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A polyphasic approach to delineate species in Bipolaris

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Fungal Diversity 2020年第3期102卷 225-256页

作者： Chitrabhanu S.Bhunjun Yang Dong Ruvishika S.Jayawardena Rajesh Jeewon Chayanard Phukhamsakda Digvijayini Bundhun Kevin D.Hyde Jun Sheng State Key Laboratory for Conservation and Utilization of Bio‑Resources in Yunnan Yunnan Agricultural UniversityKunming 650201People’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Yunnan Research Institute for Local Plateau Agriculture and Industry Kunming 650201People’s Republic of China Department of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50002Thailand Institute of Plant Health Zhongkai University of Agriculture and EngineeringHaizhu DistrictGuangzhou 510225People’s Republic of China Centre for Mountain Futures Kunming Institute of BotanyKunming 650201YunnanPeople’s Republic of China

Bipolaris species are important plant pathogens with a worldwide distribution in tropical and temperate environments.Species recognition in Bipolaris has been problematic due to a lack of molecular data from ex-type cultures,the use of few gene regions for species resolution and overlapping morphological characters.In this study,we evaluate the efficiency of different dna barcodes in species delimitation in Bipolaris by phylogenetic analyses,Automatic Barcode Gap Discovery and Objective Clustering.GAPDH is determined to be the best single marker for the genus.These approaches are used to clarify the taxonomic placement of all sequences currently named as Bipolaris in GenBank based on ITS and GAPDH gene sequence data.In checking various publications,we found that the majority of new host records of fungal species published in the Plant Disease journal from 2010 to 2019 were based on BLAST searches of the ITS sequences and up to 82%of those records could be erroneous.Therefore,relying on BLAST searches from GenBank to name species is not recommended.Editorial boards of journals and reviewers of new record papers should be aware of this problem.In naming Bipolaris species,whether new or known,it is recommended to perform phylogenetic analyses based on GAPDH using the correct taxon sampling for accurate results and the species relationship should have reliable statistical support.At least two new species are represented by molecular data in GenBank and we provide an updated taxonomic revision of Bipolaris.We accept 45 species in Bipolaris and notes are provided for all the species including hosts and geographic distribution.

关键词： Classification dna barcoding Dothideomycetes Integrative taxonomy Pairwise differences Pleosporales

鹞落坪保护区典型农林交错带传粉昆虫多样性及其与环境因子间的关系

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生物学杂志 2023年第4期40卷 70-75页

作者：姚晨晨侯银续郭东旭万霞安徽大学资源与环境工程学院合肥230601 湿地生态保护与修复安徽省重点实验室合肥230601 安徽省疾病预防控制中心合肥230601

2019年10月至2021年10月,在鹞落坪保护区典型农林交错带采集传粉昆虫2551只,通过形态学及dna barcoding互证,鉴定出传粉昆虫92种,隶属于4目34科73属。其中,中华蜜蜂(Apis cerana)、三条熊蜂(Bombus trifasciatus)、灰带管食蚜蝇(Eristal... 详细信息

2019年10月至2021年10月,在鹞落坪保护区典型农林交错带采集传粉昆虫2551只,通过形态学及dna barcoding互证,鉴定出传粉昆虫92种,隶属于4目34科73属。其中,中华蜜蜂(Apis cerana)、三条熊蜂(Bombus trifasciatus)、灰带管食蚜蝇(Eristalis cerealis)和东方菜粉蝶(Pieris canidia)是优势种。物种多样性分析结果表明,以农田为主的样线Ⅰ比以森林为主的样线Ⅱ和Ⅲ的多样性更高,多样化的农作物能为传粉昆虫提供更好的栖息地和食物来源;样线Ⅲ则因临近旅游区域而受到较多人为干扰,多样性显著较低。此外,从WorldClim数据库中下载19个环境因子(Bio1~Bio19),分析物种及系统发育多样性与研究区域内的环境因子间的相关性关系:其中,有14个环境因子(Bio1,Bio4~13,Bio16,Bio18~19)与系统发育多样性指数以及物种丰富度指数之间存在线性相关关系,冗余分析结果则支持温度因子对系统发育多样性及丰富度影响更显著,温度可能是影响鹞落坪保护区传粉昆虫多样性的重要生态因子。

关键词：传粉昆虫物种丰富度 dna barcoding 系统发育多样性环境因子

A New Species of the Genus Elaphe(Squamata: Colubridae) from Zoige County,Sichuan,China

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Asian Herpetological Research 2012年第1期3卷 38-45页

作者： Song HUANG Li DING Frank T.BURBRINK Jun YANG Jietang HUANG Chen LING Xin CHEN Yaping ZHANG College of Life and Environment Sciences Huangshan University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Huangshan Institute of Ophiology Chengdu Institute of Biology Chinese Academy of Sciences Department of Biology the College of Staten Islandthe City University of New York Department of Biology the Graduate Centerthe City University of New York School of Life Sciences Sichuan University College of Forestry Southwest Forestry University

Previous phylogenetic analyses of dna sequence data reveal a likely new species of Elaphe Fitzinger from China,which forms the sister group of all extant Elaphe. One of the three original specimens is crushed and the other two are neonates,which precludes a morphological analysis. Three adult snakes(2 females,1 male) collected from Jiangzha Hot Spring in Zoige County,Sichuan,China on 26 July 2010 now facilitate the species’ description. Mitochondrial dna nucleotide sequences of cytochrome b(cyt b),NADH dehydrogenase subunit 4(ND4),12S ribosomal RNA(12S rRNA),and cytochrome oxidase subunit 1(CO1) from the adults are identical to sequences from the crashed specimen. Interspecific uncorrected p-distances of partial CO1 gene of 26 sequences from all 11 species of Elaphe,including this new species,are large(8.5–15.2%). This new species is morphologically distinguished from all other species of Elaphe by several characters: 'M'-shaped marking on the supraoculars and adjacent frontal; four parallel series of red-brown spots on the dorsum extending from the neck to the vent; four longitudinal stripes associated with the spots; each spot is usually composed of a whole(or incomplete) red-brown scale with puce borders; spots of each stripe are similar in shape,they occur at relatively regular intervals of one or two scales,and they are slightly red-brown in color; and it has three preoculars,whereas all other species have one or two. Now Elaphe contains 11 species and this discovery highlights the need for continued exploration of temperate regions.

关键词： new species mitochondrial dna dna barcoding Zoige ratsnake

基于dna条形码技术研究鹞落坪常见传粉昆虫多样性及其资源保护

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基于DNA条形码技术研究鹞落坪常见传粉昆虫多样性及其资源保护

作者：姚晨晨安徽大学

学位级别：硕士

传粉昆虫是全球生物多样性的重要组成部分,在农林生产的增产增收、生态环境监测及生态系统的健康维持等方面扮演着重要的角色。鹞落坪国家级自然保护区地处大别山腹地,是我国北亚热带森林生态系统生物多样性保护的核心区域之一,但保护... 详细信息

传粉昆虫是全球生物多样性的重要组成部分,在农林生产的增产增收、生态环境监测及生态系统的健康维持等方面扮演着重要的角色。鹞落坪国家级自然保护区地处大别山腹地,是我国北亚热带森林生态系统生物多样性保护的核心区域之一,但保护区内的传粉昆虫多样性长期缺少系统的研究。因此,鉴于保护区蕴含的丰富生物多样及其特有的地理区位,非常有必要开展传粉昆虫多样性的研究,以期为保护区及大别山区农林生态系统的可持续发展、生态环境监测与评价以及北亚热带生物多样性保护等方面提供科学依据,对未来开发保护区传粉昆虫资源也有着较好的参考价值。本研究通过形态学及dna条形码(dna barcoding)互证,首次系统地报道了鹞落坪自然保护区传粉昆虫的多样性及组成,分析了保护区内传粉昆虫的物种多样性、系统发育多样性及其与环境因子之间的关系。主要研究结果如下:(1)本文于2019年10月～2021年10月采用样线法、马来氏网法和灯诱法对保护区以及4条不同样线(样线Ⅰ、样线Ⅱ、样线Ⅲ和样线Ⅳ)中的传粉昆虫进行了调查,共采集到常见传粉昆虫30 000余头,分别隶属于4目(膜翅目、双翅目、鞘翅目、鳞翅目)的52科130属152种。其中,利用样线法采集到开花植物上的传粉昆虫有2 551头,隶属于4目34科73属92种。中华蜜蜂(Apis cerana)、三条熊蜂(Bombus trifasciatus)、灰带管食蚜蝇(Eristalis cerealis)和东方菜粉蝶(Pieris canidia)均超过总个体数的6%,为区内的优势种。开花植物记录到的有86种,隶属36科75属,其中,菊科、蔷薇科、豆科和蓼科为保护区的重要开花植物类群。(2)物种多样性分析结果显示,不同季节(春,夏,秋)的Marglef丰富度指数的变化顺序为:夏季>秋季>春季,Shannon指数、Simpson指数以及均匀度指数的变化规律为:秋季>夏季>春季。表明保护区内传粉昆虫的Shannon指数、Simpson指数和均匀度指数随季节的变化趋势基本一致,而与丰富度指数的变化趋势大致相反。4条样线的物种多样性分析表明,以农田为主的样线Ⅰ具有比以森林为主的样线Ⅱ和Ⅲ更高的物种多样性,分析是因多样化的农作物能为传粉昆虫提供更好的栖息地和食物来源,也表明了传粉昆虫对于农田生态系统的重要性。样线Ⅲ则因临近旅游区域而受到较多人为干扰,多样性显著较低。(3)在昆虫群落相似性方面,样线Ⅰ-样线Ⅱ、样线Ⅰ-样线Ⅳ的传粉昆虫相似性都为中等相似,这说明这3条样线重叠的开花植物种类较多,重叠的植物在开花节律和蜜源时间上相同,因此,不同样线传粉昆虫组成在一定程度上具有相似性。4条样线不同季节的传粉昆虫相似性为中等不相似,说明春季,夏季和秋季的开花植物也具有一定的相似性。(4)采用线粒体COI基因作为分子标记,对保护区的228个传粉昆虫样本成功进行了PCR扩增及测序。所有序列的A+T的含量高于G+C,平均K2P遗传距离为26%,四个目的Ka/Ks值均小于1,且不同目昆虫的科内遗传距离显著小于科间遗传距离,证明dna条形码鉴别物种具有可行性。(5)从World Clim数据库中下载了19个环境因子(Bio1～Bio19),分析了物种及系统发育多样性与研究区域内的环境因子间的相关性关系:其中有14个环境因子(Bio1,Bio4～13,Bio16,Bio18～19)与系统发育多样性指数(PD)以及物种丰富度指数之间存在线性相关关系,冗余分析结果则支持温度因子对系统发育多样性及丰富度影响更显著。表明了温度是影响该地区传粉昆虫多样性的重要生态因子。

关键词：传粉昆虫物种丰富度 dna barcoding 系统发育多样性环境因子

Identification of Dian Ji Xue Teng(Kadsura interior) with dna barcodes

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World Journal of Traditional Chinese Medicine 2017年第1期3卷 11-15页

作者： Hao-Jie Guo Xi-Wen Li Yao-Dong Qi Xue-Ping Wei Ben-Gang Zhang Hai-Tao Liu Institute of Medicinal Plant Development Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences

Objective: To identify Kadsura interior(Dian Ji Xue Teng, Schisandraceae) by using dna barcoding.Methods: We analyzed five dna barcodes(ITS, ITS2, psb A-trn H, mat K and rbc L) using dna barcoding in terms of distance-based,tree-based and character-based identification to distinguish Kadsura interior and its adulterants.Results: In distance-based and tree-based identification, K. interior could be distinguished easily from the species of Schisandra and K. coccinea.In character-based identification, there are two single nucleotide polymorphisms(SNPs) in ITS and one SNP in psb A-trn H which can be used to distinguish K. interior from K. heteroclita and K. longipedunculata.Conclusion: The results indicate that dna barcoding can be used to identify K. interior. ITS and psb A-trnH sequence can be the most ideal dna barcode for discriminating K. interior and its adulterants by the combination analysis of distance-based, tree-based and character-based identification(SNPs).

关键词： dna barcoding Schisandraceae SNP Kadsura interior

Discovery of the male of Colletes yanruae from Yunnan,China(Hymenoptera:Apoidea:Colletidae)

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Zoological Systematics 2016年第3期41卷 286-293页

作者： Zeqing Niu Zongxin Ren Chaodong Zhu Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of Sciences

Several wild pollinator bees were found visiting local plants and collected in early spring in dry and eroding lands in Yunnan, China. With both morphology and dna information, we discovered the hitherto unknown male ... 详细信息

关键词： Apiformes dna barcoding taxonomy.

Screening of dna Barcode of Quarantine Phytophthora

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Agricultural Biotechnology 2017年第1期6卷 46-51,54页

作者： Ruifang GAO Yinghui CHENG Ying WANG Ying WANG Liyun GUO Guiming ZHANG Animal and Plant Inspection and Quarantine Technology Center Shenzhen Entry-Exit Inspection and Quarantine Bureau Key Laboratory of Exotic Pest Detection Technology Research of Shenzhen College of Agriculture and Biotechnology China Agricultural University

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.

关键词： Quarantine Phytophthora dna barcoding Genetic distance barcoding gap

The Potential of dna Barcode-Based Delineation Using Seven Putative Candidate Loci of the Plastid Region in Inferring Molecular Diversity of Cowpea at Sub-Species Level

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American Journal of Molecular Biology 2016年第4期6卷 138-158页

作者： Patrick Okoth John Muoma Mulaya Emmanuel Wekesa Clabe Dennis O. Omayio Paul O. Angienda Department of Zoology School of Physical and Biological Sciences Maseno University Maseno Kenya Department of Biological Sciences Masinde Muliro University of Science and Technology Kakamega Kenya Centre for Global Health Research Kenya Medical Research Institute (KEMRI) Kisumu Kenya Department of Biochemistry and Biotechnology Kenyatta University Nairobi Kenya

The novelty and suitability of the mitochondrial gene CO1 in dna barcoding as a reliable identification tool in animal species are undisputed. This is attributed to its standardized sequencing segment of the mitochondrial cytochrome c oxidase-1 gene (CO1) which has the necessary universality and variability making it a generally acceptable barcode region. CO1 is a haploid single locus that is uniparentally-inherited. Protein-coding regions are present in high-copy numbers making it an ideal barcode. The mitochondrial oxidase subunit I (COI) gene is a robust barcode with a suitable threshold for delineating animals and is not subject to drastic length variation, frequent mononucleotide repeats or microinversions. However, a low nucleotide substitution rate of plant mitochondrial genome [mtdna] precludes the use of CO1 as a universal plant dna barcode and makes the search for alternative barcode regions necessary. Currently, there exists no universal barcode for plants. The plastid region reveals leading candidate loci as appropriate dna barcodes yet to be explored in biodiversity studies in Kenya. Four of these plastid regions are portions of coding genes (matK, rbcL, rpoB, and rpoC1), and three noncoding spacers (atpF-atpH, trnH-psbA, and psbK-psbL) which emerge as ideal candidate dna loci. While different research groups propose various combinations of these loci, there exists no consensus;the lack thereof impedes progress in getting a suitable universal dna barcode. Little research has attempted to investigate and document the applicability and extend of effectiveness of different dna regions as barcodes to delineate cowpea at subspecies level. In this study we sought to test feasibility of the seven putative candidate dna loci singly and in combination in order to establish a suitable single and multi-locus barcode regions that can have universal application in delineating diverse phylogeographic groups of closely related Kenyan cowpea variants. In this study, our focus was based on genetic parameters includin

关键词： dna barcoding Plastid Region dna Sequencing Intergenic Spacers cp dna Mo-lecular Phylogenetics Intraspecific Infraspecific

New distribution record of Cyathus stercoreus(Schwein.)De Toni(Nidulariaceae)for India from Gujarat state

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Studies in Fungi 2018年第1期3卷 227-233页

作者： Patel RS Vasava AM Rajput KS Department of Botany Faculty of ScienceThe Maharaja Sayajirao University of BarodaVadodara 390002India

Cyathus stercoreus(Schwein.)De Toni(Nidulariaceae)was collected from Shoolpaneshwar Wildlife Sanctuary from the Narmada districts of Gujarat state,India.Present study reports C.stercoreus as a new distribution record from the Gujarat state.It was identified by using morphological features and further confirmation was carried out by using molecular methods with its dna barcoding.Nucleotide sequence is submitted into NCBI and molecular data are submitted into BOLD data system for dna barcoding.

关键词： Cyathus dna barcoding Gujarat Nidulariaceae