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The newly described chrysophyte, Mallomonas vietnamica, is reported for the first time in China from specimens collected in Guizhou Province, SW China. The morphological characteristics were studied using light and scanning electron microscopy. The species was described based on morphological characteristics, including cell size, scale size, dome, V-rib, and bristles. Subsequently, molecular sequencing of M. vietnamica was conducted and a phylogenetic tree was constructed based on concatenated SSU, LSU, and rbcL sequences. The phylogenetic tree led us to suggest raising a new section named Uncatusipedae for this species. This study provides new molecular data from the genus Mallomonas and enriches our understanding of the species diversity and geographical distribution of the genus Mallomonas in China. [ABSTRACT FROM AUTHOR]

Background: DNA barcoding is a powerful method for phylogenetic mapping and species identification. However, recent research has come to a consistent conclusion about the universality of DNA barcoding. We used matK and rbcL markers to test the universality of twelve accessions from different locations belonging to two Selinum species, Selinum tenuifolium Wall. C. B. Clarke and Selinum vaginatum C. B. Clarke, keeping in mind their ability to identify species and establish phylogenetic relationships within and between the accessions. Results: The success rates of PCR amplification using matK and rbcL were 75.26% ± 3.65% and 57.24% ± 4.42%, and the rate of DNA sequencing was 63.84% ± 4.32% and 50.82% ± 4.36%, respectively, suggesting that success rates of species identification of the two fragments were higher than 41.00% (matK, 41.50% ± 2.81%; rbcL, 42.88% ± 2.59%), proving that these fragments might be used to identify species. The best evolutionary tree with good supporting values was produced utilizing combinations of matK + rbcL markers when phylogenetic relationships were built with random fragment combinations. The twelve accessions of Selinum collected from different locations and their molecular sequences of matK and rbcL markers were blasted with other genera of Apiaceae family, and it was found that Selinum is most closely related to Angelica species of Apiaceae family. Conclusion: The present study has grouped twelve accessions of Selinum species using molecular markers into phylogenies, which is first-of-its-kind report that established interrelationships within different species of Apiaceae with respect to Selinum. [ABSTRACT FROM AUTHOR]

Cucumber mosaic virus (CMV) is one of the most widespread viruses that infects a large number of cultivated crops worldwide and causes severe losses. Besides vegetables and ornamental crops, it is also spreading on medicinal and aromatic plants (MAPs) at an alarming rate. Natural occurrence of green mosaic, leaf curling, necrosis, and distortion were observed on the leaves of Salvia sclarea in the experimental field of CSIR-CIMAP, Lucknow, India. Mechanical transmission assay, morphological features, CP gene, and RNA3-based genomic characterization revealed the association of a new CMV isolate with the present disease. Virus is mechanically sap transmissible to the test plants. Transmission electron microscopy showed the presence of isodiametric particles of ~ 28 nm in diameter. Phylogenetic studies revealed that RNA3 (~ 2.2 kb) belongs to the subgroup IA of CMV. Multiple sequence alignment of amino acid sequences showed that MP possesses two unique changes in the RNA-binding domain and CP was found to be the conserved one with one change only. To the best of our knowledge, this is the first report of a CMV isolate infecting S. sclarea. [ABSTRACT FROM AUTHOR]

Luffa plants showing symptoms of begomovirus infection were collected from Vehari, Punjab in 2016. RCA and PCR amplifications of begomovirus genomic components showed the presence of a typical Old World bipartite begomovirus Tomato leaf curl New Delhi virus (ToLCNDV). Interestingly, Ageratum conyzoides symptomless alphasatellite and CLCuMB were also found associated with bipartite begomoviruses in the same host, however, no monopartite begomovirus was detected. To the best of our knowledge, this is the first report of ToLCNDV with associated satellites infecting L. cylindrica in Pakistan. The importance of begomovirus extended host range with different combinations of associated satellites has been discussed. [ABSTRACT FROM AUTHOR]

Achaea janata granulovirus (AcjaGV), an insect virus belonging to Baculoviridae, infects semilooper, a widely distributed defoliating pest on castor beans ( Ricinus communis L.) and several other plant hosts in India. The propagation and purification of the Hyderabad isolate AcjaGV were performed, granulin gene from this isolate was amplified, cloned and sequenced, and its homology with other known granulin genes was assessed. The 753-bp granulin ORF of AcjaGV encoded for a granulin protein of 250 amino acids with a molecular mass of 29.5 ± 0.7 kDa. This amino acid sequence exhibited significant homology with Spodoptera litura granulovirus (SpliGV) and other GVs infecting insects in the same Noctuidae family of Lepidoptera. Peptide analysis of granulin protein indicated close homology with that of SpliGV. Virtual RFLP patterns from in silico digestions of granulin gene of 18 granuloviruses mapped by 12 restriction enzymes were used for simulated digestions. Implications of the phylogenetic relationships of granulin nucleotide and deduced amino acid sequence are discussed. We have established the sequence identity of granulin gene of AcjaGV and characterized its protein product and the phylogenetic relationship with other known GVs. Our results indicate the presence of unique restriction sites for three restriction enzymes, and this can be used as a tool for identification of AcjaGV from various sources. This is the first report from the Indian subcontinent to describe the complete granulin gene of a GV isolated from A. janata. [ABSTRACT FROM AUTHOR]

Since most microorganisms in natural environments cannot be cultured in laboratory media, due to low growth rates or their dependency on specific conditions, culture-based systems are unable to estimate the full microbial diversity of an environment. However, molecular techniques can provide this ability by analysing the diversity of macromolecules, such as proteins, RNA or DNA, present in the environment. Metagenomic methods employ sequencing procedures for the determination of the microbial diversity of a community (sequence-driven metagenomic analysis) or for examining a particular functional ability of microorganisms in the environment (function-driven metagenomic gene identification), using genomic DNA obtained directly from environmental samples. Application of metagenomic methods provides a huge amount of data that can be analysed only by using powerful computational bioinformatics tools. Currently, these bioinformatic tools are adequate to allow the ecological structure of a community and the possible functions of its members to be determined. The resulting data can be useful for phylogenetic and biotechnological studies. This paper reviews the emergence of new technologies based on sequencing environmental DNA and on bioinformatics. We assess its potential for application in environmental studies, particularly for developing new biomolecules that can be applied to degrading recalcitrant pollutants in terrestrial and aquatic systems. [ABSTRACT FROM AUTHOR]

A genomic DNA fragment ( pAA7- 2) amplified by a random amplified polymorphic DNA primer from the rice cultivar IR68 was used to assess the genetic variation and genetic relationships among the species of genus Oryza. A Southern hybridization experiment of diverse upland rice accessions using a single restriction enzyme HindIII generated unique DNA fingerprint for each accession. The differential hybridization pattern reflecting the copy number variation of pAA7- 2 in a collection of wild species and cultivated species of rice provided insight about the genetic relationships among them. All AA genome species exhibited clear banding pattern suggesting presence of fewer copies of this sequence. Strongest hybridization signal was obtained in species belonging to BB, CC, GG, BBCC, CCDD genomes, whereas weakest hybridization signal was visible in EE, FF, and HHJJ genome species. Oryza brachyantha was the most divergent species. Clear difference in banding pattern was evident between Oryza schlechteri and Oryza coarctata belonging to HHKK genome. Although pAA7- 2 had no repetitive sequences often associated with hypervariable loci, homology to a putative unclassified expressed retrotransposon distributed over several rice chromosomes was responsible for the complex banding patterns. There were more sites homologous to pAA7- 2 sequence in corn and sorghum genome compared with the rice genome. The study demonstrates the potential of pAA7- 2 as a powerful molecular tool for DNA fingerprinting, genetic diversity, phylogenetic, and evolutionary studies in Oryza sativa and its wild relatives and other grasses. [ABSTRACT FROM AUTHOR]

Comparison of the common floristic elements between the West Indies and the surrounding continents shows a mosaic of affinities that are stronger to Central America and South America as a whole than with either one of them separately or with North America. However, since only 28% of the total West Indian seed plant flora is shared with other geographic regions of the world, the referred exercise is of limited value. Numerous tables are provided to show the distribution of genera throughout the archipelago. The application of phylogenetic studies into the service of biogeography is herein regarded as the next necessary step in elucidating the origins and affinities of the West Indian flora. [ABSTRACT FROM AUTHOR]

The efficiency of enzymatic conversion of glucose into glucose-6-phosphate in fish fed carbohydrates is still a matter of debate. This study reports the first ever identification of hexokinase-family members at a molecular level in fish. The deduced amino acid sequences of six cDNA clones allowed their assignement either to hexokinase IV (glucokinase) for rainbow trout (Oncorhynchus mykiss), common carp (Cyprinus carpio) and gilthead seabream (Sparus aurata) or to hexokinase I/II for the common carp (two clones) and the gilthead seabream, based on their similarities to known members of the HK family. The evolutionary relationships among these sequences were investigated by phylogenetic analysis. These hexokinase sequences constitute potential molecular tools for analysis of interspecific differences in dietary carbohydrate utilization in fish. [ABSTRACT FROM AUTHOR]

The group 1 and group 2 σ70-type sigma factors of the green sulfur bacterium Chlorobium tepidum and of the green nonsulfur bacterium Chloroflexus aurantiacus were cloned and characterized. Cb. tepidum was found to contain one σ70-type sigma factor; the expression of the gene was analyzed by Northern blot hybridization and primer-extension mapping. Cf. aurantiacus has genes encoding four sigma factors of groups 1 and 2. The expression of these genes was examined in cells grown aerobically and anaerobically. The sigC gene was expressed at approximately equal levels under both conditions, resulting in its designation as the group 1 sigma factor of this organism. The only other detectable transcripts arose from the sigB gene, which was expressed at higher levels during aerobic growth. A phylogenetic tree was obtained using the group 1 sigma factors of Cb. tepidum, Cf. aurantiacus, and diverse eubacteria as the molecular marker. The resulting phylogenetic tree shows that Cb. tepidum and Cf. aurantiacus are related to each other and to the cyanobacteria. The relationship of the group 2 sigma factors of Cf. aurantiacus and the cyanobacteria was more specifically examined phylogenetically. The group 2 sigma factors of Cf. aurantiacus probably arose by gene duplication events after the split of the green nonsulfur bacteria from other photosynthetic eubacteria. [ABSTRACT FROM AUTHOR]

The 459-bp HindIII (pBN-4) and the 1732-bp Eco RI (pBNE8) fragments from the Brassica nigra genome were cloned and shown to be members of a dispersed repeat family. Of the three major diploid Brassica species, the repeat pBN-4 was found to be highly specific for the B. nigra genome. The family also hybridized to Sinapis arvensis showing that B. nigra had a closer relationship with the S. arvensis genome than with B. oleracea or B. campestris. The clone pBNE8 showed homology to a number of tRNA species indicating that this family of repeats may have originated from a tRNA sequence. The species-specific 459-bp repeat pBN-4 was localized on the B. nigra chromosomes using monosomic addition lines. In addition to the localization of pBN-4, the chromosomal distribution of two other species-specific repeats, pBN34 and pBNBH35 (reported earlier), was studied. The dispersed repeats pBN-4 and pBNBH35 were found to be present on all of the chromosomes, whereas the tandem repeat pBN34 was localized on two chromosomes. [ABSTRACT FROM AUTHOR]

The construction and characterization of two genome-specific recombinant DNA clones from B. nigra are described. Southern analysis showed that the two clones belong to a dispersed repeat family. They differ from each other in their length, distribution and sequence, though the average GC content is nearly the same (45%). These B genome-specific repeats have been used to analyse the phylogenetic relationships between cultivated and wild species of the family Brassicaceae. [ABSTRACT FROM AUTHOR]