Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia.
Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia.
Parasit Vectors. 2023 Jul 22;16(1):248. doi: 10.1186/s13071-023-05875-1.
DNA barcoding is a valuable taxonomic tool for rapid and accurate species identification and cryptic species discovery in black flies. Indonesia has 143 nominal species of black flies, but information on their biological aspects, including vectorial capacity and biting habits, remains underreported, in part because of identification problems. The current study represents the first comprehensive DNA barcoding of Indonesian black flies using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences.
Genomic DNA of Indonesian black fly samples were extracted and sequenced, producing 86 COI sequences in total. Two hundred four COI sequences, including 118 GenBank sequences, were analysed. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed and species delimitation analyses, including ASAP, GMYC and single PTP, were performed to determine whether the species of Indonesian black flies could be delineated. Intra- and interspecific genetic distances were also calculated and the efficacy of COI sequences for species identification was tested.
The DNA barcodes successfully distinguished most morphologically distinct species (> 80% of sampled taxa). Nonetheless, high maximum intraspecific distances (3.32-13.94%) in 11 species suggested cryptic diversity. Notably, populations of the common taxa Simulium (Gomphostilbia) cheongi, S. (Gomphostilbia) sheilae, S. (Nevermannia) feuerborni and S. (Simulium) tani in the islands of Indonesia were genetically distinct from those on the Southeast Asian mainland (Malaysia and Thailand). Integrated morphological, cytogenetic and nuclear DNA studies are warranted to clarify the taxonomic status of these more complex taxa.
The findings showed that COI barcoding is a promising taxonomic tool for Indonesian black flies. The DNA barcodes will aid in correct identification and genetic study of Indonesian black flies, which will be helpful in the control and management of potential vector species.
DNA 条形码是一种有价值的分类工具，可用于快速准确地鉴定物种并发现黑蝇中的隐种。印度尼西亚有 143 种黑蝇，但有关其生物学方面的信息，包括媒介能力和叮咬习惯，仍未得到充分报道，部分原因是鉴定问题。本研究代表了首次使用线粒体细胞色素 c 氧化酶亚基 I（COI）基因序列对印度尼西亚黑蝇进行全面 DNA 条形码分析。
提取和测序印度尼西亚黑蝇样本的基因组 DNA，共产生 86 个 COI 序列。分析了 204 个 COI 序列，包括 118 个 GenBank 序列。构建了最大似然（ML）和贝叶斯推断（BI）树，并进行了 ASAP、GMYC 和单 PTP 等物种界限分析，以确定印度尼西亚黑蝇的物种是否可以划分。还计算了种内和种间遗传距离，并测试了 COI 序列用于物种鉴定的功效。
DNA 条形码成功区分了大多数形态明显不同的物种（>80%的采样类群）。然而，11 个物种的最大种内距离较高（3.32-13.94%）表明存在隐种多样性。值得注意的是，印度尼西亚岛屿上常见种 Simulium（Gomphostilbia）cheongi、S.（Gomphostilbia）sheilae、S.（Nevermannia）feuerborni 和 S.（Simulium）tani 的种群与东南亚大陆（马来西亚和泰国）的种群在遗传上不同。有必要进行综合形态学、细胞遗传学和核 DNA 研究，以澄清这些更复杂类群的分类地位。
研究结果表明，COI 条形码是印度尼西亚黑蝇有前途的分类工具。DNA 条形码将有助于正确鉴定和遗传研究印度尼西亚黑蝇，这将有助于控制和管理潜在的媒介物种。
