Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD
Abstract Background Leishmaniasis is one of the most neglected tropical diseases in the world and remains endemic in some underdeveloped regions, including western China. The phylogeny and classification of Chinese Leishmania has not been completely clarified to date, especially within the Leishmani...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-05-01
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| Series: | BMC Infectious Diseases |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12879-021-06163-y |
| _version_ | 1819137615322939392 |
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| author | Dongmei Yuan Hanxiao Qin Dali Chen Jianping Chen |
| author_facet | Dongmei Yuan Hanxiao Qin Dali Chen Jianping Chen |
| author_sort | Dongmei Yuan |
| collection | DOAJ |
| description | Abstract Background Leishmaniasis is one of the most neglected tropical diseases in the world and remains endemic in some underdeveloped regions, including western China. The phylogeny and classification of Chinese Leishmania has not been completely clarified to date, especially within the Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers have been performed. More analytic methods and data are still needed. Random amplified polymorphic DNA (RAPD) technology can sensitively identify slight intraspecific differences, and it is a powerful tool to seek species-specific markers. This work attempted to identify Chinese Leishmania isolates from diverse geographic regions at the genomic level. Meanwhile, specific markers of the L. donovani complex were also developed by RAPD. Methods RAPD was applied to 14 Chinese Leishmania isolates from diverse geographic regions and 3 WHO reference strains. The polymorphic sites of amplification were transformed into a data matrix, based on which genetic similarity was calculated, and a UPGMA dendrogram was constructed to analyse the genetic diversity of these Leishmania isolates. Meanwhile, the specific amplification loci of the L. donovani complex were TA-cloned, sequenced and converted into sequence characterized amplified region (SCAR) markers, which were validated preliminarily in 17 available Leishmania strains in this study and analysed by bioinformatics. Results The cluster analyses showed that the three Leishmania sp. isolates SC10H2, SD and GL clustered together and apart from others, the strains of the L. donovani complex clearly divided into two clades, and the three isolates Cy, WenChuan and 801 formed a subclade. Three specific SCAR markers of the L. donovani complex, i.e., 1-AD17, 2-A816 and 3-O13, were successfully obtained and validated on 17 available Leishmania strains in this study. Through bioinformatic analyses, Marker 1-AD17 may have more specificity for PCR detection of VL, and Marker 3-O13 has the potential to encode a protein. Conclusions The RAPD results verified that the undescribed Leishmania species causing visceral leishmaniasis (VL) in China was a unique clade distinguished from L. donovani and revealed that there was genetic differentiation among Chinese L. donovani. The identification of L. donovani-specific markers may help to provide a foundation for future research attempting to develop new specific diagnostic markers of VL and identify specific gene functions. |
| first_indexed | 2024-12-22T10:53:41Z |
| format | Article |
| id | doaj.art-0174550e272a44e19e53e112edc0f2cb |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-12-22T10:53:41Z |
| publishDate | 2021-05-01 |
| publisher | BMC |
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| series | BMC Infectious Diseases |
| spelling | doaj.art-0174550e272a44e19e53e112edc0f2cb2022-12-21T18:28:40ZengBMCBMC Infectious Diseases1471-23342021-05-0121111010.1186/s12879-021-06163-yGenetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPDDongmei Yuan0Hanxiao Qin1Dali Chen2Jianping Chen3Department of Human Anatomy, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan UniversityDepartment of Parasitology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan UniversityDepartment of Parasitology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan UniversityDepartment of Parasitology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan UniversityAbstract Background Leishmaniasis is one of the most neglected tropical diseases in the world and remains endemic in some underdeveloped regions, including western China. The phylogeny and classification of Chinese Leishmania has not been completely clarified to date, especially within the Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers have been performed. More analytic methods and data are still needed. Random amplified polymorphic DNA (RAPD) technology can sensitively identify slight intraspecific differences, and it is a powerful tool to seek species-specific markers. This work attempted to identify Chinese Leishmania isolates from diverse geographic regions at the genomic level. Meanwhile, specific markers of the L. donovani complex were also developed by RAPD. Methods RAPD was applied to 14 Chinese Leishmania isolates from diverse geographic regions and 3 WHO reference strains. The polymorphic sites of amplification were transformed into a data matrix, based on which genetic similarity was calculated, and a UPGMA dendrogram was constructed to analyse the genetic diversity of these Leishmania isolates. Meanwhile, the specific amplification loci of the L. donovani complex were TA-cloned, sequenced and converted into sequence characterized amplified region (SCAR) markers, which were validated preliminarily in 17 available Leishmania strains in this study and analysed by bioinformatics. Results The cluster analyses showed that the three Leishmania sp. isolates SC10H2, SD and GL clustered together and apart from others, the strains of the L. donovani complex clearly divided into two clades, and the three isolates Cy, WenChuan and 801 formed a subclade. Three specific SCAR markers of the L. donovani complex, i.e., 1-AD17, 2-A816 and 3-O13, were successfully obtained and validated on 17 available Leishmania strains in this study. Through bioinformatic analyses, Marker 1-AD17 may have more specificity for PCR detection of VL, and Marker 3-O13 has the potential to encode a protein. Conclusions The RAPD results verified that the undescribed Leishmania species causing visceral leishmaniasis (VL) in China was a unique clade distinguished from L. donovani and revealed that there was genetic differentiation among Chinese L. donovani. The identification of L. donovani-specific markers may help to provide a foundation for future research attempting to develop new specific diagnostic markers of VL and identify specific gene functions.https://doi.org/10.1186/s12879-021-06163-yLeishmania donovaniChinaRAPDSCAR |
| spellingShingle | Dongmei Yuan Hanxiao Qin Dali Chen Jianping Chen Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD BMC Infectious Diseases Leishmania donovani China RAPD SCAR |
| title | Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD |
| title_full | Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD |
| title_fullStr | Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD |
| title_full_unstemmed | Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD |
| title_short | Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD |
| title_sort | genetic diversity analysis of chinese leishmania isolates and development of l donovani complex specific markers by rapd |
| topic | Leishmania donovani China RAPD SCAR |
| url | https://doi.org/10.1186/s12879-021-06163-y |
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