CoDa-dendrogram: A new exploratory too

The use of orthonormal coordinates in the simplex and, particularly, balance coordinates, has suggested the use of a dendrogram for the exploratory analysis of compositional data. The dendrogram is based on a sequential binary partition of a compositional vector into groups of parts. At each step of a partition, one group of parts is divided into two new groups, and a balancing axis in the simplex between both groups is defined. The set of balancing axes constitutes an orthonormal basis, and the projections of the sample on them are orthogonal coordinates. They can be represented in a dendrogram-like graph showing: (a) the way of grouping parts of the compositional vector; (b) the explanatory role of each subcomposition generated in the partition process; (c) the decomposition of the total variance into balance components associated with each binary partition; (d) a box-plot of each balance. This representation is useful to help the interpretation of balance coordinates; to identify which are the most explanatory coordinates; and to describe the whole sample in a single diagram independently of the number of parts of the sample

An analysis of assessment outcomes from eight years' operation of the Australian border weed risk assessment system

The majority of Australian weeds are exotic plant species that were intentionally introduced for a variety of horticultural and agricultural purposes. A border weed risk assessment system (WRA) was implemented in 1997 in order to reduce the high economic costs and massive environmental damage associated with introducing serious weeds. We review the behaviour of this system with regard to eight years of data collected from the assessment of species proposed for importation or held within genetic resource centres in Australia. From a taxonomic perspective, species from the Chenopodiaceae and Poaceae were most likely to be rejected and those from the Arecaceae and Flacourtiaceae were most likely to be accepted. Dendrogram analysis and classification and regression tree (TREE) models were also used to analyse the data. The latter revealed that a small subset of the 35 variables assessed was highly associated with the outcome of the original assessment. The TREE model examining all of the data contained just five variables: unintentional human dispersal, congeneric weed, weed elsewhere, tolerates or benefits from mutilation, cultivation or fire, and reproduction by vegetative propagation. It gave the same outcome as the full WRA model for 71% of species. Weed elsewhere was not the first splitting variable in this model, indicating that the WRA has a capacity for capturing species that have no history of weediness. A reduced TREE model (in which human-mediated variables had been removed) contained four variables: broad climate suitability, reproduction in less or than equal to 1 year, self-fertilisation, and tolerates and benefits from mutilation, cultivation or fire. It yielded the same outcome as the full WRA model for 65% of species. Data inconsistencies and the relative importance of questions are discussed, with some recommendations made for improving the use of the system.

The application of DArTseq technology to pineapple

DArTseq technology is potentially the most appropriate system to discover hundreds of polymorphic genomic loci, scoring thousands of unique genomic-wide DNA fragments in one single experiment, without requiring existing DNA sequence information. The DArT complexity reduction approach in combination with Illumina short read sequencing (Hiseq2000) was applied. To test the application of DArTseq technology in pineapple, a reference population of 13 Ananas genotypes from primitive wild accessions to modern cultivars was used. In a comparison of 3 systems, the combination of restriction enzymes PstI and MseI performed the best producing 18,900 DArT markers and close to 20,000 SNPs. Based on these markers genetic relationships between the samples were identified and a dendrogram was generated. The topography of the tree corresponds with our understanding of the genetic relationships between the genotypes. Importantly, the replicated samples of all genotypes have a dissimilarity of close to 0.0 and occupy the same positions on the tree, confirming high reproducibility of the markers detected. Eventually it is planned that molecular markers will be identified that are associated with resistance to Phytophthora cinnamomi (Pc), the most economically important pathogen of pineapple in Australia, as genetic resistance is known to exist within the Ananas. Marker assisted selection can then be utilized in a pineapple breeding program to develop cultivars resistant to Pc.

Differentiation of Indian, East Timorese, Papuan and Floridian Candidatus Liberibacter asiaticus' isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci

Japanese isolates of Candidatus Liberibacter asiaticus have been shown to be clearly differentiated by simple sequence repeat (SSR) profiles at four loci. In this study, 25 SSR loci, including these four loci, were selected from the whole-genome sequence and were used to differentiate non-Japanese samples of Ca. Liberibacter asiaticus (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 SSR loci, 13 were polymorphic. Dendrogram analysis using SSR loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (SNPs) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the SNPs in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using SSR loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived.

Fluoroquinolone-resistant extraintestinal pathogenic Escherichia coli, including O25b-ST131, isolated from faeces of hospitalized dogs in an Australian veterinary referral centre

To determine rates of carriage of fluoroquinolone-resistant Escherichia coli and extraintestinal pathogenic E. coli (ExPEC) among dogs in a specialist referral hospital and to examine the population structure of the isolates. Fluoroquinolone-resistant faecal E. coli isolates (n232, from 23 of 123 dogs) recovered from hospitalized dogs in a veterinary referral centre in Sydney, Australia, over 140 days in 2009 were characterized by phylogenetic grouping, virulence genotyping and random amplified polymorphic DNA (RAPD) analysis. The RAPD dendrogram for representative isolates showed one group B2-associated cluster and three group D-associated clusters; each contained isolates with closely related ExPEC-associated virulence profiles. All group B2 faecal isolates represented the O25b-ST131 clonal group and were closely related to recent canine extraintestinal ST131 clinical isolates from the east coast of Australia by RAPD analysis. Hospitalized dogs may carry fluoroquinolone-resistant ExPEC in their faeces, including those representing O25b-ST131.

At4g24160, a Soluble Acyl-Coenzyme A-Dependent Lysophosphatidic Acid Acyltransferase

Human CGI-58 (for comparative gene identification-58) and YLR099c, encoding Ict1p in Saccharomyces cerevisiae, have recently been identified as acyl-CoA-dependent lysophosphatidic acid acyltransferases. Sequence database searches for CGI-58 like proteins in Arabidopsis (Arabidopsis thaliana) revealed 24 proteins with At4g24160, a member of the alpha/beta-hydrolase family of proteins being the closest homolog. At4g24160 contains three motifs that are conserved across the plant species: a GXSXG lipase motif, a HX4D acyltransferase motif, and V(X)(3)HGF, a probable lipid binding motif. Dendrogram analysis of yeast ICT1, CGI-58, and At4g24160 placed these three polypeptides in the same group. Here, we describe and characterize At4g24160 as, to our knowledge, the first soluble lysophosphatidic acid acyltransferase in plants. A lipidomics approach revealed that At4g24160 has additional triacylglycerol lipase and phosphatidylcholine hydrolyzing enzymatic activities. These data establish At4g24160, a protein with a previously unknown function, as an enzyme that might play a pivotal role in maintaining the lipid homeostasis in plants by regulating both phospholipid and neutral lipid levels.

Molecular Characterization of Sclerospora graminicola, the Incitant of Pearl Millet Downy Mildew Using ISSR Markers

The DNA polymorphism among 22 isolates of Sclerospora graminicola, the causal agent of downy mildew disease of pearl millet was assessed using 20 inter simple sequence repeats (ISSR) primers. The objective of the study was to examine the effectiveness of using ISSR markers for unravelling the extent and pattern of genetic diversity in 22 S. graminicola isolates collected from different host cultivars in different states of India. The 19 functional ISSR primers generated 410 polymorphic bands and revealed 89% polymorphism and were able to distinguish all the 22 isolates. Polymorphic bands used to construct an unweighted pair group method of averages (UPGMA) dendrogram based on Jaccard's co-efficient of similarity and principal coordinate analysis resulted in the formation of four major clusters of 22 isolates. The standardized Nei genetic distance among the 22 isolates ranged from 0.0050 to 0.0206. The UPGMA clustering using the standardized genetic distance matrix resulted in the identification of four clusters of the 22 isolates with bootstrap values ranging from 15 to 100. The 3D-scale data supported the UPGMA results, which resulted into four clusters amounting to 70% variation among each other. However, comparing the two methods show that sub clustering by dendrogram and multi dimensional scaling plot is slightly different. All the S. graminicola isolates had distinct ISSR genotypes and cluster analysis origin. The results of ISSR fingerprints revealed significant level of genetic diversity among the isolates and that ISSR markers could be a powerful tool for fingerprinting and diversity analysis in fungal pathogens.

Structure-Based Phylogeny as a Diagnostic for Functional Characterization of Proteins with a Cupin Fold

Background: The members of cupin superfamily exhibit large variations in their sequences, functions, organization of domains, quaternary associations and the nature of bound metal ion, despite having a conserved beta-barrel structural scaffold. Here, an attempt has been made to understand structure-function relationships among the members of this diverse superfamily and identify the principles governing functional diversity. The cupin superfamily also contains proteins for which the structures are available through world-wide structural genomics initiatives but characterized as ``hypothetical''. We have explored the feasibility of obtaining clues to functions of such proteins by means of comparative analysis with cupins of known structure and function. Methodology/Principal Findings: A 3-D structure-based phylogenetic approach was undertaken. Interestingly, a dendrogram generated solely on the basis of structural dissimilarity measure at the level of domain folds was found to cluster functionally similar members. This clustering also reflects an independent evolution of the two domains in bicupins. Close examination of structural superposition of members across various functional clusters reveals structural variations in regions that not only form the active site pocket but are also involved in interaction with another domain in the same polypeptide or in the oligomer. Conclusions/Significance: Structure-based phylogeny of cupins can influence identification of functions of proteins of yet unknown function with cupin fold. This approach can be extended to other proteins with a common fold that show high evolutionary divergence. This approach is expected to have an influence on the function annotation in structural genomics initiatives.

Assessment of genetic diversity and identification of core collection in sandalwood germplasm using RAPDS

Sandalwood is an economically important aromatic tree belonging to the family Santalaceae. The trees are used mainly for their fragrant heartwood and oil that have immense potential for foreign exchange. Very little information is available on the genetic diversity in this species. Hence studies were initiated and genetic diversity estimated using RAPD markers in 51 genotypes of Santalum album procured from different geographcial regions of India and three exotic lines of S. spicatum from Australia. Eleven selected Operon primers (10mer) generated a total of 156 consistent and unambiguous amplification products ranging from 200bp to 4kb. Rare and genotype specific bands were identified which could be effectively used to distinguish the genotypes. Genetic relationships within the genotypes were evaluated by generating a dissimilarity matrix based on Ward's method (Squared Euclidean distance). The phenetic dendrogram and the Principal Component Analysis generated, separated the 51 Indian genotypes from the three Australian lines. The cluster analysis indicated that sandalwood germplasm within India constitutes a broad genetic base with values of genetic dissimilarity ranging from 15 to 91 %. A core collection of 21 selected individuals revealed the same diversity of the entire population. The results show that RAPD analysis is an efficient marker technology for estimating genetic diversity and relatedness, thereby enabling the formulation of appropriate strategies for conservation, germplasm management, and selection of diverse parents for sandalwood improvement programmes.

Allozyme variation in four hatchery populations of Thai pangas, Pangasius hypophthalmus in Bogra, Bangladesh

Genetic variation of four hatchery stocks of Thai pangas, Pangasius hypophthalmu [sic] of Bogra region, Bangladesh was studied from 1 January 2002 to 31 December 2003. Muscle samples were collected for allozyme analysis from four (Bhai-Bhai, Jahangir, Belal and Bhai-Bon) different hatchery populations. For allozyme electrophoresis, eight enzymes were used and 11 loci viz. Adh-1*, Est-1*, GJpdh-1*, Gpi-1*, Gpi-2*, Jdhp-1*, Ldh-1*, Ldh-2*, Mdh-1*, Mdh-2*and Pgm* were identified, of which three loci (Est-1*, Gpi-2*, G3pdh-1 and Pgm*) were polymorphic in all the four populations. The mean proportion of polymorphic loci per population and the mean proportion of heterozygous loci per individual was 36.36% and 13.33, respectively for all the population studied. The highest variability measured by the mean number of alleles per locus was 1.545 in Bhai-Bon hatchery population. Based on Nei's (1972) genetic distance, the dendrogram (UPGMA) shows that four populations have made two clusters by D-value (D=0.043). Bhai-Bhai and Jahangir hatchery populations have made cluster-I, and Belal Uddin and Bhai-Bon hatchery populations formed cluster-II. Among the four populations, BhaiBhai and Jahangir hatchery populations were differentiated from each other by the D-value of 0.013, and Belal Uddin and Bhai-Bon populations were differentiated from each other by the D-value of 0.002, which suggests that the four populations may be fallen into the local population or race.

Use of allozyme markers to determine the genetic structure of hatchery population of Thai pangas, Pangasius hypophthalmus of Jessore, Bangladesh

Genetic structure of hatchery population of Thai pangas (Pangasius hypophthalmus) of Jessore region, Bangladesh has been investigated from 1 January 2004 to 31 December 2004. Samples for this study were collected from five fish hatcheries viz. Asrom, Banchte Shekha, Chowdhury, Maola and Rezaul Haque. The enzymes were encoded by 15 gene loci: Adh-1*, Est-1*, G3pdh-2*, Gpi-1*, Gpi-2*, Idhp-1*, Idhp-2*, Ldh-1*, Ldh-2*, Mdh-1*, Mdh-2*, Pgm*, Sdh-1*, Sdh-2* and Sod*. Among them four (Est-1*, G3pdh-2*, Gpi-2*and Pgm*) were found to be polymorphic in different populations but only Gpi-2* was polymorphic in all the sampled populations. The mean proportion of polymorphic loci per population was the highest (26.7%) in Banchte Shekha hatchery while the mean proportion of heterozygous loci was 13.33% per individual in Banchte Shekha and Maola hatcheries. The UPGMA dendrogram of Nei's (1972) genetic distances indicated a relationship between the genetic distance and geographical difference. High genetic variability in stocks of Thai pangas was observed in the Banchte Shekha and Maola hatcheries and less variability was found in the other three hatcheries.

Allozyme and morphological variation in four hatchery stocks of Thai pangas, Pangasius hypophthalmus in Mymensingh, Bangladesh

Genetic and morphological characters of four hatchery population (Shambhuganj, Brahmaputra, Anudan and Bhai-Bhai) of Thai pangas, Pangasius hypophthalmus in Mymensingh region of Bangladesh was studied using morphological characters and allozyme markers from 29 November 2001 to 29 November 2002. A total of 14 morphometric and 6 meristic characters were verified, among which 3 morphometric (BDA, PELFL and HW) and 2 meristic characters (AFR, CFR) of Anudan hatchery population were found to be significantly higher (p>0.001) than those of the other three hatchery populations. Brahmaputra hatchery population was also significantly higher in two meristic characters (PCFR and CFR). For allozyme electrophoresis nine enzyme markers were used viz.: Esr-1*, G3pdh-2*, Gpi-1*, Gpi-2*, Ldh-1*, Ldh-2*, Mdh-1*, Mdh-2* and Pgm* where three loci (Esr-1*, Gpi-2* and Pgm*) were polymorphic (p>0.95) in Anudan and Brahmaputra hatchery populations. The mean proportion of polymorphic loci per population was higher (33.3%) in Brahmaputra and Anudan hatchery populations. Also the expected heterozygosity levels were 0.149 and 0.177 in Brahmaputra and Anudan hatchery populations, respectively. Based on Nei's (1972) genetic distances, the UPGMA dendrogram grouped the populations into two clusters. The Brahmaputra and Anudan populations are in one group; Shambhuganj, and Bhai-Bhai populations are in the second group. High genetic variation in Thai pangas was observed in the Brahmaputra and Anudan hatchery populations and less variation in the other two hatchery populations.

The genetic diversity of Acipenser stellatus populations in the Caspian Sea was studied using microsatellite technique

A total of 361 caudal fin samples were collected from adult A. stellatus specimens caught in the north Caspian Sea, including specimens from Kazakhstan (Ural River), Russia (Volga River), Azerbaijan (Kura River), specimens caught in the south Caspian Sea including specimens from Fishery Zone 1 (from Astara to Anzali), Fishery Zone 2 (from Anzali to Ramsar), Fishery Zone 3 (from Nowshahr to Babolsar), Fishery Zone 4 (from Miyankaleh to Gomishan) as well as from specimens caught in Turkmenistan (all specimens were collected during the sturgeon stock assessment survey). About 2 g of fin tissue was removed from each caudal fin sample, stored in 96% ethyl alcohol and transferred to the genetic laboratory of the International Sturgeon Research Institute. Genomic DNA was extracted using phenol-chloroform method. The quality and quantity of DNA was assessed using 1% Agarose gel electrophoresis and Polymerase Chain Reaction (PCR) was conducted on the target DNA using 15 paired microsatellite primer. PCR products were electrophoresed on polyacrylamide gels (6%) that were stained using silver nitrate. Electrophoretic patterns and DNA bands were analyzed with BioCapt software. Allele count and frequency, genetic diversity, expected heterozygosity and observed heterozygosity allele number, and the effective allele number, genetic similarity and genetic distance, FST and RST were calculated. The Hardy Wienberg Equilibrium based on X2 and Analysis of Molecular Variance (AMOVA) at 10% confidence level was calculated using the Gene Alex software. Dendrogram for genetic distances and identities were calculated using TFPGA program for any level of the hierarchy. It is evident from the results obtained that the 15 paired primers studied, polymorphism was observed in 10 pairs in 12 loci, while one locus did not produce DNA bands. Mean allele number was 13.6. Mean observed and expected heterozygosity was 0.86 and 0.642, respectively. It was also seen that specimens from all regions were not in Hardy Wienberg Equilibrium in most of the loci (P≤0.001). Highest Fst (0.063) was observed when comparing specimens from Fishery Zone 2 and Fishery Zone 4 (Nm=3.7) and lowest FST (0.028) was observed when comparing specimens from the Volga River and those from the Ural River (8.7). Significant differences (P<0.01) were observed between RST recorded in the specimens studied. Highest genetic distance (0.604) and lowest genetic resemblance (0.547) were observed between specimens from Fishery zones 2 and 4. Lowest genetic distance (0.311) and highest genetic resemblance (0.733) was observed between specimens from Turkmenistan and specimens from Fishery zone 1. Based on the genetic dendrogeram tree derived by applying UPGMA algorithm, A. stellatus specimens from Fishery zone 2 or in other words specimens from the Sepidrud River belong to one cluster which divides into two clusters, one of which includes specimens from Fishery zones 1, 3 and 4 and specimens from Turkmenistan while the other cluster includes specimens from Ural, Volga and Kura Rivers. It is thus evident that the main population of this species belongs to the Sepidrud River. Results obtained from the present study show that at least eight different populations of A. stellatus are found in the north and south Caspian Sea, four of which are known populations including the Ural River population, the Volga River population, the Kura River population and the Sepidrud River populations. The four other populations identified belonging to Fishery zones 1, 3, and 4 and to Turkmenistan are most probably late or early spawners of the spring run and autumn run of each of the major rivers mentioned. Specific markers were also identified for each of the populations identified. The Ural River population can be identified using primers Spl-68, 54b and Spl-104, 163 170, 173, the Volga River population can be identified using primers LS-54b and Spl-104, 170, 173 113a and similarly the population from the Kura River can be identified using primers LS-34, 54b and Spl-163, 173 and that from the Sepidrud River can be identified using primers LS-19, 34, 54b and Spl-105, 113b. This study gives evidence of the presence of different populations of this species and calls for serious measures to be taken to protect the genetic stocks of these populations. Considering that the population of A. stellatus in Fishery zone 2 is an independent population of the Sepidrud River in the Gilan Province, the catch of these fishes in the region needs to be controlled and regulated in order to restore the declining stocks of this species.

中国角蟾亚科十一种的同工酶电泳研究(英文)

本文用同工酶电泳的方法分析了中国产角蟾亚科3属11种,共13个地理种群样本,以探讨它们的遗传多样性及系统关系。用于分析的酶共14种,由24个基因位点编码。经过酶带的分析和计算,得出了每个种群样本在每个基因位点上的等位基因频率（见表3）。根据基因频率的分布,计算得出了各种群样本的基因多样性指数——平均杂合率（H）（见表4）,结果表明,角蟾亚科的H值平均值为0.18, 在两栖动物中是属于很高的遗传多样性水平,根据基因频率的分布,计算了所有种群样本间的Nei’s遗传距（见表5）,并通过类平均法（UPGMA）重建了进化树（dendrogram）。分析结果支持将拟角蟾属（Ophryophryne）从角蟾属（Megophrys）中分出为独立属的观点;但是对短腿蟾属（Brachytarsophrys）是否为独立属提出了疑问。在角蟾属（Mesophrys）中,可以明显地看出3个组,它们中的种间亲缘关系比较近,这3个组分别是:①白颌大角蟾（M.lateralis）、大花角蟾（M.giganticus）和长肢角蟾（M.longipes）;②粗皮角蟾（M.palpebralespinneosa）、淡肩角蟾（M.boettgeri）...