Neighbor-joining Algorithm Research Articles

Identification and Phylogeny of Cryptic Species of the Daphnia Longispina Complex (Anomopoda, Daphniidae) Using ITS2 Secondary Structure

Cladocerans of the genus Daphnia O.F. Muller (Crustacea: Cladocera) are typical members of different types of water bodies and are used as model organisms in various biological disciplines. Within the genus, a considerable number of closely related and cryptic species are noted, the identification of which by morphological traits often causes difficulties. In the present study, species identification in the Daphnia longispina complex, namely, D. longispina O.F. Muller, D. hyalina Leydig, D. umbra Taylor, Hebert et Colbourne, and D. cf. longispina, was performed using data on the predicted secondary structure of the second internal transcribed spacer (ITS2) of the nuclear rDNA. Phylogenetic analysis carried out using the Profile Neighbor-Joining algorithm and the analysis of compensatory base changes supported the species status of D. hyalina and D. cf. longispina. It was demonstrated that the data on the ITS2 secondary structure can be used to resolve complex taxonomic problems in the study of cladocerans in general and the species complexes in particular.

Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences

Abstract. Hapsari L, Trimanto, Wahyudi D. 2019. Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences. Biodiversitas 20: 1266-1283. Heliconia L. is a single genus in the family Heliconiaceae, with approximate consists of 200 species. It has wide morphological variations among and within species which led to problems in species identification. Species diversity and phylogenetic analysis using morphology and rbcL marker subjected to 17 Heliconia spp. living collections of Purwodadi Botanic Garden (PBG) have been conducted. The rbcL gene located in chloroplast genome is one of appropriate proposed marker for plant barcoding assessment. This study aimed to study morphology and genetic variability of the PBG Heliconiaceae collections, to confirms the species name for a more accurate identity record and to reveal the diversity and phylogenetics of the species. Morphological characterization showed high variability among Heliconia species, which included 3 subgenera (Heliconia, Stenochlamys, and Griggsia) and 1 hybrid. Each species possessed unique morphological characteristics. The common morphological characters which distinguished among and within Heliconia species includes leaf form, inflorescence type, and bract characteristics. Key to the Heliconia species examined is presented in this paper. However, molecular confirmation using rbcL sequences showed high conservation level (0.932) and low genetic variability. About 656 nucleotides were monomorphic and 33 positions were polymorphic which comprised 18 singleton variable sites and 15 parsimony informative sites. Twelve haplotypes were produced with haplotype diversity value 0.8952. Pairwise distance analysis shows that they were shared high similarity of rbcL sequences with very low genetic distance (0.022 to 0.000). The topology of phylogenetic tree resulted by Neighbour-Joining algorithm has the best grouping and be able to explain the relationship among species of Heliconia, although supported by low bootstrap (65). It was separated into two clades following its subgen. classification. Clade 1 consists of subgen. Heliconia and Griggsia; while clade 2 consists of subgen. Heliconia and Stenochlamys; also hybrid species. Further, separation of deeper branchings (section) was inconsistent and unclear. Upon this study, rbcL marker was considered too conserved thus less valuable for phylogenetic analysis at lower taxa among and within Heliconia spp. However, rbcL was suggested to distinguish at higher level taxa between closely related genus and above.

A Simple Genetic Algorithm for Optimizing Multiple Sequence Alignment on the Spread of the SARS Epidemic

Background:Multiple sequence alignment is a method of getting genomic relationships between 3 sequences or more. In multiple alignments, there are 3 mutation network analyses, namely topological network system, mutation region network and network system of mutation mode. In general, the three analyses show stable and unstable regions that map mutation regions. This area of ​​mutation is described further in a phylogenetic tree which simultaneously illustrates the path of the spread of an epidemic, the Severe Acute Respiratory Syndrome (SARS) epidemic. The process of spreading the SARS viruses, in this case, is described as the process of phylogenetic tree formation, and as a novelty of this research, multiple alignments in the process are analyzed in detail and then optimized with genetic algorithms.Methods:The data used to form the phylogenetic tree for the spread of the SARS epidemic are 14 DNA sequences which are then optimized by using genetic algorithms. The phylogenetic tree is constructed by using the neighbor-joining algorithm with a distance matrix that the intended distance is the genetic distance obtained from sequence alignment by using the Needleman Wunsch Algorithm.Results & Conclusion:The results of the analysis obtained 3649 stable areas and 19 unstable areas. The results of phylogenetic tree from the network system analysis indicated that the spread of the SARS epidemic extended from Guangzhou 16/12/02 to Zhongshan 27/12/02, then spread simultaneously to Guangzhou 18/02/03 and Guangzhou hospital. After that, the virus reached Metropole, Zhongshan, Hongkong, Singapore, Taiwan, Hong kong, and Hanoi which then continued to Guangzhou 01/01/03 and Toronto at once. The results of the mutation region network system demonstrate decomposition of orthogonal mutations in the 1st order arc.

Assessment of genetic diversity among low-nitrogen-tolerant early generation maize inbred lines using SNP markers

Low soil nitrogen (low-N) level is responsible for yield reduction in maize (Zea mays L.) fields in sub-Saharan Africa. A clear understanding of the genetic diversity among early generation inbred lines selected from various elite low-N- tolerant populations offers an opportunity to obtain lines that could be used in parental combinations to develop high-yielding low-N-tolerant maize hybrids. A total of 115 S3 lines derived from four low-N-tolerant populations were assessed for genetic diversity using 15 670 single nucleotide polymorphism (SNP) markers. The SNP markers were highly polymorphic with polymorphic information content ranging from 0.0 to 0.38. The genetic diversity among the inbred lines ranged from 0.0 to 0.50 and thus indicated the high level of dissimilarity among the inbred lines. The neighbour-joining clustering algorithm and model-based population structure classified the 115 lines into four distinct groups that were generally consistent with the genetic backgrounds of the inbred lines. The information obtained from this study revealed genetic diversity among the inbred lines and may guide the selection of potential parents for detailed combining ability studies and eventual use in hybrid combinations. The selected inbred lines would be invaluable in the development of low-N-tolerant hybrids.

Geographical description and molecular characterization of genetic structure and diversity using a 6K SNP array in Turkish oat germplasm

Cultivated oat (Avena sativa L. and Avena byzantina Koch) is native to Turkey, a secondary center of oat diversity. Oat breeding has received less attention relative to other cereals. In this work, the diversity of oat landraces collected from different regions of Turkey as well as obtained from different gene banks was investigated using 3293 high quality SNP markers. Expected heterozygosity (Hs), observed heterozygosity (Ho), inbreeding coefficient (Fis), and overall genetic diversity (Ht) of the oat gene pool were 0.22, 0.01, 0.96, and 0.38, respectively. The value of the genetic differentiation (Fst) metric for genetic structure was 0.41 and indicated that kinship was more of a determinant for population structure than the geographical provenance. The populations from different geographical regions shared a great proportion of genetic diversity. Clustering using model-based STRUCTURE, principal coordinates (PCoA), and neighbour-joining (NJ) algorithms were mostly comparable except for five discrepantly clustered accessions in NJ and PCoA relative to STRUCTURE, which can be attributed to the relatively reduced resolution power in the NJ and PCoA approaches. SNP markers partitioned all oat accessions into four main groups (A, B, C, and D) with 10 unclassified accessions. Some landraces were identical based on genetic distance and can represent duplications in gene banks. The data presented in this work represent the initial results on genetic diversity as investigated in Turkish oat, and are an important resource for systematicians, geneticists, and breeders interested in Turkish oat germplasm. These results are expected to open new opportunities for further studies in oat genomics and cultivar development.

Distribution of HLA DRB1, DQA1 and DQB1 Allelic Main Groups in the Vojvodina Province of Serbia: Genetic Relatedness with Other Populations

The Human Leukocyte Antigen (HLA) system represents a distinctive marker in identifying population groups since they exhibit a very high level of polymorphism that reveals remarkable frequency variation in human populations. In this study the gene frequencies of HLA class II DRB1, DQB1 and DQA1 alleles were studied in 100 randomly chosen individuals from region of Vojvodina, Serbia, with an aim to establish the genetic relationship between Vojvodina population and selected populations of European and non-European descent. DNA low resolution typing for DRB1, DQA1 and DQB1 was done using a standardized PCR-SSOP. Genetic distances between Vojvodina and 28 populations were computed based on frequency of DRB1 alleles. Phylogenetic trees were constructed using the neighbour-joining algorithm. The distribution of the observed genotypes is in Hardy–Weinberg equilibrium for all studied systems. The most frequent alleles were HLA-DQA1*01 (0.475), HLA-DQB1*05 (0.3), HLA-DRB1*11 (0.14). Two locus haplotype analysis identified HLA-DQB1*05-DQA1*01 (0.22), HLA-DQB1*03-DQA1*05 (0.135) and HLA-DQB1*06-DQA1*01 (0.1075) as the common haplotypes in Vojvodina population. Compared to other populations, Vojvodina appear to be genetically related to Balkan population, in particular Croatia, Slovenia and Bosnia and Herzegovinia. In conclusion, genetic distance matrix estimated using alleles at HLA-DRB1 locus, indicates that Vojvodina population is related to present-day nearby populations, Polish, Russians, Germans and French but not to Albanians from Kosovo and Bulgarians.

Analysis on Algorithms for Constructing Phylogenetic Trees From Distances

Neighbour-joining algorithm (NJ for short) is an used widely algorithm for constructing phylogenetic trees from distances because of its high accuracy. For NJ costs a lot of time to construct phylogenetic trees for the large input data, it does not often output a result within feasible time. Until now, there are several improved algorithms of NJ aiming for speeding up the construction of trees, but there is no research on the accuracy of those improved algorithms. The paper will analyze and compare the accuracy of NJ as well as its improved algorithms by means of the experiments. We introduce a new improved algorithm, called RandomNJ, which is an efficient method for constructing phylogenetic trees from distances. Furthermore, we design the INJ which is a web-based server for on-line constructing the phylogenetic trees using the improved algorithms and NJ. It is available from http://bioinformatics.imu.edu.cn/INJ/.

First Report of Prunus domestica as the Host of a Phytoplasma Belonging to Group 16SrI, Subgroup B/L

HomePlant DiseaseVol. 103, No. 1First Report of Prunus domestica as the Host of a Phytoplasma Belonging to Group 16SrI, Subgroup B/L PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Prunus domestica as the Host of a Phytoplasma Belonging to Group 16SrI, Subgroup B/LA. Zwolińska, N. Borodynko-Filas, D. Nowaczyk, and B. Hasiów-JaroszewskaA. Zwolińska†Corresponding author: A. Zwolińska; E-mail: E-mail Address: a.zwolinska@iorpib.poznan.plhttp://orcid.org/0000-0003-2681-2915Search for more papers by this author, N. Borodynko-FilasSearch for more papers by this author, D. NowaczykSearch for more papers by this author, and B. Hasiów-JaroszewskaSearch for more papers by this authorAffiliationsAuthors and Affiliations A. Zwolińska † N. Borodynko-Filas D. Nowaczyk B. Hasiów-Jaroszewska , Institute of Plant Protection – National Research Institute, Virology and Bacteriology Department, Poznań, Poland. Published Online:31 Oct 2018https://doi.org/10.1094/PDIS-06-18-0963-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat In July 2016 and 2017, diseased plum trees (Prunus domestica L.) were observed in the orchard localized in the Wielkopolska region of Poland. The symptoms of witches’ brooms with internode shortening, axillary bud growth, and reduced leaf size indicated a potential phytoplasma infection. Samples of shortened shoots were collected from five symptomatic and five asymptomatic plants, respectively. DNA samples were extracted from 2 g of leaf tissues using a modified cetyltrimethylammonium bromide procedure (Maixner et al. 1995) and subsequently used as templates in nested polymerase chain reaction (PCR) for the amplification of genes encoding 16S rRNA; ribosomal proteins (rp) S19, L22, and S3 and elongation factor Tu (tuf) with primers P1/P7 followed by R16F2n/R16R2; rpF1/rpR1 followed by rp(I)F1A/rp(I)R1A and fTuf1/rTuf1 followed by fTufAY/rTufAY, respectively (Duduk et al. 2013; Martini et al. 2007; Schneider et al. 1997). Amplicons of correct sizes (1.2, 1.2, and 0.9 kb) were obtained from all the diseased plants tested (samples Plum1 to Plum5), respectively. No PCR products were obtained from the asymptomatic samples. All PCR products were ligated into pGEM-T Easy Vector Systems (Promega), and plasmid DNA was sequenced by an external company (Genomed, Warsaw, Poland). The 16S rDNA, tuf, and rp genes coding sequences from Plum1 to Plum5 were identical, and therefore one representative sequence of each region was deposited in GenBank under accession numbers MH061193, MH061368, and MH061366, respectively. The R16F2n/R16R2 (MH061193) primed fragment was subjected to in silico restriction digestion using iPhyClassifier, the online tool for phytoplasma classification (https://plantpathology.ba.ars.usda.gov/cgi-bin/resource/iphyclassifier.cgi). The collective restriction fragment length polymorphism patterns indicated that diseased plants were infected by ‘Candidatus Phytoplasma asteris’ of subgroup 16SrI-L. Next, the 385-bp barcode fragments of the EF-Tu gene from representatives of different phytoplasma groups were retrieved from the GenBank database. The phylogenetic analysis was performed based on those sequences and the tuf sequence obtained in this study using the neighbor joining algorithm of MEGA 7 software (https://www.megasoftware.net/). The 1.2-kbp DNA segment containing rp genes was also analyzed. In the phylogenetic trees, the Polish isolate of plum witches’ broom phytoplasma clustered together with ‘Ca. P. asteris’ representatives of ribosomal subgroup 16SrI-B and 16SrI-B/L. Based on all the performed analyses, the plum witches’ broom phytoplasma (PlumWB) was classified as a member of group 16SrI, subgroup B/L, which consists of two heterogeneous 16Sr RNA genes (Jomantiene et al. 2010). To our knowledge, this is the first report of plums infected with ‘Ca. P. asteris’ representing subgroup I-B/L in Poland, suggesting that fruit trees can be perennial reservoirs of the phytoplasma, which has great significance in the pathogen’s epidemiology.

Phylogenetic relationship and genetic background of blueberry (Vaccinium spp.) based on retrotransposon-based SSAP molecular markers

A total length of 98 070 bp long terminal repeat retrotransposon (LTR-RT) sequences were found after preliminary prediction and subsequent screening, accounting for 3.96% of the whole blueberry genome. Thirty-three members belonged to Ty1/Copia retrotransposon family and 60 members of Ty3/Gypsy retrotransposon family were identified according to their sequence similarity to previously reported retrotransposons, accounting for 1.57% and 2.39% of the whole genome, respectively. Nineteen sequences from Ty1/Copia family and thirty-three Ty3/Gypsy sequences were used for primer design. Sixty-six pairs of primers were synthesized randomly, in which forty-two pairs of primers were screened to validate the availability and transferability of LTR-RT on 48 blueberry cultivars. We found that 4, 236 bands were amplified using 42 pairs of primers, of which 4184 were polymorphic bands. Bands at each locus ranged from 34 to 219, with an average of 101. To elucidate genetic relationship of 48 blueberry cultivars, principle coordinate analysis (PCoA) was carried out based on SSAP genotyping data. The results showed that the first two coordinates could explain 14.11% of the total variation among all cultivars, of which the first and second coordinate accounted for 8.13% and 5.98% of total variation, respectively. The first three axes accounted for 18.84% of the total variation. In order to estimate genetic background and phylogenetic relationship of these cultivars, phylogenetic tree was constructed based on neighbor-joining algorithm. The results showed that 48 cultivars could be clustered into five groups, indicating that genetic background of 48 blueberry cultivars used in this study was relatively simple. The genetic composition of highbush blueberry cultivars was similar, which consisted of a single genepool. Genetic background of rabbiteye blueberry cultivars presented multiple source of genepools, which was probably related to the involvement of several species in the artificial selection. ‘Bluegem’ resembles genetic composition with highbush blueberries, suggesting that several cultivars possibly involved in its breeding process. The original lineage from V. virgatum was supposed to be replaced gradually with repeated hybridization during cross fertilization. The cross breeding among cultivars genetically distant from one other would enrich the genetic diversity of blueberry cultivars. All these results provided valuable references for the selection of parental cultivars in blueberry breeding.

First Report of ‘Candidatus Phytoplasma asteris’ Related Strain Associated with Atractylodes lancea Malformations in Hubei Province of China

HomePlant DiseaseVol. 102, No. 12First Report of ‘Candidatus Phytoplasma asteris’ Related Strain Associated with Atractylodes lancea Malformations in Hubei Province of China PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of ‘Candidatus Phytoplasma asteris’ Related Strain Associated with Atractylodes lancea Malformations in Hubei Province of ChinaQ. Wan, L. Chen, S. Ming, L. Gong, X. Huang, K. Yu, H.-Y. Che, and D.-Q. LuoQ. WanSearch for more papers by this author, L. ChenSearch for more papers by this author, S. MingSearch for more papers by this author, L. GongSearch for more papers by this author, X. HuangSearch for more papers by this author, K. Yu†Corresponding author: K. Yu; E-mail: E-mail Address: [email protected]http://orcid.org/0000-0002-4262-4431Search for more papers by this author, H.-Y. Chehttp://orcid.org/0000-0002-9302-7784Search for more papers by this author, and D.-Q. LuoSearch for more papers by this authorAffiliationsAuthors and Affiliations Q. Wan L. Chen S. Ming L. Gong X. Huang K. Yu † , Hubei Key Laboratory of Resources and Chemistry of Chinese Medicine, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China H.-Y. Che D.-Q. Luo , Environment and Plant Protection Research Institute, Chinese Academy of Tropical Agriculture Science, Hainan, China. Published Online:10 Oct 2018https://doi.org/10.1094/PDIS-01-18-0177-PDNAboutSections ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Atractylodes lancea Thunb., a commercially cultivated plant in Hubei, Shanxi, and Henan Provinces, China, is well known for its extensive use in the practice of traditional Chinese medicine for the treatment of various diseases (Huang et al. 2016). During the investigations conducted in April 2017 in Yingshan (30°30′ to 31°08′ N; 115°32′ to 116°04′ E), Hubei Province, 100 plants of A. lancea with symptoms including stem fasciation and proliferation were noticed across the five surveyed fields. Other symptoms including floral virescence and inflorescence abnormality were also observed. Stem tissues were sampled from six symptomatic and three asymptomatic A. lancea plants, and molecular diagnostics were employed to prove possible phytoplasma infections. Total DNA was extracted using the Plant Genomic DNA Kit (Tiangen, Beijing, China) following the manufacturer’s instructions, and nested polymerase chain reaction (PCR) was performed with P1/P7 followed by R16F2n/R16R2 primer pairs (Lee et al. 1998). A phytoplasma-specific gene fragment of approximately 1,200 base pairs (bp) was amplified from all symptomatic plants. In parallel diagnostic assays, no amplicons were generated from asymptomatic plants. The amplicon of approximately 1,200 bp of the second PCR product from symptomatic samples was purified, cloned into pMD-18T vector (Takara Bio, Dalian, China), and sequenced. The sequences obtained from all six symptomatic plants were identical, and one of them was deposited in the GenBank under accession number MG257945.3. An NCBI-BLAST search indicated that it shared 99.7% identity to the sesame phyllody phytoplasma (GenBank accession no. KF728953) from India. A phylogenetic tree of phytoplasma 16S rRNA gene sequences was constructed using a neighbor-joining algorithm, and it showed that A. lancea isolates clustered with the phytoplasma strains belonging to subgroup 16SrI-B (GenBank accession nos. MG652627 and KY565572). Restriction fragment length polymorphism analyses using iPhyClassifier (Zhao et al. 2009) placed the A. lancea phytoplasma strain in the 16SrI-B subgroup because the virtual pattern was identical (similarity coefficient 0.92) to the reference pattern of 16Sr group I, subgroup B (CP000061). Although ‘Ca. Phytoplasma asteris’ 16SrI-B subgroup has been identified in various hosts (Alvarez et al. 2014), to our knowledge, this is the first report of 16SrI-B subgroup phytoplasma infecting A. lancea in China. With its rapid and widespread characteristics, the identified phytoplasma strain could pose an imminent threat and cause economic loss to A. lancea cultivation. A. lancea is widely distributed and cultivated also in Japan and Thailand (Na-Bangchang and Karbwang 2014), and a phytoplasma, detected in China, could be a potential problem for all the region and seriously affect the production of rhizomes of A. lancea, which have a great pharmacological value worldwide.

Genetic variability of Akhal-Teke horses bred in Italy.

BackgroundThe Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences.MethodsSeventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences.ResultsNucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.

Mathematical and Simulation-Based Analysis of the Behavior of Admixed Taxa in the Neighbor-Joining Algorithm.

The neighbor-joining algorithm for phylogenetic inference (NJ) has been seen to have three specific properties when applied to distance matrices that contain an admixed taxon: (1) antecedence of clustering, in which the admixed taxon agglomerates with one of its source taxa before the two source taxa agglomerate with each other; (2) intermediacy of distances, in which the distance on an inferred NJ tree between an admixed taxon and either of its source taxa is smaller than the distance between the two source taxa; and (3) intermediacy of path lengths, in which the number of edges separating the admixed taxon and either of its source taxa is less than or equal to the number of edges between the source taxa. We examine the behavior of neighbor-joining on distance matrices containing an admixed group, investigating the occurrence of antecedence of clustering, intermediacy of distances, and intermediacy of path lengths. We first mathematically predict the frequency with which the properties are satisfied for a labeled unrooted binary tree selected uniformly at random in the absence of admixture. We then introduce a taxon constructed by a linear admixture of distances from two source taxa, examining three admixture scenarios by simulation: a model in which distance matrices are chosen at random, a model in which an admixed taxon is added to a set of taxa that reflect treelike evolution, and a model that introduces a perturbation of the treelike scenario. In contrast to previous conjectures, we observe that the three properties are sometimes violated by distance matrices that include an admixed taxon. However, we also find that they are satisfied more often than is expected by chance when the distance matrix contains an admixed taxon, especially when evolution among the non-admixed taxa is treelike. The results contribute to a deeper understanding of the nature of evolutionary trees constructed from data that do not necessarily reflect a treelike evolutionary process.

Presencia de Candidatus Liberibacter solanacearum en Bactericera cockerelli Sulc asociada con enfermedades en tomate, chile y papa


 
 
 El “permanente del tomate”, “manchado del tubérculo” o “zebra chip” en papa y “brotes cloróticos” del chile, son tres enfermedades descritas en México con signos coincidentes de aborto de flor, oscurecimiento de tejido vascular en la base del tallo y raíz de las plantas. Se ha mencionado la asociación entre estas enfermedades y la bacteria emergente Candidatus Liberibacter solanacearum (CLs) así como al psílido Bactericera cockerelli como su vector. Estas enfermedades, que en inicio se localizaban en tres estados de México se han diseminado a las principales regiones productoras de solanáceas, tanto en condiciones de campo como en invernadero. El objetivo del estudio fue conocer la presencia de CLs asociado a enfermedades que afectan los cultivos de tomate, para y chile en México. La bacteria se identificó por PCR del gen 16S de ADNr, clonación y secuenciación. La alineación de secuencias nucleotídicas se realizó con el método Clustal W y el árbol filogenético se construyó con el algoritmo de Neighbor-Joining a partir de distancias calculadas con el método de Tajima-Nei y un índice de Felsenstein de 1 000 réplicas, utilizando el software MEGA versión 5.05. En total se analizaron 167 muestras, de las cuales 86 resultaron positivas, provenientes de 14 estados de México. Se obtuvieron cinco secuencias nucleotídicas de Guanajuato, San Luis Potosí y Sinaloa correspondientes al tomate, papa y chile, adultos y huevecillos de B. cockerelli. El análisis de las secuencias mostró una identidad de 99.4% al comparase entre estas y hasta 99.8% con accesiones del GenBank descritas para CLs en EUA, Nueva Zelanda y Canadá.
 
 

Olive Tree (Olea europaea L.) Diversity in Traditional Small Farms of Ficalho, Portugal

The genetic diversity of “Gama” and “Bico de Corvo”, local cultivars of olive tree (Olea europaea) from seven traditional orchards of Ficalho (Alentejo region, Portugal), was studied to characterize the local diversity and assess the level of on farm diversity. Two different analytical systems were used: endocarp morphological characteristics and genetic analysis by microsatellite markers (Simple Sequence Repeats or SSR). The seven screened loci were polymorphic and allowed the identification of 23 distinct SSR profiles within the 27 trees analyzed. A total of 52 different alleles were scored, with an average of 7.43 alleles/SSR locus, and considerable genetic diversity was found. Neighbor-Joining algorithm cluster analysis and principal co-ordinate analysis (PCoA) allowed for the identification of the genetic relationships between several accessions. The 27 Olea accessions were clearly separated into three different groups. SSR analysis was more precise than endocarp characterization in the classification of genetic diversity among the olive tree cultivars. The study shows reasonable olive tree diversity in Ficalho, indicating that these traditional orchards are important reservoirs of old minor cultivars and incubators of new genotypes.

First report of a ‘Candidatus Phytoplasma trifolii‘‐related strain associated with soybean bud proliferation and seed pod abortion in Iran

During a survey in 2016, soybean (Glycine max) plants in commercial fields in Mazandaran and Golestan provinces, Iran exhibited symptoms including bud proliferation and aborted seed pods, but showed no stunting or growth reduction (Fig. 1). Approximately 25% of plants were diseased. Leaf and pod samples were collected from five diseased plants from Golestan province and ten from Mazandarn province, and two asymptomatic plants were collected from a field without symptoms in Golestan province. Total genomic DNA was extracted using a CTAB-based method (Doyle & Doyle, 2). The DNA was used as template in direct PCR using the phytoplasma-universal primers P1/P7 (Ahrens & Seemuller, 1) designed to amplify the 16S ribosomal RNA gene, followed by nested PCR using the R16MF2/R16MR1 primers (Gundersen & Lee, 3). Reactions containing template DNA from all of the diseased plants yielded PCR products of the expected size (1,400 bp). All of the asymptomatic plants tested negative for phytoplasmas. Two isolates, one each from Golestan (SG7) and Mazandaran province (SG13), were sequenced directly using primers R16MF2/R16MR1 on both strands by Macrogen (Korea). The sequences of the two isolates were identical. Consensus nucleotide sequences of 1,250 bp were deposited in GenBank (Accession Nos. MG992479 and MG992480). A BLAST search revealed that the sequences shared 98% identity to rDNA of ‘Candidatus Phytoplasma trifolii’ (MF564268) associated with tomato disease in Turkey and ‘Ca. P. trifolii’ associated with a new disease in chilli pepper in Mexico. The new isolates (SG7 and SG13) associated with soybean bud proliferation and seed pod abortion (SBPSPA) disease have 98.24% sequence identity to the ‘Ca. P. trifolii’ reference strain (AY390261) and therefore represent a 'Ca. P. trifolii'-related strain. In a phylogenetic tree constructed using the neighbour joining algorithm, the SBPSPA phytoplasma obtained from soybean in Iran clustered with 'clover proliferation' group (16SrVI) strains. There are numerous reports of ‘Ca. P. trifolii’ in Iran, associated with cucumber and zucchini phyllody, salix proliferation and date yellows. There are reports of phytoplasmas in soybean including ‘Ca. P. asteris’ in the USA (Mollov et al., 5), and peanut witches' broom phytoplasma in Malawi and Mozambique (Lava et al., 4). To our knowledge, this is the first report of ‘Ca. P. trifolii’ in soybean worldwide.

Parallelization of Pairwise Alignment and Neighbor-Joining Algorithm in Progressive Multiple Sequence Alignment

Progressive multiple sequence alignment ClustalW is a widely used heuristic method for computing multiple sequence alignment (MSA). It has three stages: distance matrix computation using pairwise alignment, guide tree reconstruction using neighbor-joining and progressive alignment. To accelerate computing for large data, the progressive MSA algorithm needs to be parallelized. This research aims to identify, decompose and implement the pairwise alignment and neighbor-joining in progressive MSA using message passing, shared memory and hybrid programming model in the computer cluster. The experimental results obtained shared memory programming model as the best scenario implementation with speed up up to 12 times.

Identification of Protein Biomarkers for Diabetic Retinopathy using Sequence Mining Techniques

Bioinformatics and sequence mining are the application and development of data mining techniques to solve problems by comprehending biological data. Sequence analysis is the most primitive operation in sequence mining techniques. Modern sequence mining research is specialized in analyzing sequential patterns which are relevant and distinct from one another and utilizing retrieved sequences similarity and distance between different protein sequences can be analyzed. Diabetic retinopathy is the major cause of blindness in individuals mostly adults with diabetes and is it is the common problem of diabetes mellitus across the world. Various research analyses stated that there are many proteins which are found to take part in diabetic retinopathy. In this paper, we have evaluated certain proteins which are closely related with diabetic retinopathy with the help of multiple alignment tool viz. Clustal Omega and obtained a phylogenetic tree of 28 protein sequences gathered from National Center for Biotechnology Information (NCBI). In this work data mining technique called sequence mining plays a significant role in providing phylogram obtained with Neighbor-Joining algorithm. From the phylogenetic tree it was recognized that cortistatin, vitamin-D receptor and somatostatin proteins has close connection with diabetic retinopathy. Molecular docking studies have also been performed which is the most extensively used method for the calculation of protein-ligand interactions. In silico docking studies indicated that four inhibitory compounds i.e. Quercetin, Kaempferol, Naringenin and Melicitrin interact with aldose reductase which also found to have role in diabetic retinopathy. Outcomes infer that techniques intended to standardize cortistatin, vitamin-D receptor and somatostatin activities be of huge advantage and provide benefit in inhibiting diabetic retinopathy.

Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.).

Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K=2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.

Bovine leukaemia virus genotypes 5 and 6 are circulating in cattle from the state of São Paulo, Brazil.

Enzootic bovine leucosis (EBL) is a silent disease caused by a retrovirus [bovine leukaemia virus (BLV)]. BLV is classified into almost 10 genotypes that are distributed in several countries. The present research aimed to describe two BLV gp51 env sequences of strains detected in the state of São Paulo, Brazil and perform a phylogenetic analysis to compare them to other BLV gp51 env sequences of strains around the world. Two bovines from different herds were admitted to the Bovine and Small Ruminant Hospital, School of Veterinary Medicine and Animal Science, University of São Paulo, Brazil. In both, lymphosarcoma was detected and the presence of BLV was confirmed by nested PCR. The neighbour-joining algorithm distance method was used to genotype the BLV sequences by phylogenetic reconstruction, and the maximum likelihood method was used for the phylogenetic reconstruction. The phylogeny estimates were calculated by performing 1000 bootstrap replicates. Analysis of the partial envelope glycoprotein (env) gene sequences from two isolates (25 and 31) revealed two different genotypes of BLV. Isolate 25 clustered with ten genotype 6 isolates from Brazil, Argentina, Thailand and Paraguay. On the other hand, isolate 31 clustered with two genotype 5 isolates (one was also from São Paulo and one was from Costa Rica). The detected genotypes corroborate the results of previous studies conducted in the state of São Paulo, Brazil. The prediction of amino acids showed substitutions, particularly between positions 136 and 150 in 11 out of 13 sequences analysed, including sequences from GenBank. BLV is still important in Brazil and this research should be continued.

Nioella aestuarii sp. nov., of the family Rhodobacteraceae, isolated from tidal flat.

A bacterium, designated strain MME-018T, was isolated from a tidal flat of the Muui-do in the Republic of Korea and identified within the family Rhodobacteraceae. The 16S rRNA gene sequence of the isolate showed the highest similarity to that of Nioella sediminis JS7-11T (98.9 %), followed by Nioella nitratireducens SSW136T (97.1 %). In phylogenetic analyses, these taxa formed a clade at neighbour-joining, maximum-likelihood, and maximum-parsimony algorithms, in which it was separated from other genus belonging to the family Rhodobacteraceae. Ubiquinone-10 (Q-10) was the major respiratory quinone. Major polar lipids included phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, and an unidentified lipid. Major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) C16 : 0, cyclo C19 : 0ω8c, and 11-methyl C18 : 1ω7c. Genomic DNA G+C content was 61 mol%. Cells were Gram-stain negative, non-motile, aerobic, and rod-shaped. This strain grew in 1‒4 % (w/v) NaCl, at 4-40 °C and pH 6.0‒8.0, with optimal growth in 2 % (w/v) NaCl, at 25‒30 °C and pH 7.0. DNA-DNA hybridization values between strain MME-018T and Nioella sediminis KCTC 42144T and Nioella nitratireducens KCTC 32417T were 17±3 and 13±1 %, respectively. On the basis of polyphasic taxonomic analysis, strain MME-018T is proposed to represent a novel species of the genus Nioella, for which the name Nioellaaestuarii sp. nov. The type strain of Nioellaaestuarii is MME-018T (=KCCM 43135T=JCM 30752T).