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Conserve primers for sequencing complete ungulate mitochondrial cytochrome c oxidase I (COI) gene from problematic and decomposed biological samples.

ABSTRACT: We describe six novel ungulate-specific conserved primers for sequencing the complete mitochondrial cytochrome c oxidase I (COI) gene of selected threatened species from degraded samples for effective conservation planning. These primers amplified 301-1599 bp DNA fragments in various combinations. The method described may assist in the sequencing of either complete gene from moderate to good quality DNA or shorter fragment from degraded DNA.

SUBMITTER: Kumar A

PROVIDER: S-EPMC7800399 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

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Conserve primers for sequencing complete ungulate mitochondrial cytochrome c oxidase I (COI) gene from problematic and decomposed biological samples.

Kumar Ajit A Ghazi Mirza Ghazanfar Ullah MGU Singh Bhim B Hussain Syed Ainul SA Bhatt Dinesh D Gupta Sandeep Kumar SK

Mitochondrial DNA. Part B, Resources 20170206 1

We describe six novel ungulate-specific conserved primers for sequencing the complete mitochondrial cytochrome c oxidase I (COI) gene of selected threatened species from degraded samples for effective conservation planning. These primers amplified 301-1599 bp DNA fragments in various combinations. The method described may assist in the sequencing of either complete gene from moderate to good quality DNA or shorter fragment from degraded DNA. ...[more]

PMID: 33490438

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Project description:BackgroundAccurate identification of mosquito species is essential for the development and optimization of strategies to control mosquitoes and mosquito-borne diseases. Problems with the morphological identification of mosquito species have led to the use of molecular identification techniques, in particular the Folmer cytochrome c oxidase subunit I (COI) PCR system (FCOS), originally designed to identify a range of other invertebrates.MethodsAs there can be difficulties identifying mosquitoes using FCOS, we re-evaluated the FCOS primers and developed a new COI-based SYBR PCR (the Auburn COI system-AUCOS) to improve the molecular identification of mosquitoes. Sequence data in GenBank for 33 species from 10 genera of mosquitoes were used to develop our AUCOS primers. Two molecular assays (AUCOS, FCOS) and morphological identification were carried out on mosquitoes collected from the field in Auburn, Alabama (USA) and on Saint Kitts.ResultsWith a convenience sample of individual mosquitoes comprising 19 species from six genera in Saint Kitts (n = 77) and Auburn (n = 48), our AUCOS provided higher-quality sequence data than FCOS. It also proved more sensitive than FCOS, successfully amplifying 67.5% (85/126) as opposed to 16.7% (21/126) of the samples. The species determined by morphology, or genus with damaged samples, matched that as determined by AUCOS for 84.9% (62/73) of the samples. Morphological classification was confirmed by FCOS with 81.0% (17/21) of samples producing utilizable sequences. While both FCOS and AUCOS correctly identified all the Aedes, Anopheles, Deinocerites, and Uranotaenia species in the study, identification of Culex species was less successful with both methods: 50.0% (3/6) by FCOS and 35.7% (5/14) by AUCOS.ConclusionsThe AUCOS DNA barcoding system for mosquito species described in this study is superior to the existing FCOS for the identification of mosquito species. As AUCOS and FCOS amplify the same variable region of the COI, the large amount of existing data on GenBank can be used to identify mosquito species with sequences produced by either PCR.

Dataset Information

Conserve primers for sequencing complete ungulate mitochondrial cytochrome c oxidase I (COI) gene from problematic and decomposed biological samples.

Publications

Conserve primers for sequencing complete ungulate mitochondrial cytochrome c oxidase I (COI) gene from problematic and decomposed biological samples.

Similar Datasets

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