Prediction of species composition ratios in pooled specimens of the Anopheles Hyrcanus group using quantitative sequencing

Abstract Background Plasmodium vivax is transmitted by members of the Anopheles Hyrcanus Group that includes six species in the Republic of Korea: Anopheles sinensis sensu stricto (s.s.), Anopheles pullus, Anopheles kleini, Anopheles belenrae, Anopheles lesteri, and Anopheles sineroides. Individual Anopheles species within the Hyrcanus Group demonstrate differences in their geographical distributions, vector competence and insecticide resistance, making it crucial for accurate species identification. Conventional species identification conducted using individual genotyping (or barcoding) based on species-specific molecular markers requires extensive time commitment and financial resources. Results A population-based quantitative sequencing (QS) protocol developed in this study provided a rapid estimate of species composition ratios among pooled mosquitoes as a cost-effective alternative to individual genotyping. This can be accomplished by using species- or group-specific nucleotide sequences of the mitochondrial cytochrome C oxidase subunit I (COI) and the ribosomal RNA internal transcribed spacer 2 (ITS2) region as species identification alleles in a two-step prediction protocol. Standard genomic DNA fragments of COI and ITS2 genes were amplified from each Anopheles species using group-specific universal primer sets. Following sequencing of the COI or ITS2 amplicons generated from sets of standard DNA mixtures, equations were generated via linear regression to predict species-specific nucleotide sequence frequencies at different positions. Species composition ratios between An. sineroides, An. pullus and An. lesteri were estimated from QS of the COI amplicons based on the mC.260A, mC.122C and mC.525C alleles at the first step, followed by the prediction of species composition ratios between An. sinensis, An. kleini and An. belenrae based on QS of the ITS2 amplicons using the rI.370G and rI.389T alleles. The COI copy number was not significantly different between species, suggesting the reliability of COI-based prediction. In contrast, ITS2 showed a slightly but significantly higher copy number in An. belenrae, requiring an adjustment of its predicted composition ratio. A blind test proved that predicted species composition ratios either from pooled DNA specimens or pooled mosquito specimens were not statistically different from the actual values, demonstrating that the QS-based prediction is accurate and reliable. Conclusions This two-step prediction protocol will facilitate rapid estimation of the species composition ratios in field-collected Anopheles Hyrcanus Group populations and is particularly useful for studying the vector ecology of Anopheles population and epidemiology of malaria.

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Prediction of species composition ratios in pooled specimens of the Anopheles Hyrcanus Group using quantitative sequencing

10.21203/rs.3.rs-377170/v1 ◽

2021 ◽

Author(s):

Do Eun Lee ◽

Heung-Chul Kim ◽

Sung-Tae Chong ◽

Terry A. Klein ◽

Ju Hyeon Kim ◽

...

Keyword(s):

Species Composition ◽

Species Identification ◽

Its2 Region ◽

Vector Ecology ◽

Universal Primer ◽

Blind Test ◽

Individual Genotyping ◽

Composition Ratios ◽

Species Specific ◽

Specific Nucleotide

Abstract Background Vivax malaria is transmitted by members of the Anopheles Hyrcanus Group that includes six species (Anopheles sinensis s.s., An. pullus, An. kleini, An. belenrae, An. lesteri, and An. sineroides) in Republic of Korea. Individual Anopheles species within the Hyrcanus Group demonstrate differences in their geographical distributions, vector competence and insecticide resistance, making it crucial for accurate species identification. Conventional species identification conducted using individual genotyping (or barcoding) based on species specific molecular markers requires extensive time commitment and financial resources. Results A population-based quantitative sequencing (QS) protocol developed in this study provided a rapid estimate of species composition ratios among pooled mosquitoes as a cost-effective alternative to individual genotyping. This can be accomplished by using species- or group-specific nucleotide sequences of the mitochondrial cytochrome C oxidase subunit I (COI) and the ribosomal RNA internal transcribed spacer 2 (ITS2) region as species identification markers in a two-step prediction protocol. Standard genomic DNA fragments of COI and ITS2 genes were amplified from each Anopheles species using group-specific universal primer sets. Following sequencing of the COI or ITS2 amplicons generated from sets of standard DNA mixtures, equations were generated via linear regression to predict species-specific nucleotide sequence frequencies at different loci. Species composition ratios between An. sineroides, An. pullus and An. lesteri were estimated from QS of the COI amplicons based on the mC.260A, mC.122C and mC.525C markers at the first step, followed by the prediction of species composition ratios between An. sinensis, An. kleini and An. belenrae based on QS of the ITS2 amplicons using the rI.370G and rI.389T markers. A blind test proved that predicted species composition ratios were not statistically different from the actual values, demonstrating that the QS-based prediction is accurate and reliable. Conclusions This two-step prediction protocol will facilitate rapid estimation of the species composition ratios in field-collected Anopheles Hyrcanus Group populations and is particularly useful for studying the vector ecology of Anopheles population and epidemiology of malaria.

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Identification of Novel Germline and Tumor-Specific Nucleotide Variants and Copy Number Variation in Clival Chordomas by Exome Sequencing

Journal of Neurological Surgery Part B Skull Base ◽

10.1055/s-0035-1546555 ◽

2015 ◽

Vol 76 (S 01) ◽

Author(s):

Georgios Zenonos ◽

Peter Howard ◽

Maureen Lyons-Weiler ◽

Wang Eric ◽

William LaFambroise ◽

...

Keyword(s):

Copy Number Variation ◽

Exome Sequencing ◽

Copy Number ◽

Number Variation ◽

Specific Nucleotide

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Bacterial Species Identification after DNA Amplification with a Universal Primer Pair

Molecular Genetics and Metabolism ◽

10.1006/mgme.1998.2795 ◽

1999 ◽

Vol 66 (3) ◽

pp. 205-211 ◽

Cited By ~ 60

Author(s):

Kevin M. McCabe ◽

Yao-Hua Zhang ◽

Bing-Ling Huang ◽

Elizabeth A. Wagar ◽

Edward R.B. McCabe

Keyword(s):

Species Identification ◽

Bacterial Species ◽

Dna Amplification ◽

Universal Primer

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Rapid Species Identification of Cooked Poisonous Mushrooms by Using Real-Time PCR

Applied and Environmental Microbiology ◽

10.1128/aem.02082-07 ◽

2008 ◽

Vol 74 (10) ◽

pp. 3306-3309 ◽

Cited By ~ 24

Author(s):

Kazuhiko Maeta ◽

Tomoya Ochi ◽

Keisuke Tokimoto ◽

Norihiro Shimomura ◽

Nitaro Maekawa ◽

...

Keyword(s):

Real Time ◽

Species Identification ◽

Real Time Pcr ◽

Specific Test ◽

Specific Identification ◽

Specific Fluorescence ◽

Species Specific ◽

Poisonous Mushrooms

ABSTRACT Species-specific identification of the major cooked and fresh poisonous mushrooms in Japan was performed using a real-time PCR system. Specific fluorescence signals were detected, and no nonspecific signals were detected. Therefore, we succeeded in developing a species-specific test for the identification of poisonous mushrooms within 1.5 h.

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Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

Iheringia Série Zoologia ◽

10.1590/1678-4766e2017016 ◽

2017 ◽

Vol 107 (0) ◽

Author(s):

Andrea A. F. Mourão ◽

Diogo Freitas-Souza ◽

Diogo T. Hashimoto ◽

Daniela C. Ferreira ◽

Fernanda D. do Prado ◽

...

Keyword(s):

Species Delimitation ◽

Parental Species ◽

Future Research ◽

Correct Identification ◽

Pcr Multiplex ◽

Pcr Rflp ◽

Genetic Pattern ◽

Morphometric Methods ◽

Species Specific ◽

Specific Nucleotide

ABSTRACT The hybridization is a widely-discussed issue in several studies with fish species. For some authors, hybridization may be related with diversification and speciation of several groups, or also with the extinction of populations or species. Difficulties to differentiate species and hybrids may be a problem to correctly apply a management of wild species, because hybrid lineages, especially the advanced ones, may resemble the parental species. The genus Cichla Bloch & Schneider, 1801 constitutes an interesting experimental model, considering that hybridization and taxonomic uncertainties hinder a correct identification. Considering these problems, in this study, we developed genetic methodologies and applied meristic and morphometric approaches in wild samples in order to identify species and for test a possible hybridization between Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006. For this, C. kelberi, C. piquiti and potential hybrid ( carijó) individuals were collected in Paraná and Tietê rivers (SP, Brazil). For meristic and morphometric methods, the individuals were analyzed using the statistical software Pcord 5:31, while for molecular methods, primers for PCR-multiplex were designed and enzyme for PCR-RFLP were selected, under the species-specific nucleotide. All results indicated that the carijó is not an interspecific hybrid, because it presented identical genetic pattern and morphology closed to C. piquiti. Thus, we propose that carijó is a C. piquiti morphotype. In addition, this study promotes a new molecular tool that could be used in future research, monitoring and management programs of the genus Cichla.

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SPECIES COMPOSITION OF NEMATODES ON MALARIA MOSQUITOES OF THE TOMSK REGION

CONCEPTUAL AND APPLIED ASPECTS OF INVERTEBRATE SCIENTIFIC RESEARCH AND BIOLOGICAL EDUCATION ◽

10.17223/978-5-94621-931-0-2020-81 ◽

2020 ◽

Author(s):

V.S. Fedorova ◽

◽

V.A. Burlak ◽

G.N. Artemov ◽

◽

...

Keyword(s):

Species Composition ◽

Intermediate Host ◽

Geographical Location ◽

Dirofilaria Repens ◽

Tomsk Region ◽

Species Specific ◽

Malaria Mosquitoes

The species composition of nematodes and their vectors were analyzed in the Tomsk region. It has been shown that all three species of malaria mosquitoes, Anopheles messeae s.s., An. daciae and An. beklemishevi, can transmit Dirofilaria repens in 89% of confirmed cases. The species-specific infection of the intermediate host with dirofilarias depends on the geographical location.

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Odorant receptor copy number change, co-expression, and positive selection establish peripheral coding differences between fly species

10.1101/2021.09.19.460991 ◽

2021 ◽

Author(s):

Thomas O. Auer ◽

Raquel Álvarez-Ocaña ◽

Steeve Cruchet ◽

Richard Benton ◽

J. Roman Arguello

Keyword(s):

Positive Selection ◽

Sensory Neuron ◽

Copy Number ◽

Odorant Receptor ◽

Chemosensory Receptor ◽

Large Gene ◽

Neuron Populations ◽

Copy Number Changes ◽

Species Specific

Animals sample their chemical environment using sensory neurons that express diverse chemosensory receptors, which trigger responses when they bind environmental molecules. In addition to modifications in the ligand binding properties of receptors, chemosensory receptor evolution is characterized by copy number changes, often resulting in large gene family size differences between species. Though chemosensory receptor expansions and contractions are frequently described, it is unknown how this is accompanied by changes in the neural circuitry in which they are expressed. Among Drosophila's chemosensory receptor families, the Odorant receptors (Ors) are ideal for addressing this question because, other than an essential co-receptor (Orco), a large majority of Ors are uniquely expressed in single olfactory sensory neuron (OSN) populations. Between-species changes in Or copy number, therefore, may indicate diversification or reduction of peripheral sensory neuron populations. To test this possibility, we focused on a rapidly duplicated/deleted Or subfamily - named Or67a - within Drosophila melanogaster and its most closely-related sister species (D. simulans, D. sechellia, and D. mauritiana). Evolutionary genetic analyses and in vivo physiological assays demonstrate that the common ancestor of these four species possessed three Or67a paralogs that had already diverged adaptively in their odor-evoked responses. Following the group's speciation events, two Or67a paralogs were independently lost in D. melanogaster and D. sechellia, with positive selection continuing to act on the intact genes. Instead of the expected singular expression of each of the functionally diverged Ors in different neurons, we found that the three D. simulans Or67a paralogs are co-expressed in the same cells. Thus, while neuroanatomy is conserved between these species, independent selection on co-expressed receptors has contributed to species-specific peripheral coding of olfactory information. This work reveals a model of adaptive change previously not considered for olfactory evolution and raises the possibility that similar processes may be operating among the largely uninvestigated cases of Or co-expression.

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Assessing the Impacts of Species Composition on the Accuracy of Mapping Chlorophyll Content in Heterogeneous Ecosystems

Remote Sensing ◽

10.3390/rs13224671 ◽

2021 ◽

Vol 13 (22) ◽

pp. 4671

Author(s):

Bing Lu ◽

Yuhong He

Keyword(s):

Remote Sensing ◽

Species Composition ◽

Chlorophyll Content ◽

Spatial Resolution ◽

Ecosystem Management ◽

Remote Sensing Images ◽

Species Classification ◽

Growth Status ◽

Species Specific ◽

Estimation Models

Chlorophyll is an essential vegetation pigment influencing plant photosynthesis rate and growth conditions. Remote sensing images have been widely used for mapping vegetation chlorophyll content in different ecosystems (e.g., farmlands, forests, grasslands, and wetlands) for evaluating vegetation growth status and productivity of these ecosystems. Compared to farmlands and forests that are more homogeneous in terms of species composition, grasslands and wetlands are more heterogeneous with highly mixed species (e.g., various grass, forb, and shrub species). Different species contribute differently to the ecosystem services, thus, monitoring species-specific chlorophyll content is critical for better understanding their growth status, evaluating ecosystem functions, and supporting ecosystem management (e.g., control invasive species). However, previous studies in mapping chlorophyll content in heterogeneous ecosystems have rarely estimated species-specific chlorophyll content, which was partially due to the limited spatial resolution of remote sensing images commonly used in the past few decades for recognizing different species. In addition, many previous studies have used one universal model built with data of all species for mapping chlorophyll of the entire study area, which did not fully consider the impacts of species composition on the accuracy of chlorophyll estimation (i.e., establishing species-specific chlorophyll estimation models may generate higher accuracy). In this study, helicopter-acquired high-spatial resolution hyperspectral images were acquired for species classification and species-specific chlorophyll content estimation. Four estimation models, including a universal linear regression (LR) model (i.e., built with data of all species), species-specific LR models (i.e., built with data of each species, respectively), a universal random forest regression (RFR) model, and species-specific RFR models, were compared to determine their performance in mapping chlorophyll and to evaluate the impacts of species composition. The results show that species-specific models performed better than the universal models, especially for species with fewer samples in the dataset. The best performed species-specific models were then used to generate species-specific chlorophyll content maps using the species classification results. Impacts of species composition on the retrieval of chlorophyll content were further assessed to support future chlorophyll mapping in heterogeneous ecosystems and ecosystem management.

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