée de l'Homme, HNS - UMR 7206, EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, 17 place Trocadéro, 75016 Paris, France.
| | - Pierre Lozouet
- Muséum National d'Histoire Naturelle, Direction des Collections, 55, rue de Buffon, 75005 Paris, France.
| | - Philippe Bouchet
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 55 Rue Buffon, F-75231 Paris, France.
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14
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Zhang J, Chen M, Dong X, Lin R, Fan J, Chen Z. Evaluation of four commonly used DNA barcoding Loci for chinese medicinal plants of the family schisandraceae. PLoS One 2015; 10:e0125574. [PMID: 25938480 PMCID: PMC4418597 DOI: 10.1371/journal.pone.0125574] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/25/2015] [Indexed: 11/19/2022] Open
Abstract
Many species of Schisandraceae are used in traditional Chinese medicine and are faced with contamination and substitution risks due to inaccurate identification. Here, we investigated the discriminatory power of four commonly used DNA barcoding loci (ITS, trnH-psbA, matK, and rbcL) and corresponding multi-locus combinations for 135 individuals from 33 species of Schisandraceae, using distance-, tree-, similarity-, and character-based methods, at both the family level and the genus level. Our results showed that the two spacer regions (ITS and trnH-psbA) possess higher species-resolving power than the two coding regions (matK and rbcL). The degree of species resolution increased with most of the multi-locus combinations. Furthermore, our results implied that the best DNA barcode for the species discrimination at the family level might not always be the most suitable one at the genus level. Here we propose the combination of ITS+trnH-psbA+matK+rbcL as the most ideal DNA barcode for discriminating the medicinal plants of Schisandra and Kadsura, and the combination of ITS+trnH-psbA as the most suitable barcode for Illicium species. In addition, the closely related species Schisandra rubriflora Rehder & E. H. Wilson and Schisandra grandiflora Hook.f. & Thomson, were paraphyletic with each other on phylogenetic trees, suggesting that they should not be distinct species. Furthermore, the samples of these two species from the southern Hengduan Mountains region formed a distinct cluster that was separated from the samples of other regions, implying the presence of cryptic diversity. The feasibility of DNA barcodes for identification of geographical authenticity was also verified here. The database and paradigm that we provide in this study could be used as reference for the authentication of traditional Chinese medicinal plants utilizing DNA barcoding.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Min Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
- Graduate University of the Chinese Academy of Sciences, Beijing, P.R. China
| | - Xiaoyu Dong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences/Nanjing Botanical Garden Memorial Sun Yat-Sen, Nanjing, Jiangsu, P.R. China
| | - Ruozhu Lin
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, P.R. China
| | - Jianhua Fan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
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15
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Meleg IN, Zakšek V, Fišer C, Kelemen BS, Moldovan OT. Can environment predict cryptic diversity? The case of Niphargus inhabiting Western Carpathian groundwater. PLoS One 2013; 8:e76760. [PMID: 24204671 PMCID: PMC3804523 DOI: 10.1371/journal.pone.0076760] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 08/29/2013] [Indexed: 11/24/2022] Open
Abstract
In the last decade, several studies have shown that subterranean aquatic habitats harbor cryptic species with restricted geographic ranges, frequently occurring as isolated populations. Previous studies on aquatic subterranean species have implied that habitat heterogeneity can promote speciation and that speciation events can be predicted from species’ distributions. We tested the prediction that species distributed across different drainage systems and karst sectors comprise sets of distinct species. Amphipods from the genus Niphargus from 11 caves distributed along the Western Carpathians (Romania) were investigated using three independent molecular markers (COI, H3 and 28S). The results showed that: 1) the studied populations belong to eight different species that derive from two phylogenetically unrelated Niphargus clades; 2) narrow endemic species in fact comprise complexes of morphologically similar species that are indistinguishable without using a molecular approach. The concept of monophyly, concordance between mitochondrial and nuclear DNA, and the value of patristic distances were used as species delimitation criteria. The concept of cryptic species is discussed within the framework of the present work and the contribution of these species to regional biodiversity is also addressed.
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Affiliation(s)
- Ioana Nicoleta Meleg
- Emil Racoviţă Institute of Speleology, Romanian Academy, Cluj-Napoca, Romania
- * E-mail:
| | - Valerija Zakšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Beatrice Simona Kelemen
- Babeş-Bolyai University, Interdisciplinary Research Institute on Bio-Nano-Sciences, Molecular Biology Center, Cluj-Napoca, Romania
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16
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Barco A, Houart R, Bonomolo G, Crocetta F, Oliverio M. Molecular data reveal cryptic lineages within the northeastern Atlantic and Mediterranean small mussel drills of theOcinebrina edwardsiicomplex (Mollusca: Gastropoda: Muricidae). Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12069] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Barco
- Department of Biology and Biotechnology ‘C. Darwin’; University of Rome ‘La Sapienza’; Viale dell'Università 32 I-00185 Rome Italy
| | - Roland Houart
- Belgian Royal Institute of Natural Sciences; Rue Vautier, 29 B-1000 Bruxelles Belgium
| | | | - Fabio Crocetta
- Stazione Zoologica Anton Dohrn; Villa Comunale I-80121 Napoli Italy
| | - Marco Oliverio
- Department of Biology and Biotechnology ‘C. Darwin’; University of Rome ‘La Sapienza’; Viale dell'Università 32 I-00185 Rome Italy
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