【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery...【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery(ABGD)和Bayesian Poisson Tree Processes(bPTP)对3个形态种进行分子物种界定,并与形态学鉴定结果进行比较。【结果】使用ABGD方法时,cox1数据集的界定结果与形态学鉴定结果一致,cox2数据集的界定结果与形态学鉴定结果存在差异;使用bPTP方法时,2种数据集的界定结果均远高于形态学鉴定结果,且均存在不同程度的过度划分。【结论】cox1是更适合用于鉴定尤犀金龟属昆虫的DNA条形码,使用ABGD方法时,其数据集界定结果与形态学鉴定结果一致。利用分子界定与形态特征鉴定相结合,可极大地提高鉴定效率和准确性。展开更多
In 2013, the 29th Chinese National Antarctic Research Expedition（CHINARE） prospected the Prydz Bay on the Antarctic continental shelf, and the Chinese R/V Xuelong icebreaker sampled all of the examined locations. Th...In 2013, the 29th Chinese National Antarctic Research Expedition（CHINARE） prospected the Prydz Bay on the Antarctic continental shelf, and the Chinese R/V Xuelong icebreaker sampled all of the examined locations. The nature of Antarctic fish diversity in the high-latitude Prydz Bay is virtually unknown, and the accuracy of relevant estimates has not been established. Thus, it is necessary to evaluate this diversity and propose protective measures. In total, ninety-nine specimens were collected from various locations. To overcome uncertainties associated with identifying species based on morphology, DNA barcoding（COI gene） was employed to reconstruct phylogenetic relationships with delimited references from NCBI. Twenty-two species representing six families were unambiguously identified from a neighbor-joining（NJ） tree and barcoding gaps. With the morphological identification, thirteen species were identified correctly, five species were identified correctly at the genus level, and four species were identified at the close sister species level. Notothenioid dominance was not evident in the Prydz Bay, in contrast to other published studies. The low species diversity and catch biomass during this CHINARE were severely constrained by limited fishing methods and localized sites, which led to biased underestimation. Our analyses indicate that DNA barcoding is an effective tool for the identification of fish species in the Prydz Bay. The identification and distribution of Antarctic fish should be an integral component of understanding Antarctic fish biodiversity and biogeography, and large-scale studies are necessary for the further taxonomic identification of Antarctic fish.展开更多
Phytophthora is genus of plant-damaging Oomycetes, whose member species are capable of causing enormous economic losses on crops worldwide. In the present study, four candidate genes ITS, CO1, EF-1α and β-tubulin we...Phytophthora is genus of plant-damaging Oomycetes, whose member species are capable of causing enormous economic losses on crops worldwide. In the present study, four candidate genes ITS, CO1, EF-1α and β-tubulin were tested using 123 strains of 80 species of Phytophthora to investigate the feasibility of ser- ving as DNA barcoding markers. The results showed that among the four candidate genes, ITS and CO1 had the highest success rate of PCR amplification and se- quencing, up to 100% and 96.7%. There were obvious barcode gaps in ITS, CO1 andβ-tubulin, but their frequency distributions of intra- and interspecific genetic distances were slightly overlapped. Wilcoxon rank sum test on intraspecific genetic distances of the four genes showed ITS = CO1 = β - tubulin = EF-1α indicating they bad the same effect on intraspecific discrimination, while the test on interspecific genetic distances of the four genes showed ITS 〉 C01 〉 β- tubulin 〉 EF - 1α. In summary, ITS and COl should be used in combination as the primary barcodes, β-tubulin as the complementary barcede for the identification of 11 quaran- tine Phytophthora species.展开更多
A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae ar...A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intraand inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra-and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intraand inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.展开更多
文摘【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery(ABGD)和Bayesian Poisson Tree Processes(bPTP)对3个形态种进行分子物种界定,并与形态学鉴定结果进行比较。【结果】使用ABGD方法时,cox1数据集的界定结果与形态学鉴定结果一致,cox2数据集的界定结果与形态学鉴定结果存在差异;使用bPTP方法时,2种数据集的界定结果均远高于形态学鉴定结果,且均存在不同程度的过度划分。【结论】cox1是更适合用于鉴定尤犀金龟属昆虫的DNA条形码,使用ABGD方法时,其数据集界定结果与形态学鉴定结果一致。利用分子界定与形态特征鉴定相结合,可极大地提高鉴定效率和准确性。
基金Chinese Polar Environment Comprehensive Investigation and Assessment Program under contract Nos CHINARE2012-2015-01-05,CHINARE 2012-2015-04-01 and CHINARE 2017-04-03
文摘In 2013, the 29th Chinese National Antarctic Research Expedition（CHINARE） prospected the Prydz Bay on the Antarctic continental shelf, and the Chinese R/V Xuelong icebreaker sampled all of the examined locations. The nature of Antarctic fish diversity in the high-latitude Prydz Bay is virtually unknown, and the accuracy of relevant estimates has not been established. Thus, it is necessary to evaluate this diversity and propose protective measures. In total, ninety-nine specimens were collected from various locations. To overcome uncertainties associated with identifying species based on morphology, DNA barcoding（COI gene） was employed to reconstruct phylogenetic relationships with delimited references from NCBI. Twenty-two species representing six families were unambiguously identified from a neighbor-joining（NJ） tree and barcoding gaps. With the morphological identification, thirteen species were identified correctly, five species were identified correctly at the genus level, and four species were identified at the close sister species level. Notothenioid dominance was not evident in the Prydz Bay, in contrast to other published studies. The low species diversity and catch biomass during this CHINARE were severely constrained by limited fishing methods and localized sites, which led to biased underestimation. Our analyses indicate that DNA barcoding is an effective tool for the identification of fish species in the Prydz Bay. The identification and distribution of Antarctic fish should be an integral component of understanding Antarctic fish biodiversity and biogeography, and large-scale studies are necessary for the further taxonomic identification of Antarctic fish.
基金Supported by Science and Technology Plan Project of Shenzhen Entry-Exit Inspection and Quarantine Bureau(SZ2015101)National Key Technology Research and Development Program of China during the 12~(th)Five-Year Plan Period(2012BAK11B06)Science and Technology Plan Project of General Administration of Quality Supervision,Inspection and Quarantine of People's Republic of China(2016IK239)
文摘Phytophthora is genus of plant-damaging Oomycetes, whose member species are capable of causing enormous economic losses on crops worldwide. In the present study, four candidate genes ITS, CO1, EF-1α and β-tubulin were tested using 123 strains of 80 species of Phytophthora to investigate the feasibility of ser- ving as DNA barcoding markers. The results showed that among the four candidate genes, ITS and CO1 had the highest success rate of PCR amplification and se- quencing, up to 100% and 96.7%. There were obvious barcode gaps in ITS, CO1 andβ-tubulin, but their frequency distributions of intra- and interspecific genetic distances were slightly overlapped. Wilcoxon rank sum test on intraspecific genetic distances of the four genes showed ITS = CO1 = β - tubulin = EF-1α indicating they bad the same effect on intraspecific discrimination, while the test on interspecific genetic distances of the four genes showed ITS 〉 C01 〉 β- tubulin 〉 EF - 1α. In summary, ITS and COl should be used in combination as the primary barcodes, β-tubulin as the complementary barcede for the identification of 11 quaran- tine Phytophthora species.
基金supported by the National Natural Science Foundation of China (Grant No. 31070015)the Special Project for Fundamental Research (Grant No. 2006FY120100) from Ministry of Science and Technology of Chinathe Knowledge Innovation Program of Chinese Academy of Sciences (Grant No. KSCX2-EW-J-6)
文摘A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intraand inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra-and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intraand inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.
