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1.
Despite the increased and widespread usage of benthic indices for environmental health assessment, some methodological ambiguities remain to be solved. We tested the congruence and consistency of the benthic indices ITI, BO2A, BENTIX, AMBI and M-AMBI in a subtropical estuary (Paranaguá Bay, Brazil). Indices were applied to non-vegetated tidal flats increasingly contaminated by sewage to test: (i) correlations with molecular biomarkers of sewage (consistency); and (ii) evaluate the overall agreement/similarity of responses (congruence). The responses of the benthic indexes ITI, AMBI and BO2A were congruent among themselves and consistent with molecular biomarkers values. BENTIX and M-AMBI were less consistent and congruent and possibly need a readjustment of boundaries for subtropical habitats. The indices seemed robust to natural background yearly variations not related to contamination. Faecal sterols associated to nutrient contents suitably supported the validation of indices and could integrate reference conditions for sewage impacted coastal habitats. Benthic indices can successfully integrate management guidelines, but their suitable application demands further research on tolerance shifts of key indicator species. 相似文献
2.
Tulipa edulis (Liliaceae) is the botanical origin of the traditional Chinese medicine (TCM) “Guangcigu”. Due to overexploitation that induced a decline in natural sources, many dried bulbs from other species of Tulipa have been used, adulterating the medicine in recent years. This practice may cause a series of inconsistent therapeutic effects and quality control problems in the herbal medicine industry. Hence, three DNA regions (matK, psbA-trnH and rbcL) were evaluated as barcodes for identifying T. edulis and its adulterants. All candidate DNA barcodes were successfully amplified from leaf samples. Based on the sequence divergences, rbcL and psbA-trnH can assign T. edulis and its adulterants to the correct genus, while matK can accurately differentiate T. edulis and its adulterants. Thus, at the DNA level, the matK intergenic region is a more suitable, accurate and applicable identification of T. edulis and its adulterants than rbcL and psbA-trnH. 相似文献
3.
The Preliminary Study on DNA Barcoding of Mosses——A Case of Part of Genera of Meteoriaceae 
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下载免费PDF全文 We compared the performances of the candidate loci for moss DNA barcoding and the primers used in amplifying the loci. Primers for three coded loci (matK, rps4 and rbcL a) and four non coded loci (atpB rbcL, atpF H, psbK I and trnH psbA) of the chloroplast genome, one from the mitochondrial genome (nad5), and one from the nucleus genome (ITS2) were evaluated. Seventy four samples representing 14 species belonging to five genera of Trachypodoaceae (or Meteoriaceae) were screened. All primers for matK and a pair of primers for trnH psbA failed. Low successes were encountered with the primers for atpF H and psbK I. The primers for psbK I produced several bands and the PCR products of atpF H were difficult to sequence. The powers of the remaining six loci were compared using the variability, identification success and the resolutions. It was found that ITS2 is the most promising candidate for DNA barcoding for mosses. Among the chloroplast genes, atpB rbcL exhibited the highest resolution. Although trnH psbA is very variable, it is too short to be an ideal barcode alone. Combinations of chloroplast genes were also tried and Ps of both atpB rbcL+trnH psbA and rbcL a++trnH psbA were 64% using NJ method. More additions of loci did not increase the resolution. No barcoding gap exists for all these loci. Phylogenetic analyses were carried out prior to the DNA barcoding evaluation and some taxonomic problems do exist. This study exemplifies the necessity of correct species delimitation and the adoption of both plastid and nuclear loci in plant DNA barcoding. 相似文献
4.
Non-biting midges (Diptera: Chironomidae) are a diverse population that commonly causes respiratory allergies in humans. Chironomid larvae can be used to indicate freshwater pollution, but accurate identification on the basis of morphological characteristics is difficult. In this study, we constructed a mitochondrial cytochrome c oxidase subunit I (COI)-based DNA barcode library for Korean chironomids. This library consists of 211 specimens from 49 species, including adults and unidentified larvae. The interspecies and intraspecies COI sequence variations were analyzed. Sophisticated indexes were developed in order to properly evaluate indistinct barcode gaps that are created by insufficient sampling on both the interspecies and intraspecies levels and by variable mutation rates across taxa. In a variety of insect datasets, these indexes were useful for re-evaluating large barcode datasets and for defining COI barcode gaps. The COI-based DNA barcode library will provide a rapid and reliable tool for the molecular identification of Korean chironomid species. Furthermore, this reverse-taxonomic approach will be improved by the continuous addition of other speceis’ sequences to the library. 相似文献
5.
Effective management of coastal and marine resources requires knowledge of how community sensitivity varies spatially. With this in mind, we developed a benthic sensitivity index (SI), based on the distribution and abundance of five ecological groups that can be used to assess community tolerance to organic enrichment and other disturbances. The index, projected as a high-resolution map, ranks communities from those dominated by sensitive and ecologically important species (i.e. low SI values) to those composed mainly of tolerant and/or opportunistic species (i.e., high SI values). Applying our model to a multiple-use case study in southeast Brazil, we were able to show considerable variability in the sensitivity of communities across the study area that was relatively stable over time. This allowed us to evaluate the possible direct (i.e., spatially overlapping) and indirect effects (i.e., cumulative changes to the physical environment) of a range of activities on sensitive and ecologically diverse benthic communities. Our approach and the resulting high-resolution maps hold promise for a range of spatial planning applications, including the development of coastal infrastructure, assessments of the representativeness of marine protected areas and other activities such as the selection of appropriate locations for dredge spoil dumping. Overall, we present a novel and transparent way of extrapolating limited survey data to provide spatial and temporal information on the sensitivity of benthic communities in multiple-use coastal and marine areas. 相似文献
6.
Lars G. Crabo 《ZooKeys》2015,(527):51-56
A new species of Ogdoconta Butler (Lepidoptera, Noctuidae, Condicinae, Condicini) is described from the Patagonia Mountains, Santa Cruz County, Arizona, USA. Ogdoconta
margareta
sp. n., is related closely to Ogdoconta
tacna (Barnes) from Texas. Modifications are proposed to a recently published key to the Ogdoconta species north of Mexico to allow identification of the new species. 相似文献
7.
To evaluate the feasibility of morphological and genetic identification of the closely related species in the genera Misgurnus and Paramisgurnus, the morphological characters of four species in these genera and DNA barcoding of five loaches (P. dabryanus, M. anguillicaudatus, M. bipartitus, M. mohoity, and Barbatula toni) were investigated. Twelve morphological characters were measured in 542 individuals to perform the comparative analysis. Among these characters, only the caudal peduncle length (LCP) revealed significant difference (P < 0.05) among these four species. The clustering based on morphological characters formed two clusters (P. dabryanus and M. anguillicaudatus; M. bipartitus and M. mohoity). A total of 186 COI fragments for the five loaches investigated were sequenced and analyzed. The results showed that interspecific K2P distance was much higher than intraspecific distance within the five species. Bayesian inference of phylogeny showed that individuals of these species were divided into five specific clades. Meanwhile, the COI fragments exhibited 22 character attributes for the differentiation of the five loach species based on character-based method. Our results suggested that DNA barcoding based on COI can be used as an efficient identifier of these five loach species; the combination of distance-based method, Bayesian inference and character-based approach provides higher resolution of identification at species level. 相似文献
8.
《Plant Diversity》2025,47(01)
DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification. 相似文献
9.
《Plant Diversity》2025,47(01)
DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification. 相似文献
10.
Isatis indigotica Fort. (Cruciferae) is a biennial medicinal plant. In order to protect the decreasing natural genetic resources of I. indigotica, three candidate DNA barcodes (ITS2, trnL-F and rbcL) were employed to establish an accurate and effective identification system for I. indigotica. The results demonstrated that all three candidate DNA barcodes have performed very well in I. indigotica. The interspecific genetic distances were obviously greater than the intraspecific distance among I. indigotica as indicated by ITS2, trnL-F and rbcL. Sequence alignment analysis of I. indigotica genotypes revealed that four SNPs (54, 108, 146 and 181 bp) located in ITS2, three (2, 30, 709 bp) in trnL-F and one (531 bp) in rbcL, respectively. UPGMA phylogenetic tree constructed from trnL-F and rbcL could allote I. indigotica to the correct corresponding genus, whereas rbcL could not distinguish I. indigotica from its adulterants. Meanwhile, UPGMA tree of ITS2 could accurately identify I. indigotica from its adulterants according to the corresponding species. Consequently, it can be concluded that ITS2 is a more suitable and accurate DNA barcode for identifying I. Indigotica and its adulterants than trnL-F and rbcL. 相似文献
11.
Maria Pratheepa Sushil Kumar Jalali Robinson Silvester Arokiaraj Thiruvengadam Venkatesan Mandadi Nagesh Madhusmita Panda Sharath Pattar 《Bioinformation》2014,10(2):98-100
Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by theNational Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis andpublication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. Itbridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects.IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client–server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBInallows the registered users to input new information, search and view information related to DNA barcode of agriculturallyimportant insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn.
Availability
http://www.nabg-nbaii.res.in/barcode 相似文献12.
Xiphidorus amazonensis n. sp. was found in the rhizospheres of Jatropha curcas, Musa sp., Anona muricata, Cassia tora, Panicum laxum, Paspalum fasciculatum, Aeschynomene sensitiva, Saccharum officinarum, Manihot esculenta, Abelmoschus esculentus, Tamarindus indica, Mangifera indica, Vigna unguiculata, Zea mays, Commelina sp., Cyperus rotundus, Fimbristylis miliacea, Citrus sinensis, and Eichhornia crassipes on the Amazon River island of Xiborena, approximately 40 km southeast of Manaus, capital of the State of Amazonas. The type habitat is flooded annually for about 6 months by the Amazon River. Xiphidorus amazonensis n. sp. differs from the closely related species Xiphidorus yepesara Monteiro, 1976 by the larger size, by a, b, and c values, and by the rounded tail terminus. It also resembles Xiphidorus tucumanensis Chaves and Coomans, 1984, but can be distinguished by its larger size, larger a, b, and c values, more conical female tail, bilobed amphidial pouch, and the presence of a spermatheca full of sperm. 相似文献
14.
藻类DNA条形码研究进展 总被引：2，自引：0，他引：2
DNA barcode,又称为DNA条形码,是指利用短的标准DNA序列的核苷酸多样性进行物种的鉴定和快速识别.目前该方法在动物分类研究中应用广泛,其中线粒体的细胞色素c氧化酶亚基1(cytochrome c oxidase subunit 1,COI或cox 1)基因中的约700bp长度的一段被用来作为标准DNA片段.在陆地植物条形码研究中,生命-植物条形码联盟会(Consortium for the Barcode of Life-Plant Working Group,CBOL-Plant Working Group)近期推荐将植物叶绿体中的两个基因片段rbcL+ matK作为初步的陆生植物条形码,此组合能在70％的程度上进行植物物种的鉴别.在海藻的分类研究中,DNA条形码的应用较少,已有的研究主要集中在硅藻、红藻和褐藻,尚没有学者明确提出适合藻类的DNA条形码.总结了能够作为藻类DNA条形码的序列特点、应用流程及分析方法,综述了DNA条形码在藻类中的研究现状和存在的问题,展望了藻类DNA条形码的应用前景. 相似文献
15.
The red algal genus Hypnea (Gigartinales) has a wide geographical distribution along tropical and subtropical coasts around the world. The relatively simple and plastic morphology, often influenced by the conditions of its habitat, complicates the identification of Hypnea species. Therefore, the number and status of some species remain in doubt. Molecular studies have been performed to supplement traditional studies based on morphology, mainly for Hypnea species occurring in Asia. In the present study, sequence data from the DNA barcode COI-5P for 114 samples from the southeastern coast of Brazil, indicated the occurrence of six taxa. Additionally, sequence data from the UPA and rbcL markers for representatives of each of those taxa confirmed the existence of six different species. After morphological analysis and comparison with sequences available in GenBank, these species were named as follows: H. aspera, H. cervicornis, H. cf. musciformis, H. spinella, and two new species, H. flava Nauer, Cassano & M.C. Oliveira and H. edeniana Nauer, Cassano & M.C. Oliveira. Hypnea cervicornis, often considered as a later synonym of H. spinella, should be considered as a distinct species based on morphology and divergence of the three molecular markers used. Hypnea aspera is a new record for the Atlantic Ocean. 相似文献
16.
《Journal of Asia》2023,26(1):102028
This study reports the first Korean records of the genera Clusia Haliday and Clusiodes Coquillett (Diptera: Clusiidae), with four newly recorded species, Clusia intermedialis (Mamaev), Clusia nigromaculata (Mamaev), Clusia unita Mamaev, and Clusiodes flaveolus Mamaev. Morphological diagnosis is provided with a key to Korean Clusiidae. The mitochondrial cytochrome c oxidase I (COI) gene sequences of Clusia and Clusiodes are analyzed for DNA barcoding. Molecular analyses of both genera result in well-defined species clusters with significant barcode gaps, and also identify problematic data in the public database. 相似文献
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The effect of medium concentration, pollen grain concentration, pH of the media, light and temperature on the germination of Vin ca rosea pollen grains, and the growth of their pollen tubes in vitro have been studied. The pollen grains germinate best at a sucrose concentration between 14.2% and 30%; when the pollen grain concentration exceeds 800 per 0.0234 ml; at near neutral pH (6.5); in darkness and at a temperature close to 30°. Moreover buffering ions affect the growth of the pollen tubes. Pollen grains remain viable in a wide range of temperatures, and the wall of the pollen grain is capable of withstanding severe osmotic imbalance. Low temperature induces spherical swellings at the tips of the pollen tubes, followed by accumulation of a hyaline plug. 相似文献
20.
Jun Seong Jeong Min Jee Kim Sung‐Soo Kim Sei‐Woong Choi Iksoo Kim 《Entomological Research》2018,48(2):108-121
In the present study, specimens of Dendrolimus superans collected from South Korea suggest the presence of D. sibiricus, instead of D. superans. Comparisons of the wing morphology, female and male genitalia, 3′‐end region of the cytochrome c oxidase I (COI) gene sequence, and internal transcribed spacer (ITS) 2 sequence of the Korean specimens with those of the D. superans specimens from Japan consistently supported the presence of D. sibiricus in South Korea. Phylogenetic analyses of the concatenated sequences of COI and ITS2 from the available sequence types of D. sibiricus and D. superans, along with South Korean specimens, were conducted using the Bayesian inference (BI) and maximum likelihood (ML) methods. These phylogenetic analyses placed the South Korean specimens with the Russian D. sibiricus as an inclusive group, excluding the Japanese D. superans, indicating the distribution of D. sibiricus in South Korea. Nevertheless, D. superans formed a distinct group only by BI analysis (Bayesian posterior probabilities = 0.89), whereas D. sibiricus, including the South Korean samples, formed a distinct group only by the ML analysis (99%), suggesting a low genetic divergence between the two species. 相似文献