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Khatun MF, Hwang HS, Kang JH, Lee KY, Kil EJ. Genetic Diversity and DNA Barcoding of Thrips in Bangladesh. INSECTS 2024; 15:107. [PMID: 38392526 PMCID: PMC10888972 DOI: 10.3390/insects15020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Thrips are economically important pests, and some species transmit plant viruses that are widely distributed and can damage vegetables and cash crops. Although few studies on thrips species have been conducted in Bangladesh, the variation and genetic diversity of thrips species remain unknown. In this study, we collected thrips samples from 16 geographical locations throughout the country and determined the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene in 207 thrips individuals. Phylogenetic analysis revealed ten genera (Thrips, Haplothrips, Megalothrips, Scirtothrips, Frankliniella, Dendrothripoides, Astrothrips, Microcephalothrips, Ayyaria, and Bathrips) and 19 species of thrips to inhabit Bangladesh. Among these, ten species had not been previously reported in Bangladesh. Intraspecific genetic variation was diverse for each species. Notably, Thrips palmi was the most genetically diverse species, containing 14 haplotypes. The Mantel test revealed no correlation between genetic and geographical distances. This study revealed that thrips species are expanding their host ranges and geographical distributions, which provides valuable insights into monitoring the diversity of and control strategies for these pests.
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Affiliation(s)
- Mst Fatema Khatun
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Republic of Korea
- Department of Entomology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Hwal-Su Hwang
- Department of Plant Medicine, College of Agriculture and Life Science, Kyungpook National University, Daegu 37224, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 37224, Republic of Korea
| | - Jeong-Hun Kang
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Republic of Korea
| | - Kyeong-Yeoll Lee
- Department of Plant Medicine, College of Agriculture and Life Science, Kyungpook National University, Daegu 37224, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 37224, Republic of Korea
- Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 37224, Republic of Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Republic of Korea
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Cheng R, Luo A, Orr M, Ge D, Hou Z, Qu Y, Guo B, Zhang F, Sha Z, Zhao Z, Wang M, Shi X, Han H, Zhou Q, Li Y, Liu X, Shao C, Zhang A, Zhou X, Zhu C. Cryptic diversity begets challenges and opportunities in biodiversity research. Integr Zool 2024. [PMID: 38263700 DOI: 10.1111/1749-4877.12809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhong'e Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhe Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Mingqiang Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoyu Shi
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingsong Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuanning Li
- Institute of Oceanography, Shandong University, Qingdao, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chen Shao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Aibing Zhang
- College of Life Science, Capital Normal University, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences/International College, University of Chinese Academy of Sciences, Beijing, China
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3
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Li C, Gao Y, Wang D, Dang L. The extraordinary rearrangement of mitochondrial genome of the wheat pest, Aptinothrips stylifer and the mitochondrial phylogeny of Thripidae (Thysanoptera). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22086. [PMID: 38288496 DOI: 10.1002/arch.22086] [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: 10/04/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
The mitochondrial gene order in Thysanoptera is notably distinct and highly rearranged, with each species exhibiting its own unique arrangement. To elucidate the relationship between gene rearrangements and phylogeny, the complete mitochondrial genome (mitogenome) of the wheat pest, Aptinothrips stylifer, was sequenced and assembled, spanning a total length of 16,033 bp. Compared with the ancestral arthropod mitogenome, significant rearrangement differences were evident in A. stylifer, whereas the gene order between A. stylifer and Anaphothrips obscurus was similar. Phylogenetic trees were reconstructed based on all 13 protein-coding gene sequences using Bayesian inference and maximum-likelihood methods, both yielding similar topological structures. Notably, A. stylifer was robustly clustered with A. obscurus, affirming its classification within Anaphothrips genus group. This exemplifies the potential correlation between gene rearrangements and phylogeny in the Thripidae family. Additionally, the mitogenome of A. stylifer exhibited several atypical features, including: (1) Three putative control regions (CRs) in close proximity, with CR2 and CR3 displaying partial similarity, and CR1 differing in base composition; (2) Two transfer RNAs (tRNAs), trnS1 and trnV, lacking the DHU arm; (3) Two ribosomal RNA (rRNA) genes inverted and positioned distant from each other; (4) Negative AT and GC skew (AT skew = -0.001, GC skew = -0.077); (5) One transposition (nad6), one inverse transposition (trnQ), four inversions (trnF, trnH, trnC, and gene block nad1-trnL1-rrnL-trnV-rrnS), and four tandem duplication random loss events; and (6) Two protein-coding genes, nad2 and atp8, terminated with an incomplete stop codon "T".
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Affiliation(s)
- Chengwen Li
- Department of Biology, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Yuxin Gao
- Department of Biology, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Dongxue Wang
- Department of Biology, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Lihong Dang
- Department of Biology, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
- Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong, China
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Mukherjee A, Ghosh A, Tyagi K, Kumar V, Banerjee D, Naskar A. Characterization of complete mitochondrial genome of three Horse flies of the genus Tabanus (Diptera: Tabanidae): comparative analysis. Mol Biol Rep 2023; 50:9897-9908. [PMID: 37864662 DOI: 10.1007/s11033-023-08837-z] [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: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Tabanidae (Horse-Flies or Deer-Flies) are one of the most economically important as well as medically significant haematophagous insect family within the order Diptera. Members of this group are also responsible for the mortality of substantial number of live-stock every year. Due to their pathogen transmission potential and vector competencies makes them an important insect group to study. Till now, mitochondrial genome of 18 species of tabanids were available. METHODS AND RESULTS The complete mitogenome of three species T. diversifrons (15,809 bp), T. rubidus (15,878 bp) and T. tenens (15,872 bp) were generated by Next generation sequencing method. They consist 37 genes, with a positive AT skew and a negative GC skew. The gene order of these three species is similar to the typical gene arrangement of infra-order Tabanomorpha. Most of the tRNAs showed typical clover-leaf secondary structure except trnS1, which lacks the DHU arm. The sliding window analysis showed that the nad4L is the most conserved while atp8, and nad6 are the most variable genes. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated that all PCGs under the purifying selection. Phylogeny revealed Chrysops and Haematopota are monophyletic while species of Hybomitra are nested within the polyphyletic clade of Tabanus. T. diversifrons exhibits sister relationship with Atylotus miser. Two morphologically divergent species T. rubidus and T. tenens are found to be genetically similar and indistinguishable by mitochondrial genome. CONCLUSIONS The hypervariable genes like atp8 and nad6 can be used as molecular markers for the identification of recently diverged lineages of family Tabanidae. Further, to address uncertainties arising from the two morphological divergent species, it is imperative to obtain data from nuclear gene markers.
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Affiliation(s)
- Arka Mukherjee
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Abhishek Ghosh
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Dhriti Banerjee
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
| | - Atanu Naskar
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
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Palanisamy A, Marimuthu M, Narayanasamy C, Venkatasamy B, Gandhi K, Lakshmanan P. Invasive flower thrips, Thrips parvispinus (Karny) occurrence, host expansion and genetic diversification in a tropical poly-crop ecosystem. Mol Biol Rep 2023; 50:9909-9923. [PMID: 37874506 DOI: 10.1007/s11033-023-08831-5] [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: 01/21/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Invasive black flower thrips Thrips parvispinus (Karny) has recently emerged as a significant threat to Indian chilli production. Identifying T. parvispinus became difficult due to the complex presence of thrips species in Indian chilli and allied ecosystems. Pest management success depends on assessing invasive pests genetic populations and their distribution in newly habituated areas. METHODS AND RESULTS The current study investigated the genetic diversity and phylogeographic structure of T. parvispinus across major chilli-growing zones representing different agro-climatic conditions in Tamil Nadu. The species-specific chaetotaxy characteristics of T. parvispinus and molecular analysis of the mtCOI gene were used to confirm that the species T. parvispinus has expanded rapidly in three regions (North Western, Western and Cauvery delta), sparsely in one (Southern) and absent from two (hilly and high rainfall). Fifteen allied crops in chilli/capsicum growing tracts served as host plants for T. parvispinus. A shrub species, namely Littleleaf boxwood, Buxus microphylla Siebold & Zucc., is described as a host plant for the first time. On capsicum and chilli, T. parvispinus and Scirtothrips dorsalis coexisted. Thrips palmi, T. tabaci, Frankliniella schultzei, and Microcephalothrips abdominalis co-occurring alongside T. parvispinus on allied crops. CONCLUSION Molecular characterization and haplotype identification help define the genetic composition of T. parvispinus and serve as a foundation for efficient monitoring and creation of Integrated Pest Management (IPM) strategies. As a result, the genetic data presented in this work strongly argues that T. parvispinus as a population is resolving itself towards a fixed state through natural selection that spans its native range globally along with low genetic diversity [Hd: 0.771].
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Affiliation(s)
- Aishwarya Palanisamy
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Murugan Marimuthu
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India.
| | - Chitra Narayanasamy
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Balasubramani Venkatasamy
- Controller of Examinations, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Karthikeyan Gandhi
- Department of Plant Pathology, Centre for Plant Protection Studies, TNAU, Coimbatore, Tamil Nadu, 641003, India
| | - Pugalendhi Lakshmanan
- Department of Vegetables, Horticultural College & Research Institute, TNAU, Coimbatore, Tamil Nadu, 641003, India
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6
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Lindner MF, Gonçalves LT, Bianchi FM, Ferrari A, Cavalleri A. Tiny insects, big troubles: a review of BOLD's COI database for Thysanoptera (Insecta). BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:703-715. [PMID: 37614126 DOI: 10.1017/s0007485323000391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
DNA Barcoding is an important tool for disciplines such as taxonomy, phylogenetics and phylogeography, with Barcode of Life Data System (BOLD) being the largest database of partial cytochrome c oxidase subunit I (COI) sequences. We provide the first extensive revision of the information available in this database for the insect order Thysanoptera, to assess: how many COI sequences are available; how representative these sequences are for the order; and the current potential of BOLD as a reference library for specimen identification and species delimitation. The COI database at BOLD currently represents only about 5% of the over 6400 valid thrips species, with a heavy bias towards a few species of economic importance. Clear Barcode gaps were observed for 24 out of 33 genera evaluated, but many outliers were also observed. We suggest that the COI sequences available in BOLD as a reference would not allow for accurate identifications in about 30% of Thysanoptera species in this database, which rises to 40% of taxa within Thripidae, the most sampled family within the order. Thus, we call for caution and a critical evaluation in using BOLD as a reference library for thrips Barcodes, and future efforts should focus on improving the data quality of this database.
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Affiliation(s)
- Mariana F Lindner
- Department of Zoology, Laboratório de Entomologia Sistemática, Institute of Biosciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Leonardo T Gonçalves
- Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Filipe M Bianchi
- Department of Zoology, Laboratório de Entomologia Sistemática, Institute of Biosciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Augusto Ferrari
- Laboratório de Entomologia, Sistemática e Biogeografia (LESB), Matéria Zoologia, Institute of Biological Sciences, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Adriano Cavalleri
- Laboratório de Entomologia, Sistemática e Biogeografia (LESB), Matéria Zoologia, Institute of Biological Sciences, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
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Pakrashi A, Patidar A, Singha D, Kumar V, Tyagi K. Comparative analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial genome of Thrips parvispinus. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-15. [PMID: 36915951 DOI: 10.1002/arch.22010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/02/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Thrips parvispinus is a serious sucking pest on a number of economically important crops in the oriental region. It has gained importance recently for its drastic range extension distribution as an invasive pest. Here, the complete mitochondrial genome (15,067 bp) of Thrips parvispinus was sequenced and characterized. It possesses 37 genes and the putative noncoding region is duplicated. Comparative analyses of nucleotide diversity, skewness, codon usage bias, and selection pressure in mitochondrial protein-coding genes of the available 31 thrips mitogenomes (24 Terebrantia + 7 Tubulifera) were performed. Phylogenetic analysis showed a sister relationship of T. parvispinus to the clade (T. florum + T. hawaiiensis). Phylogenetic analyses formed the monophyly of subfamilies Phlaeothripinae and Idolothripinae within the family Phlaeothripidae (Suborder Tubulifera). Low nucleotide diversity was indicative of reversal of strand asymmetry in the Tubulifera. Neutrality analysis showed that directional mutation plays a major role in shaping codon usage bias in both suborders. Principal component analysis indicated distinct codon usage patterns in each suborder. Our data suggested weaker selection constrains on Terebrantia than in the Tubulifera. More tubuliferan mitogenomes are required to resolve previous classification hypotheses and elucidate genome evolution in these two suborders.
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Affiliation(s)
- Avas Pakrashi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, West Bengal, India
| | - Abhishek Patidar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, West Bengal, India
| | - Devkant Singha
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, West Bengal, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, West Bengal, India
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8
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Pal S, Patidar A, Panjaliya RK, Kumar V, Tyagi K. Species of the genus Scirtothrips from India (Thysanoptera, Thripidae). Zootaxa 2023; 5306:392-396. [PMID: 37518514 DOI: 10.11646/zootaxa.5306.3.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 08/01/2023]
Affiliation(s)
- Shash Pal
- Department of Zoology; University of Jammu; Jammu & Kashmir; India.
| | - Abhishek Patidar
- Centre for DNA Taxonomy; Molecular Systematics Division; Zoological Survey of India; West Bengal; India; Department of Zoology; University of Calcutta; Kolkata; West Bengal; India.
| | | | - Vikas Kumar
- entre for DNA Taxonomy; Molecular Systematics Division; Zoological Survey of India; West Bengal; India.
| | - Kaomud Tyagi
- entre for DNA Taxonomy; Molecular Systematics Division; Zoological Survey of India; West Bengal; India.
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9
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Mukherjee T, Sharma LK, Thakur M, Banerjee D, Chandra K. Whether curse or blessing: A counterintuitive perspective on global pest thrips infestation under climatic change with implications to agricultural economics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161349. [PMID: 36621499 DOI: 10.1016/j.scitotenv.2022.161349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
The improvement and application of pest models to predict yield losses is still a challenge for the scientific community. However, pest models were targeted chiefly towards scheduling scouting or pesticide applications to deal with pest infestation. Thysanoptera (thrips) significantly impact the productivity of many economically important crops worldwide. Until now, no comprehensive study is available on the global distribution of pest thrips, as well as on the extent of cropland vulnerability worldwide. Further, nothing is known about the climate change impacts on these insects. Thus the present study was designed to map the global distribution and quantify the extent of cropland vulnerability in the present and future climate scenarios using data of identified pest thrips within the genus, i.e., Thrips, Frankliniella, and Scirtothrips. Our found significant niche contraction under the climate change scenarios and thrips may reside primarily in their thermal tolerance thresholds. About 3,98,160 km2 of cropland globally was found to be affected in the present scenario. However, it may significantly reduce to 5530 Km2 by 2050 and 1990 km2 by 2070. Further, the thrips distribution mostly getting restricted to Eastern North America, the North-western of the Indian sub-continent, and the north of Europe. Among all realms, thrips may lose ground in the Indo-Malayan realm at the most and get restricted to only 27 out of 825 terrestrial ecoregions. The agrarian communities of the infested regions may get benefit if these pests get wiped out, but on the contrary, we may lose species diversity. Moreover, the vacated niche may attract other invasive species, which may seriously impact the species composition and agricultural productivity. The present study findings can be used in making informed decisions about prioritizing future economic and research investments on the thrips in light of anticipated climate change impacts.
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Affiliation(s)
- Tanoy Mukherjee
- Zoological Survey of India, Kolkata 700053, India-; Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
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DNA Barcoding of Fish Species Diversity in Guizhou, China. DIVERSITY 2023. [DOI: 10.3390/d15020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Guizhou is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River basins with abundant fish species. However, fish from these regions are threatened by anthropogenic activities, including overfishing and habitat destruction. Here, we assessed the fish diversity including more than half of the species from the region using DNA barcoding (partial sequence of cytochrome c oxidase subunit I (COI) gene). We obtained 800 mitochondrial COI barcode sequences from 82 genera, 18 families and 8 orders of fishes. The average Kimura two-parameter (K2P) distances within species and genera were 0.35% and 5.44%, respectively. The average interspecific distance was 15.54 times higher than the mean intraspecific distance. Moreover, DNA barcodes revealed 175 operational taxonomic units (OTUs) based on consensus demarcation schemes. Barcoding gaps were detected in 94.81% of morphospecies. Three fish species (Schistura fasciolata, Vanmanenia pingchowensis, and Misgurnus dabryanus) have considerable intraspecific variability, and each was divided into multiple molecular operational taxonomic units (MOTUs) using molecular definition methods (Automatic Barcode Gap Discovery, Refined Single Linkage, General Mixed Yule Coalescent, and Poisson Tree Processes), possibly indicating the occurrence of cryptic species. Altogether, our study reveals the complex diversity of fish species in Guizhou Province, serving as a reference for the conservation and monitoring of fish species in this region.
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11
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Zhao Y, Wang H, Huang H, Zhou Z. A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China. Zookeys 2022; 1123:147-171. [PMID: 36762040 PMCID: PMC9836636 DOI: 10.3897/zookeys.1123.86704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/06/2022] [Indexed: 11/12/2022] Open
Abstract
Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 118 BINs (Barcodes Index Numbers). Among these 90 species-level taxa, 68 corresponded with morphospecies, while the remaining 22 were identified based on reverse taxonomy using BIN assignment. Thirteen of these morphospecies were represented by a single barcode (so-called singletons), and each of 19 morphospecies were split into more than one BIN. The consensus delimitation scheme yielded 55 Molecular Operational Taxonomic Units (MOTUs). Only four morphospecies (I max > DNN) failed to be recovered as monophyletic clades (i.e., Elimaeaterminalis, Phyllomimusklapperichi, Sinochloraszechwanensis and Xizicushowardi), so it is speculated that these may be species complexes. Therefore, the diversity of katydids, cave crickets, and leaf-rolling crickets in Zhejiang Province is probably slightly higher than what current taxonomy would suggest.
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Affiliation(s)
- Yizheng Zhao
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Hui Wang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Huimin Huang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
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12
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Oh JH, Kim S, Lee S. DNA barcodes reveal population-dependent cryptic diversity and various cases of sympatry of Korean leptonetid spiders (Araneae: Leptonetidae). Sci Rep 2022; 12:15528. [PMID: 36109541 PMCID: PMC9478141 DOI: 10.1038/s41598-022-18666-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
Leptonetidae are tiny, rarely encountered spiders that mainly inhabit moist environments, such as caves, leaf litter, and rock piles. Because they are microhabitat specialists, most leptonetid species have short-range endemism, and rarely occur in sympatry. Their small size, relatively simple habitus features and reproductive organ structure increase the difficulty of identification. The identification of leptonetids and other spiders may also be time-consuming due to their sexual dimorphism, polymorphism, and lack of diagnostic characteristics in juveniles. DNA barcoding has been used as an effective tool for species identification to overcome these obstacles. Herein, we conducted a test of DNA barcoding based on 424 specimens of Korean Leptonetidae representing 76 morphospecies. A threshold of 4.2% based on maximum intraspecific genetic divergence was estimated to efficiently differentiate the morphospecies. The species assignments tested by five species delimitation methods (ABGD, ASAP, GMYC, PTP, and bPTP) were consistent with the morphological identifications for only 47 morphospecies (61.8%), indicating many cases of cryptic diversity among the remaining morphospecies. Furthermore, sympatry in leptonetids, which are known to be rare, was revealed to be common in South Korea, especially in epigean species. Our results showed that sympatries within families, congeners, and intraclades potentially occur throughout the entire region of Korea.
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13
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Li M, Liu M, Hu SY, Luo FZ, Yuan ML. Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae). Front Genet 2022; 13:974084. [PMID: 36186478 PMCID: PMC9515440 DOI: 10.3389/fgene.2022.974084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.
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Affiliation(s)
- Min Li
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Fang-Zhen Luo
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Ming-Long Yuan,
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14
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Xie YL, Mound LA, Lima ÉFB, He SQ, Zhang HR, Li YJ. Molecular Studies of Relationships and Identifications Among Insects of the Subfamily Panchaetothripinae (Thysanoptera, Thripidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:6. [PMID: 36124863 PMCID: PMC9486593 DOI: 10.1093/jisesa/ieac055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The Panchaetothripinae comprises 42 genera and 146 species of leaf-feeding thrips, some of which are horticultural pests. We examined representatives of the 18 genera that include most of these pests. For species delimitation, we used DNA barcoding to produce171 sequences for 40 morphospecies. Most species were found to be monophyletic, although cryptic diversity was evident in 8 presumptive species. A multilocus molecular phylogenetic assessment was based on one mitochondrial (COI) and three nuclear loci (EF-1α, ITS2, and 28S) from 132 specimens (18 genera and 33 species), representing all genera and ~82% of species in China. Maximum likelihood (ML) and Bayesian inference (BI) confirmed monophyly of each genus with strong support. Monophyly of tribes Panchaetothripini and Monilothripini were refuted, but the well supported tribe Tryphactothripini was confirmed. Rhipiphorothrips was recovered as a sister to the remainder of the genera of Panchaetothripinae combined. Both analyses revealed two major clades. Clade A comprised the majority of the genera, including tribe Tryphactothripini. Clade B included only four genera of which two, Helionothrips and Caliothrips, are particularly species rich. The relationships of some genera remain unresolved.
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Affiliation(s)
- Yan Lan Xie
- Plant Protection College, Yunnan Agricultural University, Jinhei Road 95, Panlong District, Kunming 650201, Yunnan, P.R. China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Jinhei Road 95, Panlong District, Kunming 650201, Yunnan, China
- Biotechnology and Engineering College, West Yunnan University, Xuefu Road 2, Linxiang District, Lincang 677000, Yunnan, P.R. China
| | - Laurence A Mound
- Australian National Insect Collection, CSIRO, PO Box 1700, Canberra, ACT 2601, Australia
| | - Élison Fabrício Bezerra Lima
- Universidade Federal do Piauí – UFPI, Campus Amílcar Ferreira Sobral, BR 343, Km 3.5, Meladão. Floriano, PI 64808-605, Brasil
| | - Shu Qi He
- Plant Protection College, Yunnan Agricultural University, Jinhei Road 95, Panlong District, Kunming 650201, Yunnan, P.R. China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Jinhei Road 95, Panlong District, Kunming 650201, Yunnan, China
| | | | - Ya Jin Li
- Corresponding author, e-mail: (H RZ), (Y JL)
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15
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Population Genetic Structure of Chlorops oryzae (Diptera, Chloropidae) in China. INSECTS 2022; 13:insects13040327. [PMID: 35447769 PMCID: PMC9032139 DOI: 10.3390/insects13040327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023]
Abstract
Frequent outbreaks have made Chlorops oryzae one of the major pests of rice in some regions. In order to understand the ecological adaptation of C. oryzae at the molecular level, and provide a scientific basis for formulating management strategies, we used two molecular markers, COI and ITS1 sequences, to systematically analyze the genetic structure of 31 populations. The higher haplotype diversity and lower nucleotide diversity indicated that the C. oryzae populations experienced rapid expansion after a “Bottleneck effect”. The results of the mismatch distribution, neutrality test (Fu’s Fs < 0, p < 0.001), and haplotype network analysis suggested that the population has recently undergone an expansion. Although genetic differentiation among C. oryzae populations was found to have existed at low/medium levels (Fst: 0.183 for COI, 0.065 for ITS1), the frequent gene flow presented as well (Nm: 2.23 for COI, 3.60 for ITS1) was supposed to be responsible for frequent local outbreaks.
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16
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Integrative Insight into Relationships between Florivorous Thrips Haplothrips leucanthemi and H. niger (Insecta, Thysanoptera). INSECTS 2022; 13:insects13030279. [PMID: 35323577 PMCID: PMC8950692 DOI: 10.3390/insects13030279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022]
Abstract
Haplothrips niger is recognized as a parthenogenetic form of H. leucanthemi and is also considered to be a pest in clover-seed plantations. On the contrary, some researchers highlight the distinctiveness of H. niger and H. leucanthemi. Taking into account these two points of view, as well as the lack of molecular studies investigating the relationship between the mentioned thrips, we decided to perform analyses of both mitochondrial (COI) and nuclear markers (28S and ITS2) to determine the genetic diversity of H. leucanthemi and H. niger. Additionally, as a part of an integrative approach, we determined and analyzed their microbiota profiles, based on high-throughput 16S rRNA gene sequencing. The results of the molecular analyses revealed high intraspecific diversity of H. leucanthemi and did not support the distinctiveness of H. niger. The identified microbiota profiles were similar in both species and the performed analyses also did not support the distinctiveness of H. niger. Significant differences were, in turn, observed between H. leucanthemi and H. niger larvae. Moreover, two known endosymbiotic bacteria were found in the analyzed microbiota profiles (i.e., Wolbachia and Rickettsia). Nevertheless, these symbionts were not predominantly found in the bacterial communities that are associated with H. niger and thus, its impact on the parthenogenetic mode of its reproduction seems less likely.
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17
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Characterizing Billbug ( Sphenophorus spp.) Seasonal Biology Using DNA Barcodes and a Simple Morphometric Analysis. INSECTS 2021; 12:insects12100930. [PMID: 34680699 PMCID: PMC8538943 DOI: 10.3390/insects12100930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Billbugs (Sphenophorus spp.) are a group of grass-feeding weevils considered to be one of the most important and widespread insect pests of turfgrass. However, our limited understanding of regional variation in billbug species composition and inability to identify the damaging larval stage to species level, has hindered our ability to resolve the seasonal biology of many billbug species and constrained development of effective management approaches. In this study, we developed a robust DNA barcoding approach for identification of morphologically cryptic billbug larvae. Using this molecular tool combined with larval head capsule measurements we characterized regional variation in billbug species and developed larval phenology charts. Our approach provides researchers with the molecular tools necessary to fill critical gaps in our understanding of billbug seasonal biology and will facilitate the development of improved turfgrass pest management programs. Abstract Billbugs (Sphenophorus spp.) are a complex of grass-feeding weevil species that reduce the aesthetic and functional qualities of turfgrass. Effective billbug monitoring and management programs rely on a clear understanding of their seasonal biology. However, our limited understanding of regional variation in the species compositions and seasonal biology of billbugs, stemming primarily from our inability to identify the damaging larval stage to species level, has hindered efforts to articulate efficient IPM strategies to growers. We used a combination of DNA barcoding methods and morphometric measures to begin filling critical gaps in our understanding of the seasonal biology of the billbug species complex across a broad geographic range. First, we developed a DNA barcoding reference library using cytochrome oxidase subunit 1 (COI) sequences from morphologically identified adult billbugs collected across Indiana, Missouri, Utah and Arizona. Next, we used our reference library for comparison and identification of unknown larval specimens collected across the growing season in Utah and Indiana. Finally, we combined our DNA barcoding approach with larval head capsule diameter, a proxy for developmental instar, to develop larval phenology charts. Adult COI sequences varied among billbug species, but variation was not influenced by geography, indicating that this locus alone was useful for resolving larval species identity. Overlaid with head capsule diameter data from specimens collected across the growing season, a better visualization of billbug species composition and seasonal biology emerged. This approach will provide researchers with the tools necessary to fill critical gaps in our understanding of billbug biology and facilitate the development of turfgrass pest management programs.
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18
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Ghosh A, Jangra S, Dietzgen RG, Yeh WB. Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms? INSECTS 2021; 12:insects12100920. [PMID: 34680689 PMCID: PMC8540714 DOI: 10.3390/insects12100920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis. Abstract Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.
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Affiliation(s)
- Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.G.); (S.J.)
| | - Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.G.); (S.J.)
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Correspondence:
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, Taichung City 402, Taiwan;
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19
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Singha D, Patidar A, Kumar V, Tyagi K. A new species of Mycterothrips Trybom (Thysanoptera: Thripidae) from India with new record of the genus Paithrips Nonaka amp; Jangvitaya. Zootaxa 2021; 5048:135-140. [PMID: 34810811 DOI: 10.11646/zootaxa.5048.1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Indexed: 11/04/2022]
Abstract
Mycterothrips nainiae sp. n. (Thripinae) is described and illustrated from India, and one genus and species, Paithrips circularis Nonaka and Jangvitaya, is newly recorded from India. A key to species of Mycterothrips from India is also provided. The DNA barcode data using partial mitochondrial cytochrome c oxidase subunit I (mtCOI) from the holotype also five sequences of Paithrips circularis were generated.
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Affiliation(s)
- Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India..
| | - Abhishek Patidar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India. Department of Zoology, University of Calcutta, Kolkata, West Bengal, India..
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India..
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India..
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20
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Pakrashi A, Tyagi K, Kumar V. The complete mitochondrial genome of Taeniothrips tigris Bhatti, 1995 (Thysanoptera: Thripidae). Mitochondrial DNA B Resour 2021; 6:2256-2257. [PMID: 34286091 PMCID: PMC8266248 DOI: 10.1080/23802359.2021.1947916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In this study, we sequenced complete mitogenome of Taeniothrips tigris Bhatti 1995. It was 15,501 bp in length containing 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes along with two non-coding regions. The overall base composition of Ta. tigris is 43.66% A, 35.20% T, 11.46% C, and 9.68% G, with a high AT bias of 78.86%. The constructed phylogeny using 19 mitogenomes revealed that the genus Taeniothrips is in close relationship with genus Thrips. This mitogenome data would help in deducing phylogenetic relationships studies in the order Thysanoptera.
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Affiliation(s)
- Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India.,Department of Zoology, University of Calcutta, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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21
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Jangra S, Baranwal VK, Dietzgen RG, Ghosh A. A rapid field-based assay using recombinase polymerase amplification for identification of Thrips palmi, a vector of tospoviruses. JOURNAL OF PEST SCIENCE 2021; 94:219-229. [PMID: 33046966 PMCID: PMC7541097 DOI: 10.1007/s10340-020-01284-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 05/03/2023]
Abstract
Thrips palmi (Thysanoptera: Thripidae) is an important pest of vegetables, ornamentals, and legumes worldwide. Besides damage caused by feeding, it transmits several tospoviruses. Identification of T. palmi at an early stage is crucial in implementing appropriate pest management strategies. Morpho-taxonomic identification of T. palmi based on the adult stage is time-consuming and needs taxonomic expertise. Here, we report a rapid, on-site, field-based assay for identification of T. palmi based on recombinase polymerase amplification (RPA), its first application in insects. RPA primers designed based on 3' polymorphisms of the Internal Transcribed Spacer 2 region efficiently discriminated T. palmi without any cross-reactivity to other predominant thrips species. RPA was performed with crude DNA, extracted from single T. palmi simply by crushing in sterile distilled water and could be completed within 20 min by holding the reaction tubes in the hand. The assay was further simplified by using fluorescent as well as colorimetric dyes thus eliminating the gel-electrophoresis steps. The presence of T. palmi was visualized by a change in color from dark blue to sky blue. The assay was validated with known thrips specimens and found to be effective in diagnosing the presence of T. palmi in natural vegetation. This on-site, rapid assay for diagnosis of T. palmi can be used by non-expert personnel in the field of quarantine and pest management.
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Affiliation(s)
- Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR—Indian Agricultural Research Institute, New Delhi, 110012 India
| | - V. K. Baranwal
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR—Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR—Indian Agricultural Research Institute, New Delhi, 110012 India
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22
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Kundu S, Kumar H, Tyagi K, Chandra K, Kumar V. DNA barcoding of selected short-horned grasshoppers (Orthoptera: Acrididae) from Indian Himalayan region. Mitochondrial DNA B Resour 2020; 5:3618-3623. [PMID: 33367033 PMCID: PMC7594861 DOI: 10.1080/23802359.2020.1830725] [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: 06/04/2020] [Accepted: 09/25/2020] [Indexed: 12/03/2022] Open
Abstract
In the context of Indian zoogeography, the DNA barcode data of short-horned grasshoppers (family Acrididae) are limited in global databases. Hence, the present study was aimed to collect selected Acridid species from the Indian Himalayan regions and generate DNA barcode data to enrich the global database. The estimated K2P genetic distances, Bayesian analysis (BA) topology and multiple species delimitation methods (ABGD, bPTP, and GMYC) clearly discriminate all the studied species. Based on high genetic distance (7.5%), multiple clades, and more than one molecular operational taxonomic unit, the present study elucidates the allopatric speciation and presence of possible cryptic diversity of Oxya japonica within India, China, and Russia. The present study suggests the collection of multiple specimens from different geographical locations and the generation of more DNA barcode data would facilitate the actual diversity of this insect group.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hirdesh Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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23
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Jiang KW, Zhang R, Zhang ZF, Pan B, Tian B. DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage. PLANT DIVERSITY 2020; 42:376-385. [PMID: 33134622 PMCID: PMC7584798 DOI: 10.1016/j.pld.2020.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Dumasia taxonomy and classification have long been problematic. Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify. In this study, we evaluated the ability of six DNA barcoding sequences, one nuclear (ITS) and five chloroplast regions (trnH-psbA, matK, rbcL, trnL-trnF, psbB-psbF), to efficiently identify Dumasia species. Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation. Most combined analyses including ITS showed good species resolution and identification efficiency. We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia. The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches, which may result from cryptic differentiation. Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.
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Affiliation(s)
- Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Fu Zhang
- Department of Wetland, Southwest Forestry University, Kunming, 650224, China
| | - Bo Pan
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China
| | - Bin Tian
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
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Gu J, Jiang B, Wang H, Wei T, Lin L, Huang Y, Huang J. Phylogeny and species delimitation of the genus Longgenacris and Fruhstorferiola viridifemorata species group (Orthoptera: Acrididae: Melanoplinae) based on molecular evidence. PLoS One 2020; 15:e0237882. [PMID: 32845927 PMCID: PMC7449498 DOI: 10.1371/journal.pone.0237882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic positions of the genus Longgenacris and one of its members, i.e. L. rufiantennus are controversial. The species boundaries within both of L. rufiantennus+Fruhstorferiola tonkinensis and F. viridifemorata species groups are unclear. In this study, we explored the phylogenetic positions of the genus Longgenacris and the species L. rufiantennus and the relationships among F. viridifemorata group based on the 658-base fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) barcode and the complete sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the nuclear ribosomal DNA. The phylogenies were reconstructed in maximum likelihood framework using IQ-TREE. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. Phylogenetic species concept and NJ tree, K2P distance, the statistical parsimony network as well as the generalized mixed Yule coalescent model (GMYC) were employed to delimitate the species boundaries in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups. The results demonstrated that the genus Longgenacris should be placed in the subfamily Melanoplinae but not Catantopinae, and L. rufiantennus should be a member of the genus Fruhstorferiola but not Longgenacris. Species boundary delimitation confirmed the presence of oversplitting in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups and suggested that each group should be treated as a single species.
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Affiliation(s)
- Jingxiao Gu
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
| | - Bing Jiang
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
| | - Haojie Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People’s Republic of China
| | - Tao Wei
- Tanxi Street Agency, Liunan Subdistrict, Liuzhou, Guangxi, People’s Republic of China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, People’s Republic of China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, People’s Republic of China
| | - Jianhua Huang
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
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Marullo R, Mercati F, Vono G. DNA Barcoding: A Reliable Method for the Identification of Thrips Species (Thysanoptera, Thripidae) Collected on Sticky Traps in Onion Fields. INSECTS 2020; 11:insects11080489. [PMID: 32752172 PMCID: PMC7469196 DOI: 10.3390/insects11080489] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 01/25/2023]
Abstract
Simple Summary Thrips species (Insecta, Thysanoptera) identification using traditional approach is not an easy. In the present study, DNA barcoding was used to support the thrips species characterization of a wide collection sampled in onion fields. Our findings confirmed the selected method as a simple and accurate approach identifying major thrips species, characterizing successfully nearly 86% of the samples collected in nine main species. The results here reported underlined the role of genetic markers as a valuable and useful method for species identification, especially when the morphological approach is unsure or even impossible. Abstract Several thrips species (Insecta, Thysanoptera) are globally known as important crop pests and vectors of viral diseases, but their identification is difficult because of their small body size and inconspicuous morphological differences. Sequencing variation in the mitochondrial cytochrome c oxidase I (COI) region has been proven to be useful for the identification of species of many groups of insect pests. Here, DNA barcoding has been used to identify thrips species collected with the use of sticky traps placed in an open onion field. A total of 238 thrips specimens were analyzed, 151 of which could be identified to species and 27 to genera belonging to the family Thripidae. Fifty-one specimens could not be assigned to any genus, with the closest BLAST match in the GenBank queries being below 98%, whilst six specimens were not recognized as Thysanoptera. The results indicate that, although there are a few pest thrips species not yet barcoded, most of the species that may cause damage to crops in Europe are represented in GenBank and other databases, enabling correct identification. Additionally, DNA barcoding can be considered a valuable alternative to the classic morphology method for identification of major thrips species.
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Affiliation(s)
- Rita Marullo
- Department of Agriculture, Mediterranean University of Reggio Calabria, Località Feo Di Vito, 89060 Reggio Calabria, Italy;
- Correspondence: ; Tel.: +39-0965-1694255
| | - Francesco Mercati
- Institute of Biosciences and Bioresources, National Research Council, 90129 Palermo, Italy;
| | - Gregorio Vono
- Department of Agriculture, Mediterranean University of Reggio Calabria, Località Feo Di Vito, 89060 Reggio Calabria, Italy;
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Kundu S, Lalremsanga HT, Purkayastha J, Biakzuala L, Chandra K, Kumar V. DNA barcoding elucidates the new altitude record and range-extension of lesser-known bullfrog ( Hoplobatrachus litoralis) in northeast India. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1787259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Mizoram, India
| | | | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Mizoram, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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Kundu S, Lalremsanga HT, Rahman MM, Ahsan MF, Biakzuala L, Kumar V, Chandra K, Siddiki AMAMZ. DNA barcoding elucidates the population genetic diversity of venomous cobra species (Reptilia: Elapidae) in Indo-Bangladesh region. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1778552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Md. Mizanur Rahman
- Venom Research Centre Bangladesh, Department of Medicine, Chittagong Medical College, Chattogram, Bangladesh
| | - Md. Farid Ahsan
- Department of Zoology, University of Chittagong, Chattogram, Bangladesh
| | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - A. M. A. M. Zonaed Siddiki
- Department of Pathology and Parasitology, Chittagong Veterinary and Animal Sciences University, Chattogram, Bangladesh
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Kim S, Lee Y, Mutanen M, Seung J, Lee S. High functionality of DNA barcodes and revealed cases of cryptic diversity in Korean curved-horn moths (Lepidoptera: Gelechioidea). Sci Rep 2020; 10:6208. [PMID: 32277166 PMCID: PMC7148304 DOI: 10.1038/s41598-020-63385-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 03/30/2020] [Indexed: 01/20/2023] Open
Abstract
Curved-horn moths or gelechioid moths (Lepidoptera: Gelechioidea) represent one of the most diverse lepidopteran groups. Due to the large number of species, generally small size of adults and subtle morphological differences, their confident identification requires tenacious and long-term dedication on their diversity. Over the past decade, DNA barcoding has repeatedly been used to elucidate boundaries of species in many large and difficult groups. Here, we conducted a test of DNA barcoding with the diverse fauna of Korean Gelechioidea with very little prior information of COI gene region from the area. Altogether 509 specimens representing 154 morphospecies were included in the study. The species assignments of all three tested species delimitation methods (ABGD, bPTP and PTP) were consistent with morphological identifications for 117 species (75.97%). A threshold of 2.5% genetic divergence was observed to differentiate the morphological species efficiently. Careful morphological examination of morphospecies exceeding 2.5% intraspecific variability prove cryptic diversity in three species (Neoblastobasis biceratala, Evippe albidoesella and Promalactis atriplagata). One morphospecies, Promalactis odaiensis, showed high intraspecific divergence while consisted of only a single MOTU. Overall, DNA barcoding was shown to provide a powerful tool to discriminate species of Korean Gelechioidea and reveal cases of cryptic diversity.
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Affiliation(s)
- Sora Kim
- Laboratory of Insect Biosystematics, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Yerim Lee
- Laboratory of Insect Biosystematics, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Marko Mutanen
- Ecology and Genetics Research Unit, PO Box 3000, FI-90014, University of Oulu, Oulu, Finland
| | - Jinbae Seung
- Laboratory of Insect Biosystematics, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seunghwan Lee
- Laboratory of Insect Biosystematics, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Hidden Genetic Variability, Can the Olive Moth Prays oleae (Lepidoptera: Yponomeutidae or Praydidae?) be a Species' Complex? INSECTS 2020; 11:insects11040204. [PMID: 32225064 PMCID: PMC7240722 DOI: 10.3390/insects11040204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 11/17/2022]
Abstract
Prays oleae is the second most important pest in Mediterranean olive groves, causing substantial damage on olive production. We used mitochondrial [cytochrome c oxidase subunit I (COI), and NADH dehydrogenase subunit 5 (nad5)] and nuclear [ribosomal protein S5 (RpS5)] amplicons to assess the population variability in five main olive producing regions from Tunisia, to support or dismiss the existence of two non-monophyletic groups within the species, as found within Portugal. Our phylogenetic analysis with cytochrome c oxidase subunit I (COI) indeed displayed two distinct and well-supported clades of P. oleae, which were corroborated by the haplotype network reconstructed with both mitochondrial and nuclear amplicons. We were also able to dismiss the hypothesis that one of the clades would not develop on olive fruits. No correlation was observed between clades differentiation and geographic distribution. The existence of cryptic species can impact on the management of agroecosystems and on the perception of how these moths responds to environmental changes.
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Jangra S, Mittal A, Dhall H, Jain RK, Ghosh A. A multiplex PCR assay for rapid identification of major tospovirus vectors reported in India. BMC Genomics 2020; 21:170. [PMID: 32070289 PMCID: PMC7029577 DOI: 10.1186/s12864-020-6560-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To date, four thrips vectors have been reported to transmit five different tospoviruses in India. Their identification at an early stage is crucial in formulating appropriate pest management strategies. Since morphometric key-based thrips identification based on the adult stage is time-consuming, there is a need to develop diagnostic tools which are rapid, accurate, and independent of developmental stages. Here, we report a multiplex PCR assay to identify four major thrips vectors viz. Thrips palmi, T. tabaci, Scirtothrips dorsalis, and Frankliniella schultzei present in India. RESULTS Cytochrome oxidase subunit III and internal transcribed spacer region 2 were utilized to design species-specific primers. Of 38 pairs of primers tested, primer pairs AG35F-AG36R, AG47F-AG48R, AG87F-AG88R, and AG79F-AG80R amplified 568 bp, 713 bp, 388 bp, and 200 bp products from the DNA templates of T. palmi, S. dorsalis, T. tabaci, and F. schultzei, respectively at same PCR conditions. The specificity of the primer pairs was validated with a large number of known specimens and no cross-reactivity was observed with other thrips species. The multiplex PCR assay with a cocktail of all the four primer pairs detected four thrips vectors efficiently and could discriminate all of them concurrently in a single reaction. CONCLUSION The multiplex PCR reported in this study could identify the major thrips vectors reported in India. The assay will be useful in ascertaining distribution profile of major thrips vectors, disease epidemiology, screening large samples, and quarantine.
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Affiliation(s)
- Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anubha Mittal
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Heena Dhall
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rakesh Kumar Jain
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Two Distinct Genotypes of Spissistilus festinus (Say, 1830) (Hemiptera, Membracidae) in the United States Revealed by Phylogenetic and Morphological Analyses. INSECTS 2020; 11:insects11020080. [PMID: 31979389 PMCID: PMC7073536 DOI: 10.3390/insects11020080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/19/2020] [Accepted: 01/21/2020] [Indexed: 11/16/2022]
Abstract
Spissistilus festinus (Say, 1830) (Hemiptera: Membracidae) is a frequent pest of leguminous crops in the Southern United States, and a vector of grapevine red blotch virus. There is currently no information on the genetic diversity of S. festinus. In this study, populations of S. festinus were collected in 2015-2017 from various crops and geographic locations in the United States, and fragments of the mitochondrial cytochrome C oxidase 1 (mt-COI) gene and the nuclear internal transcribed spacer 2 (ITS2) region were characterized by polymerase chain reaction and sequencing. Maximum-likelihood and Bayesian analyses of the mt-COI and ITS2 sequences yielded similar phylogenetic tree topologies, revealing two distinct genetic S. festinus lineages with all of the specimens from California comprising one phylogenetic clade, alongside a single GenBank entry from Arizona, and all specimens from the Southeastern United States comprising a statistically-supported distinct clade, regardless of host and year of collection. The mt-COI gene fragment showed up to 10.8% genetic distance between the two phylogenetic clades. These results suggest the existence of two genotypes within S. festinus in the United States. The only distinct morphological trait between the two genotypes was a less elevated pronotum in the representative specimens from California, compared to the representative specimens from the Southeastern United States. Since this phenotypic feature is inconspicuous, a diagnostic polymerase chain reaction targeting a variable region of the mt-COI fragment was developed to reliably distinguish between the specimens of the two genotypes of S. festinus and to facilitate their specific identification.
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Tyagi K, Kumar V, Kundu S, Pakrashi A, Prasad P, Caleb JTD, Chandra K. Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex. Sci Rep 2019; 9:14033. [PMID: 31575965 PMCID: PMC6773733 DOI: 10.1038/s41598-019-50510-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/22/2019] [Indexed: 01/01/2023] Open
Abstract
Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders.
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Affiliation(s)
- Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India.
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Priya Prasad
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - John T D Caleb
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
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Exposure to watermelon bud necrosis virus and groundnut bud necrosis virus alters the life history traits of their vector, Thrips palmi (Thysanoptera: Thripidae). Arch Virol 2019; 164:2799-2804. [PMID: 31440810 DOI: 10.1007/s00705-019-04381-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/23/2019] [Indexed: 10/26/2022]
Abstract
Thrips palmi transmits the tospoviruses watermelon bud necrosis (WBNV) and groundnut bud necrosis virus (GBNV) in persistent propagative way. Little is known about the T. palmi-WBNV and -GBNV relationship. In this study, we report the effects of WBNV and GBNV infection on the life history traits of T. palmi. Both WBNV and GBNV had some negative effects on the adult life span, fecundity and survival of T. palmi as compared to non-exposed T. palmi. Tospovirus exposure favoured a female-biased ratio in the experimental population.
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Chakraborty R, Singha D, Kumar V, Pakrashi A, Kundu S, Chandra K, Patnaik S, Tyagi K. DNA barcoding of selected Scirtothrips species (Thysanoptera) from India. Mitochondrial DNA B Resour 2019; 4:2710-2714. [PMID: 33365695 PMCID: PMC7706545 DOI: 10.1080/23802359.2019.1644547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/10/2019] [Indexed: 12/03/2022] Open
Abstract
The members of the genus Scirtothrips are highly polyphagous, including major pest and vector species. We applied both morphology and molecular approaches to delimit the selected Scirtothrips species from India. Out of 43 generated barcode sequences, six sequences of three species (S. hitam, S. mangiferae, and S. malayensis) are the novel contribution in global database. The Bayesian (BA) phylogeny clearly distinguishes all the studied species with reciprocal monophyletic criteria and represents multiple clades in S. dorsalis and S. oligochaetus. The high Kimura-2-Parameter (K2P) genetic divergences were observed between the multiple clades of S. dorsalis (4.5-8.8%) and S. oligochaetus (6.4%), which indicating possible existence of cryptic diversity. The current study also provided the morphological keys for six Scirtothrips species including S. hitam as a new record to India.
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Affiliation(s)
- Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, India
| | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, India
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, India
| | - Srinivas Patnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, India
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Kundu S, Chandra K, Tyagi K, Pakrashi A, Kumar V. DNA barcoding of freshwater fishes from Brahmaputra River in Eastern Himalaya biodiversity hotspot. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2411-2419. [PMID: 33365567 PMCID: PMC7710314 DOI: 10.1080/23802359.2019.1637290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The genetic diversity of freshwater fishes is still anonymous in several drainage systems in northeast India. Moreover, the comparative genetic analysis is largely sporadic to judge their actual diversity and true status. We generated 89 DNA barcodes of 40 morphologically identified fishes collected from two major tributaries of Brahmaputra River. The comparative study revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in Bayesian (BA) tree. Considering the genetic divergence (2%) for species discrimination boundary, the high genetic diversity (2.36–10.73%) was detected in 11 species (Macrognathus pancalus, Channa punctata, Puntius terio, Bangana ariza, Garra arupi, Badis badis, Mystus vittatus, Rita rita, Gagata cenia, Mastacembelus armatus, and Danio dangila), which signified the occurrence of concealed genetic diversity in this ecozone. However, the insignificant genetic distances were also noticed in few reportedly valid species: Channa stiktos and C. ornatipinnis (1.43%); Mystus ngasep, M. rufescens, and M. carcio (0.4%); Glyptothorax trilineatus, G. churamanii, and G. verrucosus (0.4%); Botia almorhae, B. histrionica, B. lohachata, and B. rostrata (0–0.4%); Barilius barilia and B. vagra (0.4%); Batasio merianiensis and B. tengana (1.2%); Puntius chola and P. fraseri (0%), Schistura beavani and S. paucireticulata (0%); hence to validate this species, generation of more barcode data was required from their types or topotypes. The present study would help to develop conservation schemes for the native species and collegiate ecosystem, which associated with the livelihoods of millions of ethnic communities in this region.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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Bragard C, Dehnen-Schmutz K, Di Serio F, Gonthier P, Jacques MA, Jaques Miret JA, Fejer Justesen A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Malumphy C, Czwienczek E, MacLeod A. Pest categorisation of Thrips palmi. EFSA J 2019; 17:e05620. [PMID: 32626236 PMCID: PMC7009038 DOI: 10.2903/j.efsa.2019.5620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The EFSA Panel on Plant Health (PLH) performed a pest categorisation of Thrips palmi (Thysanoptera: Thripidae), for the EU. T. palmi is listed in Annex IAI of 2000/29 EC. Using molecular methods, cryptic speciation has been shown although no new species from the group have been formally described. Here, we consider T. palmi sensu lato as a defined species native to southern Asia, which has spread to tropical and subtropical countries in Asia, the Pacific, North, Central and South America, Africa and Australia. T. palmi has been reported from many different hosts in 20 botanical families; Cucurbitaceae, Solanaceae and Orchidaceae are of primary importance. T. palmi has been intercepted many times on plants from these families. Wild and cultivated hosts are widespread in the EU. However, as a subtropical and tropical species, only a small area of the EU provides climatic conditions where establishment may be possible outdoors. Several host plants are cultivated in glasshouses where conditions may be more favourable for establishment in year-round crops. There have been past outbreaks of T. palmi in EU glasshouses and outdoors in Portugal. T. palmi causes feeding and oviposition damage and populations in Asia are competent vectors of tospoviruses. Impacts could occur on many hosts, especially Cucurbitaceae, Solanaceae and ornamental plants particularly in glasshouses. Phytosanitary measures aim to prevent the entry of T. palmi specifically on cut flowers of Orchidaceae and fruits of Momordica and Solanum melongena. The species meets all the criteria assessed by the PLH Panel to satisfy the definition of a Union quarantine pest, while it does not satisfy all the criteria for it to be regarded as a Union regulated non-quarantine pest (RNQP).
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Kumar V, Tyagi K, Kundu S, Chakraborty R, Singha D, Chandra K. The first complete mitochondrial genome of marigold pest thrips, Neohydatothrips samayunkur (Sericothripinae) and comparative analysis. Sci Rep 2019; 9:191. [PMID: 30655597 PMCID: PMC6336932 DOI: 10.1038/s41598-018-37889-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 12/10/2018] [Indexed: 11/16/2022] Open
Abstract
Complete mitogenomes from the order Thysanoptera are limited to representatives of the subfamily Thripinae. Therefore, in the present study, we sequenced the mitochondrial genome of Neohydatothrips samayunkur (15,295 bp), a member of subfamily Sericothripinae. The genome possesses the canonical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs) as well as two putative control regions (CRs). The majority strand was 77.42% A + T content, and 22.58% G + C with weakly positive AT skew (0.04) and negative GC skew (-0.03). The majority of PCGs start with ATN codons as observed in other insect mitochondrial genomes. The GCG codon (Alanine) was not used in N. samayunkur. Most tRNAs have the typical cloverleaf secondary structure, however the DHU stem and loop were absent in trnV and trnS1, while the TΨC loop was absent in trnR and trnT. The two putative control regions (CR1 and CR2) show 99% sequence similarity indicated a possible duplication, and shared 57 bp repeats were identified. N. samayunkur showed extensive gene rearrangements, with 11 PCGs, 22 tRNAs, and two rRNAs translocated when compared to the ancestral insect. The gene trnL2 was separated from the 'trnL2-cox2' gene block, which is a conserved, ancestral gene order found in all previously sequenced thrips mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees resulted in similar topologies. The phylogenetic position of N. samayunkur indicates that subfamily Sericothripinae is sister to subfamily Thripinae. More molecular data from different taxonomic groups is needed to understand thrips phylogeny and evolution.
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Affiliation(s)
- Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India.
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
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Kundu S, Kumar V, Tyagi K, Rath S, Pakrashi A, Saren PC, Kosygin L, Chandra K. Mitochondrial DNA detects Arctonyx collaris from burnt body parts: a wildlife forensic case study in Indo-Burma biodiversity hotspot. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Shibananda Rath
- Freshwater Fish Section, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | | | | | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
- Freshwater Fish Section, Zoological Survey of India, Kolkata, India
- Wildlife Section, Zoological Survey of India, Kolkata, India
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Kundu S, Sharma G, Balakrishnan S, Tyagi K, Chandra K, Kumar V. DNA barcoding identified two endangered dolphins: threats on living aquatic mammals in India. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1536467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Shantanu Kundu
- 1Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Gopal Sharma
- 2Gangetic Plains Regional Centre, Zoological Survey of India, Patna, India
| | | | - Kaomud Tyagi
- 1Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- 1Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
- 2Gangetic Plains Regional Centre, Zoological Survey of India, Patna, India
- 3Marine Aquarium and Research Centre, Zoological Survey of India, Digha, India
| | - Vikas Kumar
- 1Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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Kundu S, Pakrashi A, Laskar BA, Rahaman I, Tyagi K, Kumar V, Chandra K. DNA barcoding reveals distinct population of Plotosus canius(Siluriformes: Plotosidae) in Sundarbans waters. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systemtics Division, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systemtics Division, Zoological Survey of India, Kolkata, India
| | - Boni Amin Laskar
- Freshwater Biology Regional Centre, Zoological Survey of India, Hyderabad, India
| | - Iftikar Rahaman
- Centre for DNA Taxonomy, Molecular Systemtics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systemtics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systemtics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systemtics Division, Zoological Survey of India, Kolkata, India
- Freshwater Biology Regional Centre, Zoological Survey of India, Hyderabad, India
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Bakhoum MT, Sarr M, Fall AG, Huber K, Fall M, Sembène M, Seck MT, Labuschagne K, Gardès L, Ciss M, Gimonneau G, Bouyer J, Baldet T, Garros C. DNA barcoding and molecular identification of field-collected Culicoides larvae in the Niayes area of Senegal. Parasit Vectors 2018; 11:615. [PMID: 30509304 PMCID: PMC6276223 DOI: 10.1186/s13071-018-3176-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/28/2018] [Indexed: 12/26/2022] Open
Abstract
Background Biting midge species of the genus Culicoides Latreille (Diptera: Ceratopogonidae) comprise more than 1300 species distributed worldwide. Several species of Culicoides are vectors of various viruses that can affect animals, like the African horse sickness virus (AHSV), known to be endemic in sub-Saharan Africa. The ecological and veterinary interest of Culicoides emphasizes the need for rapid and reliable identification of vector species. However, morphology-based identification has limitations and warrants integration of molecular data. DNA barcoding based on the mitochondrial gene cytochrome c oxidase subunit 1 (cox1) is used as a rapid and authentic tool for species identification in a wide variety of animal taxa across the globe. In this study, our objectives were as follows: (i) establish a reference DNA barcode for Afrotropical Culicoides species; (ii) assess the accuracy of cox1 in identifying Afrotropical Culicoides species; and (iii) test the applicability of DNA barcoding for species identification on a large number of samples of Culicoides larvae from the Niayes area of Senegal, West Africa. Results A database of 230 cox1 sequences belonging to 42 Afrotropical Culicoides species was found to be reliable for species-level assignments, which enabled us to identify cox1 sequences of Culicoides larvae from the Niayes area of Senegal. Of the 933 cox1 sequences of Culicoides larvae analyzed, 906 were correctly identified by their barcode sequences corresponding to eight species of Culicoides. A total of 1131 cox1 sequences of adult and larval Culicoides were analyzed, and a hierarchical increase in mean divergence was observed according to two taxonomic levels: within species (mean = 1.92%, SE = 0.00), and within genus (mean = 17.82%, SE = 0.00). Conclusions Our study proves the efficiency of DNA barcoding for studying Culicoides larval diversity in field samples. Such a diagnostic tool offers great opportunities for investigating Culicoides immature stages ecology and biology, a prerequisite for the implementation of eco-epidemiological studies to better control AHSV in the Niayes region of Senegal, and more generally in sub-Saharan Africa. Electronic supplementary material The online version of this article (10.1186/s13071-018-3176-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mame Thierno Bakhoum
- Institut Sénégalais de Recherches Agricoles, Laboratoire National de l'Elevage et de Recherches Vétérinaires, BP 2057, Dakar, Sénégal. .,CIRAD, UMR ASTRE, F-34398, Montpellier, France. .,ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France.
| | - Mamadou Sarr
- Institut Sénégalais de Recherches Agricoles, Laboratoire National de l'Elevage et de Recherches Vétérinaires, BP 2057, Dakar, Sénégal
| | - Assane Gueye Fall
- Institut Sénégalais de Recherches Agricoles, Laboratoire National de l'Elevage et de Recherches Vétérinaires, BP 2057, Dakar, Sénégal
| | - Karine Huber
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Moussa Fall
- Institut Sénégalais de Recherches Agricoles, Laboratoire National de l'Elevage et de Recherches Vétérinaires, BP 2057, Dakar, Sénégal
| | - Mbacké Sembène
- Département de Biologie Animale, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Momar Talla Seck
- Institut Sénégalais de Recherches Agricoles, Laboratoire National de l'Elevage et de Recherches Vétérinaires, BP 2057, Dakar, Sénégal
| | - Karien Labuschagne
- Agricultural Research Council-Onderstepoort Veterinary Research, Epidemiology, Parasites and Vectors, Onderstepoort, ZA-0110, South Africa.,Department of Zoology and Entomology, University of Pretoria, Pretoria, ZA-0002, South Africa
| | - Laetitia Gardès
- CIRAD, UMR ASTRE, F-34398, Montpellier, France.,ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Mamadou Ciss
- Institut Sénégalais de Recherches Agricoles, Laboratoire National de l'Elevage et de Recherches Vétérinaires, BP 2057, Dakar, Sénégal
| | - Geoffrey Gimonneau
- CIRAD, UMR INTERTRYP, F-34398, Montpellier, France.,Centre International de Recherche - Développement sur l'Elevage en zone subhumide, Bobo-Dioulasso 01, BP 454, Burkina Faso
| | - Jérémy Bouyer
- CIRAD, UMR ASTRE, F-34398, Montpellier, France.,ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Thierry Baldet
- CIRAD, UMR ASTRE, F-34398, Montpellier, France.,ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Claire Garros
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France.,CIRAD, UMR ASTRE, Sainte Clotilde, F- 97491, Réunion, France
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Singha D, V VK, Chakraborty R, Kundu S, Hosamani A, Kumar V, Tyagi K. Molecular footprint of Frankliniella occidentalis from India: a vector of Tospoviruses. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 4:39-42. [PMID: 33365412 PMCID: PMC7510648 DOI: 10.1080/23802359.2018.1536446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/20/2018] [Indexed: 11/10/2022]
Abstract
The western flower thrips, F. occidentalis is a vector of Tospoviruses and native to Western North America and Mexico. The present study is based on collected F. occidentalis specimens from Karnataka state in southern India and morphologically identified through available keys. The generated DNA barcode data show 99–100% similarity with the database sequences of F. occidentalis. The phylogenetic analysis (NJ, ML, and BA) shows three distinct clades of F. occidentalis in the present dataset with high bootstrap supports and posterior probabilities. The K2P genetic distances further depicted high similarity of the generated sequences from India and Netherlands. The Clade-1 (India + Netherlands) also shows a close relationship with Clade-2 (Kenya) rather than Clade-3 (Canada + USA). This study recorded the first genetic footprint of F. occidentalis in India and indicated the gene flow from the Netherlands to India. The similar molecular techniques may help to detect the invasion of many alien species in the near future and assists the quarantine regulations to protect the native ecosystem.
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Affiliation(s)
- Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematic Division, Zoological Survey of India, New Alipore, Kolkata, India
| | - Vishal Kumar V
- University of Agricultural Sciences, Raichur, Karnataka, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematic Division, Zoological Survey of India, New Alipore, Kolkata, India
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematic Division, Zoological Survey of India, New Alipore, Kolkata, India
| | | | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematic Division, Zoological Survey of India, New Alipore, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematic Division, Zoological Survey of India, New Alipore, Kolkata, India
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Chakraborty R, Tyagi K, Kundu S, Rahaman I, Singha D, Chandra K, Patnaik S, Kumar V. The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae): Comparative analysis. PLoS One 2018; 13:e0199404. [PMID: 30379813 PMCID: PMC6209132 DOI: 10.1371/journal.pone.0199404] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/21/2018] [Indexed: 11/19/2022] Open
Abstract
The melon thrips, Thrips palmi is a serious pest and vector for plant viruses on a wide range of economically important crops. DNA barcoding evidenced the presence of cryptic diversity in T. palmi and that warrants exhaustive molecular studies. Our present study is on decoding the first complete mitochondrial genome of T. palmi (15,333 bp) through next-generation sequencing (NGS). The T. palmi mt genome contains 37 genes, including 13 Protein coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA (tRNAs), and two control regions (CRs). The majority strand of T. palmi revealed 78.29% A+T content, and 21.72% G+C content with positive AT skew (0.09) and negative GC skew (-0.06). The ATN initiation codons were observed in 12 PCGs except for cox1 which have unique start codon (TTG). The relative synonymous codon usage (RSCU) analysis revealed Phe, Leu, Ile, Tyr, Asn, Lys and Met were the most frequently used amino acids in all PCGs. The codon (CGG) which is assigned to Arginine in most insects but absent in T. palmi. The Ka/Ks ratio ranges from 0.078 in cox1 to 0.913 in atp8. We observed the typical cloverleaf secondary structure in most of the tRNA genes with a few exceptions; absence of DHU stem and loop in trnV and trnS, absence of DHU loop in trnE, lack of T-arm and loop in trnN. The T. palmi gene order (GO) was compared with ancestral GO and observed an extensive gene arrangement in PCGs, tRNAs and rRNAs. The cox2 gene was separated from the gene block 'cox2-trnL2' in T. palmi as compared with the other thrips mt genomes, including ancestor GO. Further, the nad1, trnQ, trnC, trnL1, trnV, trnF, rrnS, and rrnL were inversely transpositioned in T. palmi GO. The gene blocks 'trnQ-trnS2-trnD' and 'trnN-trnE-trnS1-trnL1' seems to be genus specific. The T. palmi mt genome contained 24 intergenic spacer regions and 12 overlapping regions. The 62 bp of CR2 shows the similarity with CR1 indicating a possible duplication. The occurrence of multiple CRs in thrips mt genomes seems to be a derived trait which needs further investigation. Although, the study depicted extensive gene rearrangements in T. palmi mt genome, but the negative GC skew reflects only strand asymmetry. Both the ML and BI phylogenetic trees revealed the close relationships of Thrips with Scirtothrips as compared to Frankliniella. Thus, more mt genomes of the diverse thrips species are required to understand the in-depth phylogenetic and evolutionary relationships.
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Affiliation(s)
- Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
| | - Iftikar Rahaman
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
| | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
| | - Srinivas Patnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
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Kaczmarczyk A, Kucharczyk H, Kucharczyk M, Kapusta P, Sell J, Zielińska S. First insight into microbiome profile of fungivorous thrips Hoplothrips carpathicus (Insecta: Thysanoptera) at different developmental stages: molecular evidence of Wolbachia endosymbiosis. Sci Rep 2018; 8:14376. [PMID: 30258200 PMCID: PMC6158184 DOI: 10.1038/s41598-018-32747-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022] Open
Abstract
Insects' exoskeleton, gut, hemocoel, and cells are colonized by various microorganisms that often play important roles in their host life. Moreover, insects are frequently infected by vertically transmitted symbionts that can manipulate their reproduction. The aims of this study were the characterization of bacterial communities of four developmental stages of the fungivorous species Hoplothrips carpathicus (Thysanoptera: Phlaeothripidae), verification of the presence of Wolbachia, in silico prediction of metabolic potentials of the microorganisms, and sequencing its mitochondrial COI barcode. Taxonomy-based analysis indicated that the bacterial community of H. carpathicus contained 21 bacterial phyla. The most abundant phyla were Proteobacteria, Actinobacteria, Bacterioidetes and Firmicutes, and the most abundant classes were Alphaproteobacteria, Actinobacteria, Gammaproteobacteria and Betaproteobacteria, with different proportions in the total share. For pupa and imago (adult) the most abundant genus was Wolbachia, which comprised 69.95% and 56.11% of total bacterial population respectively. Moreover, similarity analysis of bacterial communities showed that changes in microbiome composition are congruent with the successive stages of H. carpathicus development. PICRUSt analysis predicted that each bacterial community should be rich in genes involved in membrane transport, amino acid metabolism, carbohydrate metabolism, replication and repair processes.
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Affiliation(s)
- Agnieszka Kaczmarczyk
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Halina Kucharczyk
- Department of Zoology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Marek Kucharczyk
- Department of Nature Protection, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Przemysław Kapusta
- Center for Medical Genomics - OMICRON, Jagiellonian University Medical College, Kopernika 7c, 31-034, Kraków, Poland
| | - Jerzy Sell
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Sylwia Zielińska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
- Phage Consultants, Partyzantow 10/18, 80-254, Gdansk, Poland
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Wu W, Ng WL, Yang JX, Li WM, Ge XJ. High cryptic species diversity is revealed by genome-wide polymorphisms in a wild relative of banana, Musa itinerans, and implications for its conservation in subtropical China. BMC PLANT BIOLOGY 2018; 18:194. [PMID: 30217175 PMCID: PMC6137913 DOI: 10.1186/s12870-018-1410-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown. RESULTS Using genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event. CONCLUSION Our results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&P.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Wei-Lun Ng
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Jun-Xin Yang
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wei-Ming Li
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650 China
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