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Thrombin-like enzymes from venom gland of Deinagkistrodon acutus:cDNA cloning,mechanism of diversity and phylogenetic tree construc-tion

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Acta Pharmacologica Sinica 2006年第2期27卷 184-192页

作者： Xiang-dong ZHA~(2,3,7) He-sheng HUANG~(4,7) Li-zhi ZHOU~(2,3) Jing LIU~5 Kang-sen XU~6 ~2School of Life Sciences,Anhui University,Hefei 230039,China ~3Anhui Key Laboratory of Eco-Engineering and Bio-techniques,Hefei 230039,China ~4Department of Pharmacology,Anhui Medical University.Hefei 230022,China ~5School of Life Sciences,University of Science and Technology of China,Hefei 230026,China ~6Institute for Control of Pharmaceuticals and Biological Products,Beijing 100050,China SchoolofLifeSciences AnhuiUniversityHefei230039China AnhuiKeyLaboratoryofEco-EngineeringandBio-techniques Hefei230039China DepartmentofPharmacology AnhuiMedicalUniversityHefei230022China

Aim:To clone cDNAs of thrombin-like enzymes(TLEs)from venom gland ofDeinagkistrodon acutus and analyze the mechanisms by which their structuraldiversity ***:Reverse transcription-polymerase chain reaction andgene cloning techniques were used,and the cloned sequences were analyzed byusing bioinformatics ***:Novel cDNAs of snake venom TLEs *** possibilities of post-transcriptional recombination and horizontalgene transfer are discussed.A phylogenetic tree was ***:The cDNAs of snake venom TLEs exhibit great *** are severaltypes of structural *** variations may be attributable to certainmechanisms including recombination.

关键词： thrombin-like enzymes structural diversity RNA recombination phylogenetic tree

PoIntree: A Polar and Interactive phylogenetic tree

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Genomics, Proteomics & Bioinformatics 2005年第1期3卷 58-60页

作者： Carreras Marco Gianti Eleonora Sartori Luca Plyte Simon Edward Isacchi Antonella Bosotti Roberta Nerviano Medical Sciences srl 20014 Nerviano (MI) Italy.Nerviano Medical Sciences srl 20014 Nerviano (MI) Italy.Nerviano Medical Sciences srl 20014 Nerviano (MI) Italy.Nerviano Medical Sciences srl 20014 Nerviano (MI) Italy.Nerviano Medical Sciences srl 20014 Nerviano (MI) Italy.Nerviano Medical Sciences srl 20014 Nerviano (MI) Italy.

PoIntree （Polar and Interactive tree） is an application that allows to build, visualize, and customize phylogenetic trees in a polar, interactive, and highly flexible view. It takes as input a FASTA file or multiple alignment formats. phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining （N J） algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoIntree, nodes can be dynamically opened and closed and distances between genes are graphically represented. tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component （Steema software）.

关键词： phylogenetic tree tree visualizer tree builder

A simple method for constructing phylogenetic tree

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A simple method for constructing phylogenetic tree

phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant ‘tree of life’

大连理工大学生物医学工程学会研讨会

作者： TANG Nan-nan , LI Chun ( Departmenl of Applied Mathematics, University of Technology, Dalian 116024, P R china Department of Mathematics, Bohai University, Jinzhou 121000, P R China)

＜正＞Based on the directed graphical representation of DNA sequences, we associate a DNA sequence with a 3-compoent vector whose entries are the normalized ALE-index of the upper triangular matrices of the directed graphs. By giving a new distance of pairs of points in 3-D space, we obtain a similarity matrix of 20 mtDNA sequences belonging to different species. The entries of the similarity matrix are used to construct phylogenetic tree. The proposed approach does not require sequence alignment and is totally automatic.

关键词： DNA phylogenetic tree Directed graph ALE-index

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National Science Review 2021年第4期8卷 66-77页

作者： Yongzeng Zhang Tao Deng Lu Sun Jacob B.Landis Michael J.Moore Hengchang Wang Yuehua Wang Xiaojiang Hao Jijun Chen Shenghong Li Maonian Xu Pema-Tenzin Puno Peter H.Raven Hang Sun CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences University of the Chinese Academy of Sciences Department of Botany and Plant Sciences University of California Riverside School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell University Department of Biology Oberlin College CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Chinese Academy of Sciences School of Life Science Yunnan University State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of BotanyChinese Academy of Sciences Pharmaceutical Sciences University of Iceland Missouri Botanical Garden

To evaluate the phylogenetic patterns of the distribution and evolution of plant secondary metabolites(PSMs), we selected 8 classes of PSMs and mapped them onto an updated phylogenetic tree including 437 families of seed plants. A significant phylogenetic signal was detected in 17 of the 18 tested seed-plant clades for at least 1 of the 8 PSM classes using the D statistic. The phylogenetic signal, nevertheless, indicated weak clustering of PSMs compared to a random distribution across all seed plants. The observed signal suggests strong diversifying selection during seed-plant evolution and/or relatively weak evolutionary constraints on the evolution of PSMs. In the survey of the current phylogenetic distributions of PSMs, we found that multiple origins of PSM biosynthesis due to external selective forces for diverse genetic pathways may have played important roles. In contrast, a single origin of PSMs seems rather uncommon. The distribution patterns for PSMs observed in this study may also be useful in the search for natural compounds for medicinal purposes.

关键词： secondary metabolites phylogenetic tree phylogenetic signal co-diversification evolution bioprospecting seed plants

Fast algorithm for constructing neighbor-joining phylogenetic trees

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Journal of Southeast University(English Edition) 2006年第2期22卷 176-179页

作者：陈宁涛王能超施保昌华中科技大学计算机科学与技术学院武汉430074 华中科技大学并行计算研究所武汉430074

To improve the performance of Saitou and Nei＇s algorithm （SN） and Studier and Keppler＇s improved algorithm （SK） for constructing neighbor-joining phylogenetic trees and reduce the time complexity of the computation, a fast algorithm is proposed. The proposed algorithm includes three techniques. First, a linear array A[N] is introduced to store the sum of every row of the distance matrix （the same as SK）, which can eliminate many repeated computations. Secondly, the value of A [i] is computed only once at the beginning of the algorithm, and is updated by three elements in the iteration. Thirdly, a very compact formula for the sum of all the branch lengths of operational taxonomic units （OTUs） i and j is designed, and the correctness of the formula is proved. The experimental results show that the proposed algorithm is from tens to hundreds times faster than SN and roughly two times faster than SK when N increases, constructing a tree with 2 000 OTUs in 3 min on a current desktop computer. To earn the time with the cost of the space and reduce the computations in the innermost loop are the basic solutions for algorithms with many loops.

关键词： phylogenetic tree neighbor-joining method fast algorithm progressive multiple alignment

Using DNA Sequences and phylogenetic trees as Tools for Teaching Entomology to Undergraduate Students: A Simple Approach

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Advances in Entomology 2021年第4期9卷 147-154页

作者： Mohammad Ali Al-Deeb Biology Department United Arab Emirates University Al Ain UAE

This technical note aims to show how any instructor teaching entomology can use the Basic Local Alignment Search Tool (BLAST) and the “one click” mode of *** to teach undergraduate students about insect DNA similarity in a simple way. Teaching an entomology course requires the use of numerous tools to help students grasp different concepts. Knowing that there are more than one million described species of insects means that teaching students about insect identification and taxonomy can be challenging. However, here we present two easy exercises that could be used as classroom or take-home assignments to demonstrate various levels of DNA similarity among different insect taxa. Such exercises unlock students’ creativity and break the barrier of fear of bioinformatics. Moreover, they open up new ways for them to understand insect taxonomy through molecular biology and allow them to develop new skills that contribute to strengthening their scientific performance in the future, especially when they do research as graduate students. Finally, this note is an example of how to integrate simple bioinformatics tools into the teaching of entomology.

关键词： DNA Sequence phylogenetic tree GenBank Teaching Entomology

phylogenetic analysis and biological characteristic tests of marine bacteria isolated from Southern Ocean(Indian sector)water

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Acta Oceanologica Sinica 2015年第8期34卷 73-82页

作者： GUPTA Pratibha BALAJI Raju PARANI M CHANDRA T S SHUKLA P KUMAR Anil BANDOPADHYAY Rajib Department of Bio-Engineering Birla Institute of Technology Department of Genetic Engineering Kattankulathur Campus SRM University Microbiology and Genetics Laboratory Department of Biotechnology Indian Institute of Technology Madras Department of Microbiology Maharshi Dayanand University OSSG Department National Centre for Antarctic and Ocean Research Ministry of Earth Sciences Government of India UGC Centre of Advanced Study Department of Botany the University of Burdwan

Fifty-seven bacteria were isolated from Southern Ocean （Indian sector） water samples which were collected from different latitude and longitude of the ocean. All the isolates were able to grow at 4℃, 20℃, 37℃ and tolerable NaCI concentration up to 13.5% （w/v）. 29 out of 57 isolates were identified using 16S rDNA amplification and the sequences were submitted to National Center for Biotechnology Information （NCBI）. All the isolates were classified by using Ribosomal Database Project （RDP） and found that isolates belongs to Proteobacteria and Bacteriodes. The average G＋C content was 56.4%. The isolates were screened for the presence of extracellular enzymes, viz. amylase, catalase, urease, esterase, lipase and protease. The disc diffusion method is used to screen antibiotic production by the isolates against four pathogenic bacteria, viz. Salmonella typhimurium （NCIM 2501）, Staphylococcus aureus （NCIM 2122）, Bacillus subtilis （NCIM 2193）, and Pseudomonas aeruginosa （NCIM 2036）. Nine out of 29 were found to be antibiotic producer.

关键词： Southern Ocean marine bacteria 16S rDNA phylogenetic tree antibacterial

Sequence Divergence of Microsatellites and Phylogeny Analysis in Tetraploid Cotton Species and Their Putative Diploid Ancestors

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Journal of Integrative Plant Biology 2005年第12期47卷 1418-1430页

作者： Wang-Zhen GUO Dong FANG Wen-Duo YU Tian-Zhen ZHANG State Key Laboratory of Crop Genetics and Germplasm Enhancement Cotton Research Institute Nanjing Agricultural University Nanjing 210095 China

To determine the level of microsatellite sequence differences and to use the information to construct a phylogenetic relationship for cultivated tetraploid cotton （Gossypium spp.） species and their putative diploid ancestors, 10 genome-derived microsatellite primer pairs were used to amplify eight species, including two tetraploid and six diploid species, in Gossypium. A total of 92 unique amplicons were resolved using polyacrylamide gel electrophoresis. Each amplicon was cloned, sequenced, and analyzed using standard phylogenetic software. Allelic diversities were caused mostly by changes in the number of simple sequence repeat （SSR） motif repeats and only a small proportion resulted from interruption of the SSR motif within the locus for the same genome. The frequency of base substitutions was 0.5%-1.0% in different genomes, with only few indels found. Based on the combined 10 SSR flanking sequence data, the homology of A-genome diploid species averaged 98.9%, even though most of the amplicons were of the same size, and the sequence homology between G. gossypioides （Ulbr.） Standl. and three other D-genome species （G. raimondii Ulbr., G. davidsonii Kell., and G. thurberi Tod.） was 98.5%, 98.6%, and 98.5%, respectively. phylogenetic trees of the two allotetraploid species and their putative diploid progenitors showed that homoelogous sequences from the A- and D-subgenome were still present in the polyploid subgenomes and they evolved independently. Meanwhile, homoelogous sequence interaction that duplicated loci in the polyploid subgenomes became phylogenetic sisters was also found in the evolutionary history of tetraploid cotton species. The results of the present study suggest that evaluation of SSR variation at the sequence level can be effective in exploring the evolutionary relationships among Gossypuim species.

关键词： diploid Gossypium microsatellite phylogenetic tree simple sequence repeat (SSR) tetraploid.

Population genetic structure of Sitobion miscanthi in China

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Journal of Integrative Agriculture 2022年第1期21卷 178-187页

作者： SUN Jing-xuan LI Qian TAN Xiao-ling FAN Jia ZHANG Yong QIN Yao-guo Frédéric FRANCIS CHEN Ju-lian State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193P.R.China Department of Functional and Evolutionary Entomology Gembloux Agro-Bio TechUniversity of LiègeGembloux 5030Belgium Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences Mudanjiang 157000P.R.China

The wheat aphid, Sitobion miscanthi, is one of the most destructive pests of wheat plants in the temperate regions of China. Little is known about the genetic structure evolution of the different geographic populations of S. miscanthi with its migration. In this study, we investigated the population genetic structure and demographic history of S. miscanthi by analysing 18 geographical populations across China using one mitochondrial gene, COI;one nuclear gene, EF-1α;and two endosymbiont Buchnera genes, gnd and trpA. Analysis of data from the various groups showed high haplotype diversity and low nucleotide variation. SAMOVA analysis did not find a correlation between genetic distance and geographic distance. However, areas with high population diversity exhibited high haplotype diversity. Therefore, we speculate that there are two main natural migration pathways of S. miscanthi in China. One is from Yunnan to the Sichuan Basin, and the other is from Wuhan, Xinyang and Jiaodong Peninsula areas to the northwest. Based on this hypothesis, we inferred that these aphid populations appear first in the southwestern and southern regions and spread to the north with the help of the southeastern and southwestern monsoons, which occur in spring and summer. In autumn, the aphids spread southward with the northeastern and northwestern monsoons.

关键词： Sitobion miscanthi molecular marker COI symbiotic bacteria phylogenetic tree