National Institute for Biotechnology and Genetic Engineering

About: National Institute for Biotechnology and Genetic Engineering is a education organization based out in Faisalabad, Pakistan. It is known for research contribution in the topics: Begomovirus & Leaf curl. The organization has 842 authors who have published 1397 publications receiving 43346 citations.

The Sorghum bicolor genome and the diversification of grasses

Abstract: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Abstract: Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.

Aligned two- and three-dimensional structures by directional freezing of polymers and nanoparticles

Abstract: Aligned two- and three-dimensional structures by directional freezing of polymers and nanoparticles

Geminivirus strain demarcation and nomenclature

Abstract: Geminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al in Arch Virol 145:1743–1761, 2000, Arch Virol 148:405–421, 2003) A system to standardize virus names, and corresponding guidelines, has been proposed (Fauquet et al in Arch Virol 145:1743–1761, 2000) This system is now followed by a large number of geminivirologists in the world, making geminivirus nomenclature more transparent and useful In 2003, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species This threshold has been utilised since with general satisfaction More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5] The present publication is proposing demarcation criteria and guidelines to classify and name geminiviruses below the species level Using the Clustal V algorithm (DNAStar MegAlign software), the distribution of pairwise sequence comparisons, for pairs of sequences below the species taxonomic level, identified two peaks: one at 85–94% nt identity that is proposed to correspond to “strain” comparisons and one at 92–100% identity that corresponds to “variant” comparisons Guidelines for descriptors for each of these levels are proposed to standardize nomenclature under the species level In this publication we review the status of geminivirus species and strain demarcation as well as providing updated isolate descriptors for a total of 672 begomovirus isolates As a consequence, we have revised the status of some virus isolates to classify them as “strains”, whereas several others previously classified as “strains” have been upgraded to “species” In all other respects, the classification system has remained robust, and we therefore propose to continue using it An updated list of all geminivirus isolates and a phylogenetic tree with one representative isolate per species are provided

Geminiviruses: masters at redirecting and reprogramming plant processes

Abstract: The family Geminiviridae is one of the largest and most important families of plant viruses. The small, single-stranded DNA genomes of geminiviruses encode 5-7 proteins that redirect host machineries and processes to establish a productive infection. These interactions reprogramme plant cell cycle and transcriptional controls, inhibit cell death pathways, interfere with cell signalling and protein turnover, and suppress defence pathways. This Review describes our current knowledge of how geminiviruses interact with their plant hosts and the functional consequences of these interactions.