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Dai W, Leng H, Li J, Li A, Li Z, Zhu Y, Li X, Jin L, Sun K, Feng J. The role of host traits and geography in shaping the gut microbiome of insectivorous bats. mSphere 2024; 9:e0008724. [PMID: 38509042 PMCID: PMC11036801 DOI: 10.1128/msphere.00087-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The gut microbiome is a symbiotic microbial community associated with the host and plays multiple important roles in host physiology, nutrition, and health. A number of factors have been shown to influence the gut microbiome, among which diet is considered to be one of the most important; however, the relationship between diet composition and gut microbiota in wild mammals is still not well recognized. Herein, we characterized the gut microbiota of bats and examined the effects of diet, host taxa, body size, gender, elevation, and latitude on the gut microbiota. The cytochrome C oxidase subunit I (COI) gene and 16S rRNA gene amplicons were sequenced from the feces of eight insectivorous bat species in southern China, including Miniopterus fuliginosus, Aselliscus stoliczkanus, Myotis laniger, Rhinolophus episcopus, Rhinolophus osgoodi, Rhinolophus ferrumequinum, Rhinolophus affinis, and Rhinolophus pusillus. The results showed that the composition of gut microbiome and diet exhibited significant differences among bat species. Diet composition and gut microbiota were significantly correlated at the order, family, genus, and operational taxonomic unit levels, while certain insects had a marked effect on the gut microbiome at specific taxonomic levels. In addition, elevation, latitude, body weight of bats, and host species had significant effects on the gut microbiome, but phylosymbiosis between host phylogeny and gut microbiome was lacking. These findings clarify the relationship between gut microbiome and diet and contribute to improving our understanding of host ecology and the evolution of the gut microbiome in wild mammals. IMPORTANCE The gut microbiome is critical for the adaptation of wildlife to the dynamic environment. Bats are the second-largest group of mammals with short intestinal tract, yet their gut microbiome is still poorly studied. Herein, we explored the relationships between gut microbiome and food composition, host taxa, body size, gender, elevation, and latitude. We found a significant association between diet composition and gut microbiome in insectivorous bats, with certain insect species having major impacts on gut microbiome. Factors like species taxa, body weight, elevation, and latitude also affected the gut microbiome, but we failed to detect phylosymbiosis between the host phylogeny and the gut microbiome. Overall, our study presents novel insights into how multiple factors shape the bat's gut microbiome together and provides a study case on host-microbe interactions in wildlife.
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Affiliation(s)
- Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jun Li
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Aoqiang Li
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhongle Li
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Yue Zhu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Xiaolin Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Life Science, Jilin Agricultural University, Changchun, China
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Archidona-Yuste A, Clavero-Camacho I, Ruiz-Cuenca AN, Cantalapiedra-Navarrete C, Liebanas G, Castillo P, Palomares-Rius JE. The more we search, the more we find: discovering and expanding the biodiversity in the ring nematode genus Xenocriconemella De Grisse and Loof, 1965 (Nematoda: Criconematidae). ZOOLOGICAL LETTERS 2024; 10:8. [PMID: 38528566 DOI: 10.1186/s40851-024-00230-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024]
Abstract
The ring nematode genus Xenocriconemella De Grisse and Loof, 1965 comprises only one nominal species, Xenocriconemella macrodora (Taylor, 1936) De Grisse and Loof, 1965. The initial objective of the present study was to investigate the morphological-morphometric and molecular diversity of 28 X. macrodora populations in the Iberian Peninsula associated with tree forests (mainly Quercus spp.). However, a detailed integrative taxonomic analysis (morphological-morphometric and molecular data) from each population and analysis of this data using principal component analysis (PCA) for morphometric data (including these 28 populations and other 25 X. macrodora populations around the world) and molecular and phylogenetic species delimitation methods revealed that X. macrodora forms a species complex. This species complex is composed by species that are morphometricly and morphologically similar, but clearly different at the molecular level. Three new species are described applying integrative taxonomy, namely as Xenocriconemella iberica sp. nov., Xenocriconemella paraiberica sp. nov. and Xenocriconemella pradense sp. nov. However, the molecular diversity of this species in USA and Italy confirmed that additional species are likely present in this species complex, and the diversity of this group may be higher than expected. The study of X. macrodora topotypes can clarify the position of this species using molecular markers under an integrative approach.
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Affiliation(s)
- A Archidona-Yuste
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain.
| | - I Clavero-Camacho
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
| | - A N Ruiz-Cuenca
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
- Department of Animal, Plant Biology and Ecology, University of Jaén, Campus Las Lagunillas, Jaén, Spain
| | - C Cantalapiedra-Navarrete
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
| | - G Liebanas
- Department of Animal, Plant Biology and Ecology, University of Jaén, Campus Las Lagunillas, Jaén, Spain
| | - P Castillo
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
| | - J E Palomares-Rius
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
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Liu ZW, Zhou J. DNA barcoding of Notopterygii Rhizoma et Radix (Qiang-huo) and identification of adulteration in its medicinal services. Sci Rep 2024; 14:2879. [PMID: 38311607 PMCID: PMC10838912 DOI: 10.1038/s41598-024-53008-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/25/2024] [Indexed: 02/06/2024] Open
Abstract
Safety concerns, stemming from the presence of complex and unpredictable adulterants, permeate the entire industrial chain of traditional Chinese medicines (TCMs). The Notopterygii Rhizoma et Radix (NReR) from the Apiaceae family, commonly known as "Qiang-huo", is a widely used herbal medicine. The recent surge in its demand has given rise to a proliferation of counterfeit and substituted products in the market. Traditional identification presents inherent limitations, while DNA mini-barcoding, reliant on sequencing a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In this study, we constructed a comprehensive Internal Transcribed Spacer 2 (ITS2) matrix encompassing genuine NReR and their commonly found adulterants for the first time. Leveraging this matrix, we conducted a thorough assessment of the genetic profiles and sources of NReR available in the Chinese herbal medicine market. Following established DNA barcoding protocols, the intra-specific genetic divergences within NReR species were found to be lower than the inter-specific genetic divergences from other species. Among the 120 samples that were successfully amplified, ITS2 exhibits an outstanding species-level identification efficiency of 100% when evaluated using both the BLASTN and neighbor-joining (NJ) tree methods. We concluded that ITS2 is a mini-barcode that has shown its potential and may become a universal mini-barcode for the quality control of "Qiang-huo", thereby ensuring the safety of clinical medication.
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Affiliation(s)
- Zhen-Wen Liu
- Yunnan Key Laboratory of Biodiversity of Gaoligong Mountain, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
- Gaoligong Mountain, Forest Ecosystem, Observation and Research Station of Yunnan Province, Kunming, 650201, China
| | - Jing Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China.
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Wang W, Chen B, Ma R, Qiao M, Fu Y. The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain. BMC PLANT BIOLOGY 2023; 23:546. [PMID: 37936056 PMCID: PMC10629101 DOI: 10.1186/s12870-023-04513-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method. RESULTS Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2 + trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2 + trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades. CONCLUSIONS The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2 + trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis.
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Affiliation(s)
- Weijie Wang
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Baixu Chen
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Ruoke Ma
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Mengji Qiao
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China.
| | - Yunlin Fu
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China.
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Lin A, Li J, Hu Y, Zhong M, Yu M, Ma N, Wei T, Luo J, Feng J. Contrasting laboratory and field outcomes of bat-moth interactions. Mol Ecol 2023; 32:5864-5876. [PMID: 37789799 DOI: 10.1111/mec.17150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
Predator-prey interactions are important but difficult to study in the field. Therefore, laboratory studies are often used to examine the outcomes of predator-prey interactions. Previous laboratory studies have shown that moth hearing and ultrasound production can help prey avoid being eaten by bats. We report here that laboratory behavioural outcomes may not accurately reflect the outcomes of field bat-moth interactions. We tested the success rates of two bat species capturing moths with distinct anti-bat tactics using behavioural experiments. We compared the results with the dietary composition of field bats using next-generation DNA sequencing. Rhinolophus episcopus and Rhinolophus osgoodi had a lower rate of capture success when hunting for moths that produce anti-bat clicks than for silent eared moths and earless moths. Unexpectedly, the success rates of the bats capturing silent eared moths and earless moths did not differ significantly from each other. However, the field bats had a higher proportion of silent eared moths than that of earless moths and that of clicking moths in their diets. The difference between the proportions of silent eared moths and earless moths in the bat diets can be explained by the difference between their abundance in bat foraging habitats. These findings suggest that moth defensive tactics, bat countertactics and moth availability collectively shape the diets of insectivorous bats. This study illustrates the importance of using a combination of behavioural experiments and molecular genetic techniques to reveal the complex interactions between predators and prey in nature.
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Affiliation(s)
- Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiqian Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Yinli Hu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Maojun Zhong
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Minglun Yu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Nina Ma
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Tingting Wei
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Jinhong Luo
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun, China
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Gruppi C, Sanzenbacher P, Balekjian K, Hagar R, Hagen S, Rayne C, Schweizer TM, Bossu CM, Cooper D, Dietsch T, Smith TB, Ruegg K, Harrigan RJ. Genetic identification of avian samples recovered from solar energy installations. PLoS One 2023; 18:e0289949. [PMID: 37672506 PMCID: PMC10482291 DOI: 10.1371/journal.pone.0289949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/30/2023] [Indexed: 09/08/2023] Open
Abstract
Renewable energy production and development will drastically affect how we meet global energy demands, while simultaneously reducing the impact of climate change. Although the possible effects of renewable energy production (mainly from solar- and wind-energy facilities) on wildlife have been explored, knowledge gaps still exist, and collecting data from wildlife remains (when negative interactions occur) at energy installations can act as a first step regarding the study of species and communities interacting with facilities. In the case of avian species, samples can be collected relatively easily (as compared to other sampling methods), but may only be able to be identified when morphological characteristics are diagnostic for a species. Therefore, many samples that appear as partial remains, or "feather spots"-known to be of avian origin but not readily assignable to species via morphology-may remain unidentified, reducing the efficiency of sample collection and the accuracy of patterns observed. To obtain data from these samples and ensure their identification and inclusion in subsequent analyses, we applied, for the first time, a DNA barcoding approach that uses mitochondrial genetic data to identify unknown avian samples collected at solar facilities to species. We also verified and compared identifications obtained by our genetic method to traditional morphological identifications using a blind test, and discuss discrepancies observed. Our results suggest that this genetic tool can be used to verify, correct, and supplement identifications made in the field and can produce data that allow accurate comparisons of avian interactions across facilities, locations, or technology types. We recommend implementing this genetic approach to ensure that unknown samples collected are efficiently identified and contribute to a better understanding of wildlife impacts at renewable energy projects.
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Affiliation(s)
- Cristian Gruppi
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Peter Sanzenbacher
- U.S. Fish and Wildlife Service, Palm Springs, California, United States of America
| | - Karina Balekjian
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Rachel Hagar
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Sierra Hagen
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Christine Rayne
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Teia M. Schweizer
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Christen M. Bossu
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Daniel Cooper
- Resource Conservation District, Santa Monica Mountains, Topanga, California, United States of America
| | - Thomas Dietsch
- U.S. Fish and Wildlife Service, Carlsbad, California, United States of America
| | - Thomas B. Smith
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
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Putt QY, Ya'cob Z, Adler PH, Chen CD, Hew YX, Izwan-Anas N, Lau KW, Sofian-Azirun M, Pham XD, Takaoka H, Low VL. From bites to barcodes: uncovering the hidden diversity of black flies (Diptera: Simuliidae) in Vietnam. Parasit Vectors 2023; 16:266. [PMID: 37545007 PMCID: PMC10405495 DOI: 10.1186/s13071-023-05892-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Prompt and precise identification of black flies (Simuliidae) is crucial, given their biting behaviour and significant impact on human and animal health. To address the challenges presented by morphology and chromosomes in black fly taxonomy, along with the limited availability of molecular data pertaining to the black fly fauna in Vietnam, this study employed DNA-based approaches. Specifically, we used mitochondrial and nuclear-encoded genes to distinguish nominal species of black flies in Vietnam. METHODS In this study, 135 mitochondrial cytochrome c oxidase subunit I (COI) sequences were established for 45 species in the genus Simulium in Vietnam, encompassing three subgenera (Gomphostilbia, Nevermannia, and Simulium), with 64 paratypes of 27 species and 16 topotypes of six species. Of these COI sequences, 71, representing 27 species, are reported for the first time. RESULTS Combined with GenBank sequences of specimens from Malaysia, Myanmar, Thailand, and Vietnam, a total of 234 DNA barcodes of 53 nominal species resulted in a 71% success rate for species identification. Species from the non-monophyletic Simulium asakoae, S. feuerborni, S. multistriatum, S. striatum, S. tuberosum, and S. variegatum species groups were associated with ambiguous or incorrect identifications. Pairwise distances, phylogenetics, and species delimitation analyses revealed a high level of cryptic diversity, with discovery of 15 cryptic taxa. The current study also revealed the limited utility of a fast-evolving nuclear gene, big zinc finger (BZF), in discriminating closely related, morphologically similar nominal species of the S. asakoae species group. CONCLUSION This study represents the first comprehensive molecular genetic analysis of the black fly fauna in Vietnam to our knowledge, providing a foundation for future research. DNA barcoding exhibits varying levels of differentiating efficiency across species groups but is valuable in the discovery of cryptic diversity.
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Affiliation(s)
- Qi Yan Putt
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
- Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Zubaidah Ya'cob
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Peter H Adler
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Chee Dhang Chen
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Yan Xin Hew
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
- Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Noor Izwan-Anas
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
- Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Koon Weng Lau
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mohd Sofian-Azirun
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Xuan Da Pham
- Research Center for Genetics and Reproductive Health, School of Medicine, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hiroyuki Takaoka
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Van Lun Low
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia.
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Kamdem MM, Ramoejane M, Voua Otomo P. Local-Scale DNA Barcoding of Afrotropical Hoverflies (Diptera: Syrphidae): A Case Study of the Eastern Free State of South Africa. INSECTS 2023; 14:692. [PMID: 37623402 PMCID: PMC10455394 DOI: 10.3390/insects14080692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023]
Abstract
The Afrotropical hoverflies remain an understudied group of hoverflies. One of the reasons for the lack of studies on this group resides in the difficulties to delimit the species using the available identification keys. DNA barcoding has been found useful in such cases of taxonomical uncertainty. Here, we present a molecular study of hoverfly species from the eastern Free State of South Africa using the mitochondrial cytochrome-c oxidase subunit I gene (COI). The identification of 78 specimens was achieved through three analytical approaches: genetic distances analysis, species delimitation models and phylogenetic reconstructions. In this study, 15 nominal species from nine genera were recorded. Of these species, five had not been previously reported to occur in South Africa, namely, Betasyrphus inflaticornis Bezzi, 1915, Mesembrius strigilatus Bezzi, 1912, Eristalinus tabanoides Jaennicke, 1876, Eristalinus vicarians Bezzi, 1915 and Eristalinus fuscicornis Karsch, 1887. Intra- and interspecific variations were found and were congruent between neighbour-joining and maximum likelihood analyses, except for the genus Allograpta Osten Sacken, 1875, where identification seemed problematic, with a relatively high (1.56%) intraspecific LogDet distance observed in Allograpta nasuta Macquart, 1842. Within the 78 specimens analysed, the assembled species by automatic partitioning (ASAP) estimated the presence of 14-17 species, while the Poisson tree processes based on the MPTP and SPTP models estimated 15 and 16 species. The three models showed similar results (10 species) for the Eristalinae subfamily, while for the Syrphinae subfamily, 5 and 6 species were suggested through MPTP and SPTP, respectively. Our results highlight the necessity of using different species delimitation models in DNA barcoding for species diagnoses.
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Affiliation(s)
- Michel Mathurin Kamdem
- Department of Zoology and Entomology, University of the Free State, Private Bag x13, Phuthaditjhaba 9866, South Africa; (M.R.); (P.V.O.)
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Archidona-Yuste A, Palomares-Rius JE, Clavero-Camacho I, Cantalapiedra-Navarrete C, Liébanas G, Castillo P. A Blind-Identification Test on Criconema annuliferum (de Man, 1921) Micoletzky, 1925 Species Complex Corroborate the Hyper-Cryptic Species Diversity Using Integrative Taxonomy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1044. [PMID: 36903905 PMCID: PMC10005498 DOI: 10.3390/plants12051044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Ring nematodes are obligate ectoparasites on crops and natural herbaceous and woody plants, and some species are of economic importance and cause damage to roots of several crops. Recent integrative taxonomical analyses recognized the existence of two cryptic species within the Criconema annuliferum morphotype in Spain. In this study, we corroborated that morphometric, morphological and a multi-locus analysis (including the ribosomal markers D2-D3 expansion segments of 28S rRNA, ITS rRNA, 18S RNA, and the mitochondrial DNA cytochrome oxidase I gene) identified a new lineage clearly separated from C. annuliferum, C. paraannuliferum and C. plesioannuliferum. The new lineage was described herein as Criconema pseudoannuliferum sp. nov., confirming that C. annuliferum species complex species complex comprises a hyper-cryptic species complex. This research analysed soil samples from the rhizosphere of maritime pine (Pinus pinaster Ait.) forests in Bermeja-Crestellina Mountain, located at the western part of Málaga province, southern Spain. The integrative taxonomical analyses revealed the occurrence of a new cryptic species identified using females, males and juveniles with detailed morphology, morphometry and molecular markers, described herein as Criconema pseudoannuliferum sp. nov. All molecular markers (D2-D3, ITS, 18S and COI) were obtained from the same individual that was also used for morphological and morphometric analyses. This research demonstrated the hidden diversity within the C. annuliferum species complex species complex can reach to four lineages under ribosomal and mitochondrial gene markers for one morphospecies group, which includes four species, viz. C. annuliferum, C. paraannuliferum, C. plesioannuliferum, and C. pseudoannuliferum sp. nov. Criconema pseudoannuliferum sp. nov. was detected in moderate soil density in two maritime pine forests (5 and 25 nematodes/500 cm3 of soil) suggesting that does not cause damage to maritime pine.
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Affiliation(s)
- Antonio Archidona-Yuste
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| | - Juan Emilio Palomares-Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| | - Ilenia Clavero-Camacho
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| | - Carolina Cantalapiedra-Navarrete
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| | - Gracia Liébanas
- Department of Animal Biology, Plant Biology and Ecology, University of Jaén, Campus ‘Las Lagunillas’ s/n, Edificio B3, 23071 Jaén, Spain
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
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Clavero-Camacho I, Palomares-Rius JE, Cantalapiedra-Navarrete C, Castillo P, Liébanas G, Archidona-Yuste A. A Proposed New Species Complex within the Cosmopolitan Ring Nematode Criconema annuliferum (de Man, 1921) Micoletzky, 1925. PLANTS (BASEL, SWITZERLAND) 2022; 11:1977. [PMID: 35956456 PMCID: PMC9370717 DOI: 10.3390/plants11151977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Ring nematodes are obligate ectoparasites on cultivated and wild herbaceous and woody plants, inhabiting many types of soil, but particularly sandy soils. This study explored the morphometrical and molecular diversity of ring nematodes resembling Criconema annuliferum in 222 soil samples from fruit crops in Spain, including almond, apricot, peach and plum, as well as populations from cultivated and wild olives, and common yew. Ring nematodes of the genus Criconema were detected in 12 samples from under Prunus spp. (5.5%), showing a low to moderate nematode soil densities in several localities from southeastern and northeastern Spain. The soil population densities of Criconema associated with Prunus spp. ranged from 1 nematode/500 cm3 of soil in apricot at Sástago (Zaragoza province) to 7950 and 42,491 nematodes/500 cm3 of soil in peach at Ricla and Calasparra (Murcia province), respectively. The integrative taxonomical analyses reveal the presence of two cryptic species identified using females, males (when available), and juveniles with detailed morphology, morphometry, and molecular markers (D2-D3, ITS, 18S, and COI), described herein as Criconema paraannuliferum sp. nov. and Criconema plesioannuliferum sp. nov. All molecular markers from each species were obtained from the same individuals, and these individuals were also used for morphological and morphometric analyses. Criconema paraannuliferum sp. nov. was found in a high soil density in two peach fields (7950 and 42,491 nematodes/500 cm3 of soil) showing the possibility of being pathogenic in some circumstances.
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Affiliation(s)
- Ilenia Clavero-Camacho
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain; (I.C.-C.); (J.E.P.-R.); (C.C.-N.); (P.C.)
| | - Juan Emilio Palomares-Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain; (I.C.-C.); (J.E.P.-R.); (C.C.-N.); (P.C.)
| | - Carolina Cantalapiedra-Navarrete
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain; (I.C.-C.); (J.E.P.-R.); (C.C.-N.); (P.C.)
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain; (I.C.-C.); (J.E.P.-R.); (C.C.-N.); (P.C.)
| | - Gracia Liébanas
- Department of Animal Biology, Plant Biology and Ecology, University of Jaén, Campus ‘Las Lagunillas’ s/n, Edificio B3, 23071 Jaén, Spain;
| | - Antonio Archidona-Yuste
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Centro Alameda del Obispo, 14004 Córdoba, Spain
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The phytogeography and genetic diversity of the weedy hydrophyte, Pistia stratiotes L. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02798-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Ecological and morphological differentiation among COI haplotype groups in the plant parasitic nematode species Mesocriconema xenoplax. J Nematol 2022; 54:20220009. [PMID: 35860518 PMCID: PMC9260820 DOI: 10.2478/jofnem-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Indexed: 11/20/2022] Open
Abstract
DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species delimitation metrics largely supported the genetic integrity of the HG. Discriminant function analysis of HG morphological traits identified stylet length, total body length, and stylet knob width as the strongest distinguishing features among the seven groups, with stylet length as the strongest single distinguishing morphological feature. Multivariate analysis identified land cover, ecoregion, and maximum temperature as predictors of 53.6% of the total variation (P = 0.001). Within land cover, HG categorized under “herbaceous,” “woody wetlands,” and “deciduous forest” were distinct in DAPC and RDA analyses and were significantly different (analysis of molecular variance P = 0.001). These results provide empirical evidence for molecular, morphological, and ecological differentiation associated with HG within the monophyletic clade that represents the species Mesocriconema xenoplax.
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Miller JP, Delicado D, García-Guerrero F, Ramos MA. Recurrent founder-event speciation across the Mediterranean likely shaped the species diversity and geographic distribution of the freshwater snail genus Mercuria Boeters, 1971 (Caenogastropoda: Hydrobiidae). Mol Phylogenet Evol 2022; 173:107524. [DOI: 10.1016/j.ympev.2022.107524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/31/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
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Salata S, Fisher BL. Taxonomic revision of the Pheidole megacephala species-group (Hymenoptera, Formicidae) from the Malagasy Region. PeerJ 2022; 10:e13263. [PMID: 35497190 PMCID: PMC9053301 DOI: 10.7717/peerj.13263] [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] [Received: 12/09/2021] [Accepted: 03/22/2022] [Indexed: 01/13/2023] Open
Abstract
Background The Malagasy Region, one of the top megadiversity regions, hosts one of the highest numbers of endemic and threatened organisms on earth. One of the most spectacular examples of ant radiation on the island has occurred in the hyperdiverse genus Pheidole. To this date, there are 135 described Madagascan Pheidole divided into 16 species-groups, and 97% of Malagasy species are endemic to the island. This study is a taxonomic revision of the Pheidole megacephala group, one of only two species-groups comprising a combination of native, endemic taxa and widely distributed introduced species. Methods The diversity of the Malagasy members of the megacephala group was assessed via application of qualitative morphological and DNA sequence data. Qualitative, external morphological characteristics (e.g., head shape, gaster sculpture, body colouration) were evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. Mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were analyzed to test the putative species previously delimited by morphological analyses. Results We recognize three species belonging to the megacephala group: P. megacephala (Fabricius, 1793), P. megatron Fischer & Fisher, 2013 and P. spinosa Forel, 1891 stat. nov. Pheidole spinosa is redescribed and elevated to the species level. The following names are recognized as junior synonyms of P. spinosa: P. megacephala scabrior Forel, 1891 syn. nov., P. picata Forel, 1891 syn. nov., P. picata gietleni Forel, 1905 syn. nov., P. picata bernhardae Emery, 1915 syn. nov., and P. decepticon Fischer & Fisher, 2013 syn. nov. The results are supplemented with an identification key to species for major workers of the megacephala group, high-resolution images for major and minor workers, and comments on the distribution and biology of all Malagasy members of the group. Our study revealed that Pheidole megacephala, a species listed among the 100 worst invasive species worldwide, occurs in both natural and disturbed sites in the Malagasy region. The two remaining members of the megacephala group, most likely endemic to this region, are also present in anthropogenic habitats and often co-occur with P. megacephala. It appears that the Malagasy members of the group are generalists and dominant in anthropogenic habitats. Additionally, we documented the presence of supermajors in colonies of P. spinosa-a phenomenon previously not known for this group.
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Affiliation(s)
- Sebastian Salata
- California Academy of Sciences, San Francisco, CA, USA,Myrmecological Laboratory, Department of Biodiversity and Evolutionary Taxonomy, University of Wroclaw, Wroclaw, Lower Silesia, Poland
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Malik S, Babbar S, Chaudhary M, Sharma S, Raina SN, Babbar SB. Authentication and deciphering interrelationships of Hippophae species using DNA barcodes. THE NUCLEUS 2022. [DOI: 10.1007/s13237-021-00382-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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16
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Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT. Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PHYTOKEYS 2022; 188:1-18. [PMID: 35095289 PMCID: PMC8758638 DOI: 10.3897/phytokeys.188.75937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Certain species within the genus Panax L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panaxvietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.
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Affiliation(s)
- Nguyen Nhat Linh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Pham Le Bich Hang
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Huynh Thi Thu Hue
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Ha Hong Hanh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Le Thi Thu Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
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Chen Q, Hu H, Zhang D. DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:764255. [PMID: 35283910 PMCID: PMC8914171 DOI: 10.3389/fpls.2022.764255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/21/2022] [Indexed: 05/10/2023]
Abstract
The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.
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Affiliation(s)
- Qi Chen
- College of Pharmacy, Dali University, Dali, China
| | - Haisu Hu
- College of Pharmacy, Dali University, Dali, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, China
- Institute of Materia Medica, Dali University, Dali, China
- *Correspondence: Dequan Zhang,
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Maloupa E, Karapatzak E, Ganopoulos I, Karydas A, Papanastasi K, Kyrkas D, Yfanti P, Nikisianis N, Zahariadis A, Kosma IS, Badeka AV, Patakioutas G, Fotakis D, Krigas N. Molecular Authentication, Phytochemical Evaluation and Asexual Propagation of Wild-Growing Rosa canina L. (Rosaceae) Genotypes of Northern Greece for Sustainable Exploitation. PLANTS (BASEL, SWITZERLAND) 2021; 10:2634. [PMID: 34961105 PMCID: PMC8704562 DOI: 10.3390/plants10122634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/19/2021] [Accepted: 11/28/2021] [Indexed: 11/23/2022]
Abstract
Dogroses belong to a taxonomically difficult genus and family and represent important phytogenetic resources associated with high ornamental, pharmaceutical-cosmetic and nutritional values, thus suggesting a potentially high exploitation merit. Triggered by these prospects, wild-growing Rosa canina populations of Greece were selected for investigation and evaluation of their potential for integrated domestication. We collected ripe rosehips from Greek native wild-growing populations (samples from seven genotypes) for phytochemical analysis (total phenolics, total flavonoids, antioxidant activity and vitamin C content), leaf samples for DNA analysis using the ITS2 sequence (nine genotypes) and fresh soft-wood stem cuttings for propagation trials (seven genotypes). After evaluation of these materials, this study reports for the first-time distinct DNA-fingerprinted genotypes from Greece with interesting phytochemical profiles mainly in terms of Vitamic C content (up to 500.22 ± 0.15 mg of ascorbic acid equivalents/100 g of sample) as well as effective asexual propagation protocols for prioritized R. canina genotypes via cuttings. The latter highlights the importance of the levels of external hormone application (2000 ppm of indole-3-butyric acid), the effect of season (highly-effective spring trials) and genotype-specific differences in rooting capacities of the studied genotypes. All inclusive, this study offers new artificially selected material of Greek native R. canina with a consolidated identity and interesting phytochemical profile. These materials are currently under ex-situ conservation for further evaluation and characterization in pilot field studies, thus facilitating its sustainable exploitation for applications in the agro-alimentary, medicinal-cosmetic, and ornamental sectors.
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Affiliation(s)
- Eleni Maloupa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, P.O. Box 60458, 57001 Thermi, Thessaloniki, Greece; (E.M.); (E.K.); (I.G.); (A.K.); (K.P.)
| | - Eleftherios Karapatzak
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, P.O. Box 60458, 57001 Thermi, Thessaloniki, Greece; (E.M.); (E.K.); (I.G.); (A.K.); (K.P.)
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, P.O. Box 60458, 57001 Thermi, Thessaloniki, Greece; (E.M.); (E.K.); (I.G.); (A.K.); (K.P.)
| | - Antonis Karydas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, P.O. Box 60458, 57001 Thermi, Thessaloniki, Greece; (E.M.); (E.K.); (I.G.); (A.K.); (K.P.)
| | - Katerina Papanastasi
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, P.O. Box 60458, 57001 Thermi, Thessaloniki, Greece; (E.M.); (E.K.); (I.G.); (A.K.); (K.P.)
| | - Dimitris Kyrkas
- Department of Agriculture, University of Ioannina, 47100 Arta, Greece; (D.K.); (P.Y.); (G.P.)
| | - Paraskevi Yfanti
- Department of Agriculture, University of Ioannina, 47100 Arta, Greece; (D.K.); (P.Y.); (G.P.)
| | - Nikos Nikisianis
- Systada General Partnership, 55133 Kalamaria, Thessaloniki, Greece;
| | | | - Ioanna S. Kosma
- Laboratory of Food Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (I.S.K.); (A.V.B.)
| | - Anastasia V. Badeka
- Laboratory of Food Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (I.S.K.); (A.V.B.)
| | - Giorgos Patakioutas
- Department of Agriculture, University of Ioannina, 47100 Arta, Greece; (D.K.); (P.Y.); (G.P.)
| | - Dimitrios Fotakis
- Forest Research Institute, Hellenic Agricultural Organization Dimitra, 57006 Vassilika, Thessaloniki, Greece;
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, P.O. Box 60458, 57001 Thermi, Thessaloniki, Greece; (E.M.); (E.K.); (I.G.); (A.K.); (K.P.)
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Mortimer K, Kongsrud JA, Willassen E. Integrative taxonomy of West African Magelona (Annelida: Magelonidae): species with thoracic pigmentation. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab070] [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]
Abstract
Abstract
Benthic samples collected during several cruises from shelf areas along the West African coast from Morocco to Angola, have highlighted a huge diversity of magelonid species (over 20 species), many of which are undescribed. The majority of samples were taken as part of two large-scale projects in the region: the Canary Current Large Marine Ecosystem project (CCLME) and the Guinea Current Large Marine Ecosystem project (GCLME). Six magelonid species bearing posterior thoracic pigmentation have been highlighted, Magelona alleni and five species new to science: Magelona fasciata sp. nov., Magelona guineensis sp. nov., Magelona mackiei sp. nov., Magelona nanseni sp. nov. and Magelona picta sp. nov. West African magelonids and comparative material from the UK and Norway have been investigated using COI, 16S and 28S markers. An integrated taxonomic approach is used to delineate species of Magelona carrying posterior thoracic pigmentation. These species from West African waters constitute a well-supported monophyletic group, with the species M. alleni being sister to the new species herein described. Our 41 COI DNA-barcode-sequences had between species distances from 9.3 to 26.8% and were allocated to ten different BINs in Boldsystems.org.
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Affiliation(s)
- Kate Mortimer
- Department of Natural Sciences, Amgueddfa Cymru — National Museum Wales, Cathays Park, Cardiff CF10 3NP, Wales, UK
| | - Jon Anders Kongsrud
- Department of Natural History, University Museum of Bergen, P.O. Box 7800, N-5020 Bergen, Norway
| | - Endre Willassen
- Department of Natural History, University Museum of Bergen, P.O. Box 7800, N-5020 Bergen, Norway
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Yanaso S, Phrutivorapongkul A, Hongwiset D, Piyamongkol S, Intharuksa A. Verification of Thai ethnobotanical medicine "Kamlang Suea Khrong" driven by multiplex PCR and powerful TLC techniques. PLoS One 2021; 16:e0257243. [PMID: 34534243 PMCID: PMC8448358 DOI: 10.1371/journal.pone.0257243] [Citation(s) in RCA: 2] [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: 03/31/2021] [Accepted: 08/26/2021] [Indexed: 11/18/2022] Open
Abstract
Kamlang Suea Khrong (KSK) crude drug, a traditional Thai medicine used for oral tonic and analgesic purposes, is obtained from three origins: the inner stem bark of Betula alnoides (BA) or the stems of Strychnos axillaris (SA) or Ziziphus attopensis (ZA). According to the previous reports, SA contains strychnine-type alkaloids that probably cause poisoning; however, only organoleptic approaches are insufficient to differentiate SA from the other plant materials. To ensure the botanical origin of KSK crude drug, powerful and reliable tools are desperately needed. Therefore, molecular and chemical identification methods, DNA barcoding and thin-layer chromatography (TLC), were investigated. Reference databases, i.e., the ITS region and phytochemical profile of the authentic plant species, were conducted. In case of molecular analysis, multiplex polymerase chain reaction (PCR) based on species-specific primers was applied. Regarding species-specific primers designation, the suitability of three candidate barcode regions (ITS, ITS1, and ITS2) was evaluated by genetic distance using K2P model. ITS2 presented the highest interspecific variability was verified its discrimination power by tree topology. Accordingly, ITS2 was used to create primers that successfully specified plant species of authentic samples. For chemical analysis, TLC with toluene:ethyl acetate:ammonia (1:9:0.025) and hierarchical clustering were operated to identify the authentic crude drugs. The developed multiplex PCR and TLC methods were then applied to identify five commercial KSK crude drugs (CK1-CK5). Both methods correspondingly indicated that CK1-CK2 and CK3-CK5 were originated from BA and ZA, respectively. Molecular and chemical approaches are convenient and effective identification methods that can be performed for the routine quality-control of the KSK crude drugs for consumer reliance. According to chemical analysis, the results indicated BA, SA, and ZA have distinct chemical profiles, leading to differences in pharmacological activities. Consequently, further scientific investigations are required to ensure the quality and safety of Thai ethnobotanical medicine known as KSK.
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Affiliation(s)
- Suthira Yanaso
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmaceutical Sciences, Huachiew Chalermprakiet University, Bang Phli, Samutprakan, Thailand
| | - Ampai Phrutivorapongkul
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
| | - Darunee Hongwiset
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
| | - Sirivipa Piyamongkol
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
| | - Aekkhaluck Intharuksa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
- * E-mail:
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21
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Hansen S, Addison P, Benoit L, Haran JM. Barcoding pest species in a biodiversity hot-spot: the South African polyphagous broad-nosed weevils (Coleoptera, Curculionidae, Entiminae). Biodivers Data J 2021; 9:e66452. [PMID: 34257510 PMCID: PMC8263552 DOI: 10.3897/bdj.9.e66452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/09/2021] [Indexed: 11/25/2022] Open
Abstract
Polyphagous broad nosed weevils (Curculionidae: Entiminae) constitute a large and taxonomically challenging subfamily that contains economically significant agricultural pests worldwide. South Africa is a hot-spot for biodiversity and several species of indigenous and endemic genera of Entiminae have shifted on to cultivated plants, with some being phytosanitary pests. The sporadic pest status of many species (where the species has an occasional economic impact on the agricultural industry, but is not encountered often enough that is is readily recognisable by researchers and agricultural extension workers) and the presence of pest complexes and cryptic species represent an identification challenge to non-specialists. Furthermore, no comprehensive identification tools exist to identify immature stages that may be found in crops/soil. In this paper, a curated barcoding database with 70 COI sequences from 41 species (39 Entiminae, 2 Cyclominae) is initiated, to assist with the complexity of identification of species in this group.
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Affiliation(s)
- Steffan Hansen
- Stellenbosch University, Stellenbosch, South AfricaStellenbosch UniversityStellenboschSouth Africa
| | - Pia Addison
- University of Stellenbosch, Stellenbosch, South AfricaUniversity of StellenboschStellenboschSouth Africa
| | - Laure Benoit
- CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Montpellier University, Montpellier, FranceCBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Montpellier UniversityMontpellierFrance
| | - Julien M Haran
- CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Montpellier University, Montpellier, FranceCBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Montpellier UniversityMontpellierFrance
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22
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Rossi G, Plazzi F, Zuffi G, Marchi A, De Bonis S, Valli M, Marinšek P, Falconi R. Mitochondrial phylogeny and taxonomic revision of Italian and Slovenian fluvio-lacustrine barbels, Barbus sp. (Cypriniformes, Cyprinidae). BMC ZOOL 2021; 6:8. [PMID: 37170173 PMCID: PMC10127354 DOI: 10.1186/s40850-021-00073-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Barbels are ray finned cyprinid fishes of the Old-World with partially unresolved, intricate taxonomy. Within the Barbus sensu lato paraphyletic assemblage, Barbus sensu stricto is a monophyletic tetraploid lineage of Europe, northern Africa and Middle East, including two monophyletic sibling genera: Barbus and Luciobarbus. Italy, Slovenia and northern Croatia are natively inhabited by several entities of the genus Barbus, whose relationships and taxonomic ranks are still unclear. Aim of the present work is to focus on phylogeography of Italian and Slovenian barbels, with an appraisal of their current taxonomy.
Results
One hundred fifty specimens were collected in 78 sampling sites from 33 main watersheds, widely distributed along Italian and Slovenian ichthyogeographic districts. We amplified two mitochondrial markers, cytochrome b (cytb) and control region (D-loop), to infer a robust phylogeny for our sample and investigate on species delimitation.
Our results strongly indicate all Italian and Adriatic Slovenian fluvio-lacustrine barbels to be comprised into at least three distinct species. We provide a proposal of taxonomic revision and a list of synonymies for two of them and a new description under the International Code of Zoological Nomenclature rules for the third one.
Conclusions
If nuclear data will confirm our findings, at least three specific entities should be acknowledged across our sampling area. Namely, the three species are (i) Barbus plebejus, in the Padano-Venetian district; (ii) Barbus tyberinus, in the Tuscany-Latium district; (iii) Barbus oscensis Rossi & Plazzi sp. nov., in the Tyrrhenian and southernmost-Adriatic parts of Apulia-Campania district. Finally, we briefly discuss the implications of such a taxonomic scenario on conservation policies.
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D'Ercole J, Dincă V, Opler PA, Kondla N, Schmidt C, Phillips JD, Robbins R, Burns JM, Miller SE, Grishin N, Zakharov EV, DeWaard JR, Ratnasingham S, Hebert PDN. A DNA barcode library for the butterflies of North America. PeerJ 2021; 9:e11157. [PMID: 33976967 PMCID: PMC8061581 DOI: 10.7717/peerj.11157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.
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Affiliation(s)
- Jacopo D'Ercole
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Paul A Opler
- Colorado State University, Fort Collins, CO, United States of America
| | | | - Christian Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food, Guelph, Ontario, Canada
| | - Jarrett D Phillips
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,School of Computer Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert Robbins
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - John M Burns
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - Scott E Miller
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States of America.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States of America
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jeremy R DeWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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van Bemmelen van der Plaat A, van Treuren R, van Hintum TJL. Reliable genomic strategies for species classification of plant genetic resources. BMC Bioinformatics 2021; 22:173. [PMID: 33789577 PMCID: PMC8011391 DOI: 10.1186/s12859-021-04018-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 02/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To address the need for easy and reliable species classification in plant genetic resources collections, we assessed the potential of five classifiers (Random Forest, Neighbour-Joining, 1-Nearest Neighbour, a conservative variety of 3-Nearest Neighbours and Naive Bayes) We investigated the effects of the number of accessions per species and misclassification rate on classification success, and validated theirs generic value results with three complete datasets. RESULTS We found the conservative variety of 3-Nearest Neighbours to be the most reliable classifier when varying species representation and misclassification rate. Through the analysis of the three complete datasets, this finding showed generic value. Additionally, we present various options for marker selection for classification taks such as these. CONCLUSIONS Large-scale genomic data are increasingly being produced for genetic resources collections. These data are useful to address species classification issues regarding crop wild relatives, and improve genebank documentation. Implementation of a classification method that can improve the quality of bad datasets without gold standard training data is considered an innovative and efficient method to improve gene bank documentation.
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Affiliation(s)
| | - Rob van Treuren
- Centre for Genetic Resources, Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Theo J L van Hintum
- Centre for Genetic Resources, Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
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Csősz S, Loss AC, Fisher BL. Taxonomic revision of the Malagasy Aphaenogaster swammerdami group (Hymenoptera: Formicidae). PeerJ 2021; 9:e10900. [PMID: 33717685 PMCID: PMC7934650 DOI: 10.7717/peerj.10900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/13/2021] [Indexed: 11/20/2022] Open
Abstract
Background Madagascar is famous for its extremely rich biodiversity; the island harbors predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Continuing ongoing efforts to inventory the Malagasy ant fauna, we revise the species currently placed in the myrmicine genus Aphaenogaster Mayr. One species described from Madagascar, Aphaenogaster friederichsi Forel, is synonymized with the Palearctic A. subterranea Latreille syn. nov. This species is considered neither native to Madagascar nor established in the region. This revision focuses on the balance of species in the A. swammerdami group which are all endemic to Madagascar. Methods The diversity of the Malagasy Aphaenogaster fauna was assessed via application of multiple lines of evidence involving quantitative morphometric, qualitative morphological, and DNA sequence data. (1) Morphometric investigation was based on hypothesis-free Nest Centroid clustering (NC-clustering) combined with PArtitioning based on Recursive Thresholding (PART) to estimate the number of morphological clusters and determine the most probable boundaries between them. This protocol provides a repeatable and testable approach to find patterns in continuous morphometric data. Species boundaries and the reliability of morphological clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). (2) Qualitative, external morphological characteristics (e.g., shape, coloration patterns, setae number) were subjectively evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. (3) Species delimitation analyses based on mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were carried out to test the putative species previously delimited by morphological and morphometric analyses. Results Five species can be inferred based on the integrated evaluation of multiple lines of evidence; of these, three are new to science: Aphaenogaster bresslerisp. n., A. gonacantha (Emery, 1899), A. makaysp. n., A. sahafinasp. n., and A. swammerdamiForel, 1886. In addition, three new synonymies were found for A. swammerdami Forel, 1886 (A. swammerdami clara Santschi, 1915 syn. n., A. swammerdami curta Forel, 1891 syn. n. and A. swammerdami spinipes Santschi, 1911 syn. n.). Descriptions and redefinitions for each taxon and an identification key for their worker castes using qualitative traits and morphometric data are given. Geographic maps depicting species distributions and biological information regarding nesting habits for the species are also provided.
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Affiliation(s)
- Sandor Csősz
- Evolutionary Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | - Ana C Loss
- National Institute of the Atlantic Forest, Santa Teresa, Brazil
| | - Brian L Fisher
- Entomology, California Academy of Sciences, San Francisco, CA, USA
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Lv YN, Yang CY, Shi LC, Zhang ZL, Xu AS, Zhang LX, Li XL, Li HT. Identification of medicinal plants within the Apocynaceae family using ITS2 and psbA-trnH barcodes. Chin J Nat Med 2021; 18:594-605. [PMID: 32768166 DOI: 10.1016/s1875-5364(20)30071-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Indexed: 02/02/2023]
Abstract
To ensure the safety of medications, it is vital to accurately authenticate species of the Apocynaceae family, which is rich in poisonous medicinal plants. We identified Apocynaceae species by using nuclear internal transcribed spacer 2 (ITS2) and psbA-trnH based on experimental data. The identification ability of ITS2 and psbA-trnH was assessed using specific genetic divergence, BLAST1, and neighbor-joining trees. For DNA barcoding, ITS2 and psbA-trnH regions of 122 plant samples of 31 species from 19 genera in the Apocynaceae family were amplified. The PCR amplification for ITS2 and psbA-trnH sequences was 100%. The sequencing success rates for ITS2 and psbA-trnH sequences were 81% and 61%, respectively. Additional data involved 53 sequences of the ITS2 region and 38 sequences of the psbA-trnH region were downloaded from GenBank. Moreover, the analysis showed that the inter-specific divergence of Apocynaceae species was greater than its intra-specific variations. The results indicated that, using the BLAST1 method, ITS2 showed a high identification efficiency of 97% and 100% of the samples at the species and genus levels, respectively, via BLAST1, and psbA-trnH successfully identified 95% and 100% of the samples at the species and genus levels, respectively. The barcode combination of ITS2/psbA-trnH successfully identified 98% and 100% of samples at the species and genus levels, respectively. Subsequently, the neighbor joining tree method also showed that barcode ITS2 and psbA-trnH could distinguish among the species within the Apocynaceae family. ITS2 is a core barcode and psbA-trnH is a supplementary barcode for identifying species in the Apocynaceae family. These results will help to improve DNA barcoding reference databases for herbal drugs and other herbal raw materials.
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Affiliation(s)
- Ya-Na Lv
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Chun-Yong Yang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Lin-Chun Shi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zhong-Lian Zhang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - An-Shun Xu
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Li-Xia Zhang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xue-Lan Li
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Hai-Tao Li
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Damian D, Damas M, Wensman JJ, Berg M. Genetic Relationship Between Hard Ticks ( Ixodidae) Infesting Cattle from Select Areas of a Wildlife-Livestock Interface Ecosystem at Mikumi National Park, Tanzania. Vector Borne Zoonotic Dis 2021; 21:191-199. [PMID: 33450167 DOI: 10.1089/vbz.2020.2706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: There has recently been a substantial increase in the number of tick species and tick-borne infectious agents in Tanzania. Owing to their impact on human, livestock, and wild animal health, increased knowledge of ticks is needed. So far, no published data on the genetic relationship between hard tick (Ixodidae) sequences collected from cattle are available in Tanzania. Methods: Ticks from cattle in the wards, which lie at the border of Mikumi National Park, were collected in the dry season, November to December 2019. Morphological identification of ticks was initially performed at the genus level. To identify ticks at the species level, molecular analysis based on the 16S rRNA gene was performed. Evolutionary relationships and genetic distances between ticks were determined using MaximumLikelihood and Kimura 2-parameter methods, respectively. Results: Based on morphology, two genera (Rhipicephalus and Hyalomma) were identified in the 630 adult ticks collected from a total of 252 cattle. Six species (Rhipicephalus microplus, Rhipicephalus evertsi, Hyalomma marginatum, Hyalomma rufipes, Hyalomma truncatum, and Hyalomma turanicum) were confirmed by BLASTn and phylogenetic analyses. Considerable mean and pairwise genetic distances were observed for Rhipicephalus and Hyalomma genera. Conclusion: The presence of different phylogenetic clusters and considerable mean and pairwise genetic distances observed reflect possible biological diversity of hard ticks present in the study area. Considering the value of the cattle in the livelihoods and economies of people and the country, the outcomes of this study will be useful in planning integrated control strategies for ticks and tick-borne diseases in Tanzania.
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Affiliation(s)
- Donath Damian
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, United Republic of Tanzania
| | - Modester Damas
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, United Republic of Tanzania
| | - Jonas Johansson Wensman
- Section of Ruminant Medicine, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Burgar JM, Hitchen Y, Prince J. Effectiveness of bat boxes for bat conservation and insect suppression in a Western Australian urban riverine reserve. AUSTRAL ECOL 2020. [DOI: 10.1111/aec.12980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Yvette Hitchen
- School of Biological Sciences The University of Western Australia Crawley Western AustraliaAustralia
- Helix Molecular Solutions Leederville Western Australia Australia
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Jakoby G, Rog I, Megidish S, Klein T. Enhanced root exudation of mature broadleaf and conifer trees in a Mediterranean forest during the dry season. TREE PHYSIOLOGY 2020; 40:1595-1605. [PMID: 32705136 DOI: 10.1093/treephys/tpaa092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/19/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Root exudates are part of the rhizodeposition process, which is the major source of soil organic carbon (C) released by plant roots. This flux of C is believed to have profound effects on C and nutrient cycling in ecosystems. The quantity of root exudates depends on the plant species, the period throughout the year, and external biotic and abiotic factors. Since root exudates of mature trees are difficult to collect in field conditions, very little is known about their flux, especially in water-limited ecosystems, such as the seasonally hot and dry Mediterranean maquis. Here, we collected exudates from DNA-identified roots in the forest from the gymnosperm Cupressus sempervirens L. and the evergreen angiosperm Pistacia lentiscus L. by 48-h incubations on a monthly temporal resolution throughout the year. We examined relationships of the root exudate C flux to abiotic parameters of the soil (water content, water potential, temperature) and atmosphere (vapor pressure deficit, temperature). We also studied relationships to C fluxes through the leaves as indicators of tree C balance. Root exudation rates varied significantly along the year, increasing from 6 μg C cm -2 root day-1 in both species in the wet season to 4- and 11-fold rates in Pistacia and Cupressus, respectively, in the dry season. A stepwise linear mixed-effects model showed that the three soil parameters were the most influential on exudation rates. Among biotic factors, there was a significant negative correlation of exudation rate with leaf assimilation in Cupressus and a significant negative correlation with leaf respiration in Pistacia. Our observation of enhanced exudation flux during the dry season indicates that exudation dynamics in the field are less sensitive to the low tree C availability in the dry season. The two key Mediterranean forest species seem to respond to seasonal changes in the rhizosphere such as drying and warming, and therefore invest C in the rhizosphere under seasonal drought.
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Affiliation(s)
- Gilad Jakoby
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ido Rog
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shacham Megidish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamir Klein
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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Dhivya S, Ashutosh S, Gowtham I, Baskar V, Harini AB, Mukunthakumar S, Sathishkumar R. Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes. BMC Genomics 2020; 21:659. [PMID: 32972362 PMCID: PMC7513480 DOI: 10.1186/s12864-020-07036-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/30/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements. RESULTS Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana. CONCLUSION Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.
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Affiliation(s)
- S Dhivya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - S Ashutosh
- Technologico de Monterrey, Centre of Bioengineering, Epigmenio Gonzalez #500, Fracc. San Pablo, Campus Queretaro, Santiago de Querétaro, Queretaro, Mexico
| | - I Gowtham
- Plant Biofarming Laboratory, DRDO-BU Centre for Life Sciences, Bharathiar University, Coimbatore, 641046, India
| | - V Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - A Baala Harini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - S Mukunthakumar
- Biotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical Botanic Garden & Research Institute, Palode, Thiruvananthapuram, Kerala, 695 562, India
| | - R Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India.
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Kolter A, Gemeinholzer B. Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases. Genome 2020; 64:265-298. [PMID: 32649839 DOI: 10.1139/gen-2019-0198] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The problem of low species-level identification rates in plants by DNA barcoding is exacerbated by the fact that reference databases are far from being comprehensive. We investigate the impact of increased sampling depth on identification success by analyzing the efficacy of established plant barcode marker sequences (rbcL, matK, trnL-trnF, psbA-trnH, ITS). Adding sequences of the same species to the reference database led to an increase in correct species assignment of +10.9% for rbcL and +19.0% for ITS. Simultaneously, erroneous identification dropped from ∼40% to ∼12.5%. Despite its evolutionary constraints, ITS showed the highest identification rate and identification gain by increased sampling effort, which makes it a very suitable marker in the planning phase of a barcode study. The limited sequence availability of trnL-trnF is problematic for an otherwise very promising plastid plant barcoding marker. Future developments in machine learning algorithms have the potential to give new impetus to plant barcoding, but are dependent on extensive reference databases. We expect that our results will be incorporated into future plans for the development of DNA barcoding reference databases and will lead to these being developed with greater depth and taxonomic coverage.
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Affiliation(s)
- Andreas Kolter
- Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany.,Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany
| | - Birgit Gemeinholzer
- Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany.,Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany
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MacDonald AM, Gibson DJ, Barta JR, Poulson R, Brown JD, Allison AB, Nemeth NM. Bayesian Phylogenetic Analysis of Avipoxviruses from North American Wild Birds Demonstrates New Insights into Host Specificity and Interspecies Transmission. Avian Dis 2020; 63:427-432. [PMID: 31967425 DOI: 10.1637/12023-010619-reg.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/11/2019] [Indexed: 11/05/2022]
Abstract
Avian pox is commonly diagnosed in a variety of North American wild and domestic birds, yet little is known about the evolutionary relationships among the causative poxviruses. This study aimed to determine the phylogenetic relationships among isolates identified in different avian host species to better characterize the host range of specific viral strains and compare the genetic variability within and between viral clades. Skin lesions grossly and microscopically consistent with poxvirus infection from 82 birds collected in Canada, the United States, and the U.S. Virgin Islands were included in this study. A total of 12 avian species were represented; the most common species sampled were wild turkeys (Meleagris gallopavo), mourning doves (Zenaida macroura), and American crows (Corvus brachyrhynchos). Poxvirus samples from these birds were genotyped using PCR that targeted the 4b core protein gene followed by amplicon sequencing. Bayesian phylogenetic analyses of these viruses, in conjunction with publicly available sequences, representing avipoxvirus strains from six continents revealed statistically significant monophyletic clades based on genetic distances of sequences within and between observed clades. Genetic variation within the fowlpox clade was low compared to the canarypox clade. Host and geographic origins of viral isolates revealed overall clustering of viral strains within avian species, with a few exceptions. No genetic differences were observed between viruses from Canada and the United States within individual species. These results are novel in their characterization and comparison of the phylogenetic relationships of poxvirus isolates in wild bird species from North America. Further, we provide new data on the level of host specificity and specific strains circulating in North America.
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Affiliation(s)
- Amanda M MacDonald
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada, NIG 2W1, .,Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada, NIG 2W1, .,These authors contributed equally to this work
| | - Daniel J Gibson
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada, NIG 2W1.,These authors contributed equally to this work
| | - John R Barta
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada, NIG 2W1
| | - Rebecca Poulson
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, GA 30602
| | - Justin D Brown
- Pennsylvania Game Commission, Animal Diagnostic Laboratory, University Park, PA 16802
| | - Andrew B Allison
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610
| | - Nicole M Nemeth
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, GA 30602
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Yang CQ, Lv Q, Zhang AB. Sixteen Years of DNA Barcoding in China: What Has Been Done? What Can Be Done? Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Weng YM, Veire BM, Dudko RY, Medeiros MJ, Kavanaugh DH, Schoville SD. Rapid speciation and ecological divergence into North American alpine habitats: the Nippononebria (Coleoptera: Carabidae) species complex. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
The climate-driven species pump hypothesis has been supported in a number of phylogeographic studies of alpine species. Climate-driven shifts in distribution, coupled with rapid demographic change, have led to strong genetic drift and lineage diversification. Although the species pump has been linked to rapid speciation in a number of studies, few studies have demonstrated that ecological divergence accompanies rapid speciation. Here we examine genetic, morphological and physiological variation in members of the ground beetle taxon Nippononebria, to test three competing hypotheses of evolutionary diversification: isolation and incomplete lineage sorting (no speciation), recent speciation without ecological divergence, or recent speciation with ecological divergence into alpine habitats. Genetic data are consistent with recent divergence, with major lineages forming in the last million years. A species tree analysis, in conjunction with morphological divergence in male reproductive traits, support the formation of three recognized Nippononebria taxa. Furthermore, both morphological and physiological traits demonstrate ecological divergence in alpine lineages, with convergent shifts in body shape and thermal tolerance breadth. This provides strong evidence that the climate-driven species pump can generate ecological novelty, though it is argued that spatial scale may be a key determinant of broader patterns of macroevolution in alpine communities.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Benton M Veire
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Roman Yu Dudko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Tomsk State University, Tomsk, Russia
| | - Matthew J Medeiros
- Urban School of San Francisco, San Francisco, CA, USA
- School of Life Sciences, University of Nevada Las Vegas, S. Maryland Parkway, Las Vegas, NV, USA
| | - David H Kavanaugh
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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Ajene IJ, Khamis FM, van Asch B, Pietersen G, Seid N, Rwomushana I, Ombura FLO, Momanyi G, Finyange P, Rasowo BA, Tanga CM, Mohammed S, Ekesi S. Distribution of Candidatus Liberibacter species in Eastern Africa, and the First Report of Candidatus Liberibacter asiaticus in Kenya. Sci Rep 2020; 10:3919. [PMID: 32127552 PMCID: PMC7054587 DOI: 10.1038/s41598-020-60712-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/11/2020] [Indexed: 01/18/2023] Open
Abstract
Huanglongbing (HLB) is a serious disease of Citrus sp. worldwide. In Africa and the Mascarene Islands, a similar disease is known as African citrus greening (ACG) and is associated with the bacterium Candidatus Liberibacter africanus (Laf). In recent years, Candidatus Liberibacter asiaticus (Las) associated with the severe HLB has been reported in Ethiopia. Thus, we aimed to identify the Liberibacter species affecting citrus, the associated vectors in Eastern Africa and their ecological distribution. We assessed the presence of generic Liberibacter in symptomatic leaf samples by quantitative PCR. Subsequently, we sequenced the 50 S ribosomal protein L10 (rplJ) gene region in samples positive for Liberibacters and identified the species by comparison with public sequence data using phylogenetic reconstruction and genetic distances. We detected generic Liberibacter in 26%, 21% and 66% of plants tested from Uganda, Ethiopia and Kenya, respectively. The rplJ sequences revealed the most prevalent Liberibacters in Uganda and Ethiopia were LafCl (22%) and Las (17%), respectively. We detected Las in Kenya for the first time from three sites in the coastal region. Finally, we modelled the potential habitat suitability of Las in Eastern Africa using MaxEnt. The projection showed large areas of suitability for the pathogen in the three countries surveyed. Moreover, the potential distribution in Eastern Africa covered important citrus-producing parts of Ethiopia, Kenya, Uganda and Tanzania, and included regions where the disease has not been reported. These findings will guide in the development of an integrated pest management strategy to ACG/HLB management in Africa.
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Affiliation(s)
- Inusa J Ajene
- International Center of Insect Physiology and Ecology, Nairobi, Kenya.,Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.,Department of Crop Protection, Faculty of Agriculture Ahmadu Bello University, Zaria, Nigeria
| | - Fathiya M Khamis
- International Center of Insect Physiology and Ecology, Nairobi, Kenya.
| | - Barbara van Asch
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Gerhard Pietersen
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | | | | | | | - Pole Finyange
- Kenya Agricultural and Livestock Research Organization, Matuga, Kenya
| | - Brenda A Rasowo
- International Center of Insect Physiology and Ecology, Nairobi, Kenya
| | | | - Samira Mohammed
- International Center of Insect Physiology and Ecology, Nairobi, Kenya
| | - Sunday Ekesi
- International Center of Insect Physiology and Ecology, Nairobi, Kenya
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Liu M, Li XW, Liao BS, Luo L, Ren YY. Species identification of poisonous medicinal plant using DNA barcoding. Chin J Nat Med 2020; 17:585-590. [PMID: 31472895 DOI: 10.1016/s1875-5364(19)30060-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 11/24/2022]
Abstract
The aim is to select a universal DNA barcode for identifying all poisonous medicinal plants in Chinese pharmacopoeia and their poisonous related species or adulterants. We chose 4 commonly used regions as candidate DNA barcodes (ITS2, psbA-trnH, matK and rbcL) and compared their identification efficiency in 106 species from 27 families and 65 genera totally. Data analysis was performed including the information of sequence alignment, inter/intra-specific genetic distance and data distribution, identification efficiency and the situation of Neighbor-Joining (NJ) phylogenetic trees. We found ITS2 sequence region had high variation, stable genetic distance and identification efficiency relatively. The topological structure of NJ phylogenetic tree showed monophyletic. Our findings show that ITS2 can be applied as a universal barcode for identifying poisonous medicinal plants in Chinese pharmacopoeia and their poisonous related species or adulterants.
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Affiliation(s)
- Miao Liu
- College of Chinese Medicine Materials, Jilin Agriculture University, Changchun 130118, China; Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xi-Wen Li
- Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Bao-Sheng Liao
- Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lu Luo
- Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yue-Ying Ren
- College of Chinese Medicine Materials, Jilin Agriculture University, Changchun 130118, China.
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Phillips JD, French SH, Hanner RH, Gillis DJ. HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves. PeerJ Comput Sci 2020; 6:e243. [PMID: 33816897 PMCID: PMC7924493 DOI: 10.7717/peerj-cs.243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/07/2019] [Indexed: 05/25/2023]
Abstract
Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5-10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.
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Affiliation(s)
| | - Steven H. French
- School of Computer Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert H. Hanner
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Daniel J. Gillis
- School of Computer Science, University of Guelph, Guelph, Ontario, Canada
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38
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Conti M, Cinget B, Vivancos J, Oudemans P, Bélanger RR. A Molecular Assay Allows the Simultaneous Detection of 12 Fungi Causing Fruit Rot in Cranberry. PLANT DISEASE 2019; 103:2843-2850. [PMID: 31469361 DOI: 10.1094/pdis-03-19-0531-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cranberry fruit rot (CFR) is arguably one of the most limiting factors of cranberry (Vaccinium macrocarpon) production throughout its growing areas. The disease is caused by a group of closely related fungi that require identification using long and cumbersome steps of isolation and microscopic observations of structural features. The objective of this study was to develop a molecular assay to simultaneously detect and discriminate 12 of the most important fungal species reported to be pathogenic on cranberry fruit to facilitate the diagnosis of CFR. As the first approach, internal transcribed spacers and large subunit regions of all fungi were sequenced and confirmed with sequences available in the NCBI database. These data were used to develop primers able to differentiate seven of the 12 species. The five remaining species, including three in the Phacidiaceae family and two in the Glomerellaceae family, were differentiated on the basis of a more discriminant marker, the translation elongation factor 1-α. Two PCR reactions were optimized to clearly delineate the 12 species. The multiplex test was first validated using pure fungal cultures; it was subsequently validated using fruit collected in cranberry beds in eastern Canada. In the latter case, the test was rigorous enough to clearly discriminate the fungal pathogens from contaminants. Within the tested samples, Physalospora vaccinii and Coleophoma empetri were most commonly found. This molecular test offers scientists, diagnosticians, and growers a powerful tool that can rapidly and precisely identify fungi causing CFR so they can implement appropriate control methods.
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Affiliation(s)
- Matteo Conti
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
| | - Benjamin Cinget
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
| | - Julien Vivancos
- Laboratoire d'expertise et de Diagnostic en Phytoprotection, Quebec City, Québec, Canada
| | - Peter Oudemans
- Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, The State University of New Jersey, Chatsworth, NJ, U.S.A
| | - Richard R Bélanger
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
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Silatsa BA, Simo G, Githaka N, Mwaura S, Kamga RM, Oumarou F, Keambou C, Bishop RP, Djikeng A, Kuiate JR, Njiokou F, Pelle R. A comprehensive survey of the prevalence and spatial distribution of ticks infesting cattle in different agro-ecological zones of Cameroon. Parasit Vectors 2019; 12:489. [PMID: 31623642 PMCID: PMC6796472 DOI: 10.1186/s13071-019-3738-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 10/09/2019] [Indexed: 11/10/2022] Open
Abstract
Background Ticks and tick-borne diseases are a major impediment to livestock production worldwide. Cattle trade and transnational transhumance create risks for the spread of ticks and tick-borne diseases and threaten cattle production in the absence of an effective tick control program. Few studies have been undertaken on cattle ticks in the Central African region; therefore, the need to assess the occurrence and the spatial distribution of tick vectors with the aim of establishing a baseline for monitoring future spread of tick borne-diseases in the region is urgent. Results A total of 7091 ixodid ticks were collected during a countrywide cross-sectional field survey and identified using morphological criteria. Of these, 4210 (59.4%) ticks were Amblyomma variegatum, 1112 (15.6%) Rhipicephalus (Boophilus) microplus, 708 (10.0%) Rhipicephalus (Boophilus) decoloratus, 28 (0.4%) Rhipicephalus (Boophilus) annulatus, 210 (3.0%) Hyalomma rufipes, 768 (10.8%) Hyalomma truncatum, and 19 (0.3%) Rhipicephalus sanguineus. Three ticks of the genus Hyalomma spp. and 33 of the genus Rhipicephalus spp. were not identified to the species level. Cytochrome c oxidase subunit 1 (cox1) gene sequencing supported the data from morphological examination and led to identification of three additional species, namely Hyalomma dromedarii, Rhipicephalus sulcatus and Rhipicephalus pusillus. The finding of the invasive tick species R. microplus in such large numbers and the apparent displacement of the indigenous R. decoloratus is highly significant since R. microplus is a highly efficient vector of Babesia bovis. Conclusions This study reports the occurrence and current geographical distribution of important tick vectors associated with cattle in Cameroon. It appears that R. microplus is now well established and may be displacing native Rhipicephalus (Boophilus) species, such as R. decoloratus. This calls for an urgent response to safeguard the livestock sector in western central Africa.
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Affiliation(s)
- Barberine A Silatsa
- Department of Biochemistry, Faculty of Sciences, University of Dschang, P.O. Box 67, Dschang, Cameroon. .,Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of Sciences, University of Dschang, P.O. Box 67, Dschang, Cameroon. .,Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) hub, P.O. Box 30709-00100, Nairobi, Kenya.
| | - Gustave Simo
- Department of Biochemistry, Faculty of Sciences, University of Dschang, P.O. Box 67, Dschang, Cameroon.,Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of Sciences, University of Dschang, P.O. Box 67, Dschang, Cameroon
| | - Naftaly Githaka
- Bioscience, International Livestock Research Institute (ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Stephen Mwaura
- Bioscience, International Livestock Research Institute (ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Rolin M Kamga
- Department of Biochemistry, Faculty of Sciences, University of Dschang, P.O. Box 67, Dschang, Cameroon.,Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of Sciences, University of Dschang, P.O. Box 67, Dschang, Cameroon
| | - Farikou Oumarou
- Special Mission for Eradication of Tsetse Flies, Regional Tsetse Division of Adamawa, B.P 263, Ngaoundere, Cameroon
| | - Christian Keambou
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) hub, P.O. Box 30709-00100, Nairobi, Kenya
| | - Richard P Bishop
- Veterinary Microbiology and Pathology (VMP), Washington State University, 100 Dairy Road, Pullman, WA, 99164, USA
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute & Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, EH25 9RG, UK
| | - Jules-Roger Kuiate
- Department of Biochemistry, Faculty of Sciences, University of Dschang, P.O. Box 67, Dschang, Cameroon
| | - Flobert Njiokou
- Laboratory of General Biology, Faculty of Sciences, University of Yaounde I, P.O. Box 812, Yaounde, Cameroon
| | - Roger Pelle
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) hub, P.O. Box 30709-00100, Nairobi, Kenya.
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40
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The combination of ITS2 and psbA-trnH region is powerful DNA barcode markers for authentication of medicinal Terminalia plants from Thailand. J Nat Med 2019; 74:282-293. [DOI: 10.1007/s11418-019-01365-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023]
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Wang S, Guo J, Hou F. Identification of the original species of cubilose based on DNA barcode. Mitochondrial DNA B Resour 2019; 4:3079-3082. [PMID: 33365864 PMCID: PMC7706791 DOI: 10.1080/23802359.2019.1666681] [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] [Received: 07/16/2019] [Accepted: 08/16/2019] [Indexed: 10/26/2022] Open
Abstract
Cubilose, a valuable traditional Chinese medicine, is mainly composed of the saliva by several species of Aerodramus or Collocalia in the Apodidae. Due to rarity, high economic value and huge market demand, its fake or adulteration is frequently found in the market. Therefore, it is urgent to establish a simple and accurate method for authenticating cubilose. DNA barcoding, which is an easy, quick and reliable method, is widely used to trace the origin of traditional Chinese medicine. For identifying the original species of cubilose, cytb gene of 18 cubilose samples including 15 officer cubilose and 3 feather cubilose were amplified and entered into the GenBank database using the BLAST search tool. The genetic distances among 18 cubilose samples were calculated based on the Kimura two parameter (K2P) model. To construct the reference database, 18 cytb sequences of Aerodramus or Collocalia were downloaded from GenBank. The neighbor-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) trees were constructed based on sequences from GenBank and our dataset. Blast analysis showed that all cubilose samples had the highest similarity with A. fuciphagus, and the sequence similarity reached over 99%. Genetic distance of 18 cubilose samples ranged from 0.000-0.010. Trees constructed by NJ and UPGMA gave similar topology: all cubilose samples clustered together with A. fuciphagus. These result demonstrated that the original species of all 18 cubilose samples were A. fuciphagus, and cytb gene is a good candidate for identifying cubilose.
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Affiliation(s)
- Shasha Wang
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jinlin Guo
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Feixia Hou
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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Bezeng BS, van der Bank HF. DNA barcoding of southern African crustaceans reveals a mix of invasive species and potential cryptic diversity. PLoS One 2019; 14:e0222047. [PMID: 31525221 PMCID: PMC6746381 DOI: 10.1371/journal.pone.0222047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/20/2019] [Indexed: 11/27/2022] Open
Abstract
Globally, crustaceans represent one of the most taxonomically diverse and economically important invertebrate group. Notwithstanding, the diversity within this group is poorly known because most crustaceans are often associated with varied habits, forms, sizes and habitats; making species identification by conventional methods extremely challenging. In addition, progress towards understanding the diversity within this group especially in southern Africa has been severely hampered by the declining number of trained taxonomists, the presence of invasive alien species, over exploitation, etc. However, the advent of molecular techniques such as “DNA barcoding and Metabarcoding” can accelerate species identification and the discovery of new species. To contribute to the growing body of knowledge on crustacean diversity, we collected data from five southern African countries and used a DNA barcoding approach to build the first DNA barcode reference library for southern African crustaceans. We tested the reliability of this DNA barcode reference library to facilitate species identification using two approaches. We recovered high efficacy of specimen identification/discrimination; supported by both barcode gap and tree-base species identification methods. In addition, we identified alien invasive species and specimens with ‘no ID” in our DNA barcode reference library. The later; highlighting specimens requiring (i) further investigation and/or (ii) the potential presence of cryptic diversity or (iii) misidentifications. This unique data set although with some sampling gaps presents many opportunities for exploring the effect and extent of invasive alien species, the role of the pet trade as a pathway for crustacean species introduction into novel environments, sea food authentication, phylogenetic relationships within the larger crustacean groupings and the discovery of new species.
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Affiliation(s)
- Bezeng S. Bezeng
- African Centre for DNA Barcoding, University of Johannesburg, Auckland Park, Johannesburg, South Africa
- School of Mathematics & Natural Sciences, University of Venda, P. Thohoyandou, Venda, South Africa
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Auckland Park, Johannesburg, South Africa
- * E-mail:
| | - Herman F. van der Bank
- African Centre for DNA Barcoding, University of Johannesburg, Auckland Park, Johannesburg, South Africa
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Ahmad AA, Shabbir MAB, Xin Y, Ikram M, Hafeez MA, Wang C, Zhang T, Zhou C, Yan X, Hassan M, Hu M. Characterization of the Complete Mitochondrial Genome of a Whipworm Trichuris skrjabini (Nematoda: Trichuridae). Genes (Basel) 2019; 10:E438. [PMID: 31181837 PMCID: PMC6627073 DOI: 10.3390/genes10060438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 01/30/2023] Open
Abstract
The complete mitochondrial (mt) genome of Trichuris skrjabini has been determined in the current study and subsequently compared with closely related species by phylogenetic analysis based on concatenated datasets of mt amino acid sequences. The whole mt genome of T. skrjabini is circular and 14,011 bp in length. It consists of a total of 37 genes including 13 protein coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNAs) genes, and two non-coding regions. The gene arrangement and contents were consistent with other members of the Trichuridae family including Trichuris suis, Trichuris trichiura, Trichuris ovis, and Trichuris discolor. Phylogenetic analysis based on concatenated datasets of amino acids of the 12 PCGs predicted the distinctiveness of Trichuris skrjabini as compared to other members of the Trichuridae family. Overall, our study supports the hypothesis that T. skrjabini is a distinct species. The provision of molecular data of whole mt genome of T. skrjabini delivers novel genetic markers for future studies of diagnostics, systematics, population genetics, and molecular epidemiology of T. skrjabini.
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Affiliation(s)
- Awais Ali Ahmad
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Muhammad Abu Bakr Shabbir
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Yang Xin
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Muhammad Ikram
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Mian Abdul Hafeez
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan.
| | - Chunqun Wang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Ting Zhang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Caixian Zhou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Xingrun Yan
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Mubashar Hassan
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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44
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Sarikaya DP, Church SH, Lagomarsino LP, Magnacca KN, Montgomery SL, Price DK, Kaneshiro KY, Extavour CG. Reproductive Capacity Evolves in Response to Ecology through Common Changes in Cell Number in Hawaiian Drosophila. Curr Biol 2019; 29:1877-1884.e6. [PMID: 31130459 PMCID: PMC6673671 DOI: 10.1016/j.cub.2019.04.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/01/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023]
Abstract
Lifetime reproductive capacity is a critical fitness component. In insects, female reproductive capacity is largely determined by the number of ovarioles, the egg-producing subunits of the ovary [e.g., 1]. Recent work has provided insights into ovariole number regulation in Drosophila melanogaster. However, whether mechanisms discovered under laboratory conditions explain evolutionary variation in natural populations is an outstanding question. We investigated potential effects of ecology on the developmental processes underlying ovariole number evolution among Hawaiian Drosophila, a large adaptive radiation wherein the highest and lowest ovariole numbers of the family have evolved within 25 million years. Previous studies proposed that ovariole number correlated with oviposition substrate [2-4] but sampled largely one clade of these flies and were limited by a provisional phylogeny and the available comparative methods. We test this hypothesis by applying phylogenetic modeling to an expanded sampling of ovariole numbers and substrate types and show support for these predictions across all major groups of Hawaiian Drosophila, wherein ovariole number variation is best explained by adaptation to specific substrates. Furthermore, we show that oviposition substrate evolution is linked to changes in the allometric relationship between body size and ovariole number. Finally, we provide evidence that the major changes in ovarian cell number that regulate D. melanogaster ovariole number also regulate ovariole number in Hawaiian drosophilids. Thus, we provide evidence that this remarkable adaptive radiation is linked to evolutionary changes in a key reproductive trait regulated at least partly by variation in the same developmental parameters that operate in the model species D. melanogaster.
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Affiliation(s)
- Didem P Sarikaya
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.
| | - Samuel H Church
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA
| | - Laura P Lagomarsino
- Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | | | | | - Donald K Price
- Biology Department, University of Hawai'i at Hilo, 200 W. Kawili St., Hilo, HI 96720, USA
| | - Kenneth Y Kaneshiro
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, 1993 East-West Rd., Manoa, HI 96822, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA.
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45
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Chang Y, Song S, Li A, Zhang Y, Li Z, Xiao Y, Jiang T, Feng J, Lin A. The roles of morphological traits, resource variation and resource partitioning associated with the dietary niche expansion in the fish-eating bat Myotis pilosus. Mol Ecol 2019; 28:2944-2954. [PMID: 31063664 DOI: 10.1111/mec.15127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 04/27/2019] [Accepted: 04/29/2019] [Indexed: 12/29/2022]
Abstract
Niche expansion and shifts are involved in the response and adaptation to environmental changes. However, it is unclear how niche breadth evolves and changes toward higher-quality resources. Myotis pilosus is both an insectivore and a piscivore. We examined the dietary composition and seasonality in M. pilosus and the closely related Myotis fimbriatus using next-generation DNA sequencing. We tested whether resource variation or resource partitioning help explain the dietary expansion from insects to fish in M. pilosus. While diet composition and diversity varied significantly between summer and autumn, the proportion of fish-eating individuals did not significantly change between seasons in M. pilosus. Dietary overlap between M. pilosus and M. fimbriatus during the same seasons was much higher than within individual species across seasons. We recorded a larger body size, hind foot length, and body mass in M. pilosus than in M. fimbriatus and other insectivorous trawling bats from China. Similar morphological differences were found between worldwide fishing bats and nonfishing trawling bats. Our results suggest that variation in insect availability or interspecific competition may not play important roles in the dietary expansion from insects to fish in M. pilosus. Myotis pilosus has morphological advantages that may help it use fish as a diet component. The morphological advantage promoting dietary niche evolution toward higher quality resources may be more important than variation in the original resource and the effects of interspecific competition.
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Affiliation(s)
- Yang Chang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Shengjing Song
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Yu Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Zhongle Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,College of Life Science, Jilin Agricultural University, Changchun, China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun, China.,College of Life Science, Jilin Agricultural University, Changchun, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,Acoustic and Functional Ecology Group, Max Planck Institute for Ornithology, Seewiesen, Germany
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46
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Moore MK, Frazier K. Humans Are Animals, Too: Critical Commonalities and Differences Between Human and Wildlife Forensic Genetics. J Forensic Sci 2019; 64:1603-1621. [DOI: 10.1111/1556-4029.14066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/10/2019] [Accepted: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- M. Katherine Moore
- Forensic Laboratory Conservation Biology Division Northwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration 219 Fort Johnson Road Charleston SC29412
| | - Kim Frazier
- Wyoming Game and Fish Wildlife Forensic and Fish Health Laboratory 1212 South Adams Street Laramie WY 82070
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He T, Jiao L, Wiedenhoeft AC, Yin Y. Machine learning approaches outperform distance- and tree-based methods for DNA barcoding of Pterocarpus wood. PLANTA 2019; 249:1617-1625. [PMID: 30825008 DOI: 10.1007/s00425-019-03116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/20/2019] [Indexed: 05/10/2023]
Abstract
Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal logging and associated trade, and the development of reliable and efficient analytical methods is essential for its extensive application in the trade of wood and in the forensics of natural materials more broadly. In this study, 120 DNA sequences of four barcodes (ITS2, matK, ndhF-rpl32, and rbcL) generated in our previous study and 85 downloaded from National Center for Biotechnology Information (NCBI) were collected to establish a reference data set for six commercial Pterocarpus woods. MLAs (BLOG, BP-neural network, SMO and J48) were compared with distance- (TaxonDNA) and tree-based (NJ tree) methods based on identification accuracy and cost-effectiveness across these six species, and also were applied to discriminate the CITES-listed species Pterocarpus santalinus from its anatomically similar species P. tinctorius for forensic identification. MLAs provided higher identification accuracy (30.8-100%) than distance- (15.1-97.4%) and tree-based methods (11.1-87.5%), with SMO performing the best among the machine learning classifiers. The two-locus combination ITS2 + matK when using SMO classifier exhibited the highest resolution (100%) with the fewest barcodes for discriminating the six Pterocarpus species. The CITES-listed species P. santalinus was discriminated successfully from P. tinctorius using MLAs with a single barcode, ndhF-rpl32. This study shows that MLAs provided higher identification accuracy and cost-effectiveness for forensic application over other analytical methods in DNA barcoding of Pterocarpus wood.
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Affiliation(s)
- Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and National Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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48
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Cryer J, Wynne F, Price SJ, Puschendorf R. Cryptic diversity in Lithobateswarszewitschii (Amphibia, Anura, Ranidae). Zookeys 2019; 838:49-69. [PMID: 31048968 PMCID: PMC6477815 DOI: 10.3897/zookeys.838.29635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/25/2019] [Indexed: 11/12/2022] Open
Abstract
Lithobateswarszewitschii is a species of ranid frog distributed from southern Honduras to Panama. This species suffered severe population declines at higher elevations (above 500 m a.s.l.) from the 1980s to early 1990s, but there is more recent evidence of recovery in parts of its range. Here we advocate for the status of Lithobateswarszewitschii as a candidate cryptic species complex based on sequence data from mitochondrial genes CO1 and 16S. Using concatenated phylogenies, nucleotide diversity (K2P-π), net between group mean distance (NBGMD) (πnet) and species delimitation methods, we further elucidate cryptic diversity within this species. All phylogenies display polyphyletic lineages within Costa Rica and Panama. At both loci, observed genetic polymorphism (K2P-π) is also high within and between geographic populations, surpassing proposed species threshold values for amphibians. Additionally, patterns of phylogeographic structure are complicated for this species, and do not appear to be explained by geographic barriers or isolation by distance. These preliminary findings suggest L.warszewitschii is a wide-ranging species complex. Therefore, we propose further research within its wider range, and recommend integrative taxonomic assessment is merited to assess species status.
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Affiliation(s)
- James Cryer
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
| | - Felicity Wynne
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
| | - Stephen J. Price
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UKUCL Genetics InstituteLondonUnited Kingdom
- Institute of Zoology, ZSL, Regents Park, London NW1 4RY, UKInstitute of Zoology, ZSLLondonUnited Kingdom
| | - Robert Puschendorf
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
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49
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Next generation sequencing from Hepatozoon canis (Apicomplexa: Coccidia: Adeleorina): Complete apicoplast genome and multiple mitochondrion-associated sequences. Int J Parasitol 2019; 49:375-387. [DOI: 10.1016/j.ijpara.2018.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/29/2018] [Accepted: 12/01/2018] [Indexed: 11/21/2022]
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50
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Powell C, Caleca V, Sinno M, van Staden M, van Noort S, Rhode C, Allsopp E, van Asch B. Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa. Genome 2019; 62:183-199. [DOI: 10.1139/gen-2018-0068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era. In this study, a dual approach combining morphological and DNA-based methods was used for the identification of adult specimens reared from olive fruits. Four species of Braconidae and six species of Chalcidoidea were identified, and DNA barcoding methodologies were used to investigate conspecificity among individuals, based on randomly selected representative specimens. Morphological identifications were congruent with DNA data, as NJ and ML trees correctly placed the sequences for each species either at the genus or species level, depending on the available taxa coverage, and genetic distances strongly supported conspecificity. No clear evidence of cryptic diversity was found. Overall seed infestation and parasitism rates were higher in wild olives compared to cultivated olives, and highest for Eupelmus spermophilus and Utetes africanus. These results can be used for early DNA-based detection of wasp larvae in olives and to further investigate the biology and ecology of these species.
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Affiliation(s)
- Chante Powell
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Virgilio Caleca
- Department of Agricultural and Forestry Sciences, University of Palermo, Italy
| | - Martina Sinno
- Department of Agricultural Sciences, University of Naples “Federico II”, Naples, Italy
| | - Michaela van Staden
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Simon van Noort
- Division of Entomology, Department of Natural History, Iziko South African Museum, Cape Town, South Africa
| | - Clint Rhode
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Elleunorah Allsopp
- Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch, South Africa
| | - Barbara van Asch
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
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