Wood transcriptome analysis and expression variation of lignin biosynthetic pathway transcripts in Roxb., a multi-purpose tropical tree species.

Safety matches are an essential consumer commodity which faces considerable shortage of raw material due to specific requirements like color, wax stability, consistent burning and splinting ability in wood. Roxb. is a multi-purpose tropical tree species which is predominantly used for production of match splints.

Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation.

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E.

Reference-based assembly of chloroplast genome from leaf transcriptome data of .

Unlabelled: Chloroplast genome sequencing is an essential tool to understand genome evolution and phylogenetic relationship. The available methods for constructing chloroplast genome include chloroplast enrichment followed by long overlapping PCR or extraction and assembly of chloroplast-specific reads from whole-genome datasets. In the present study, we propose an alternate strategy of extraction and assembly of chloroplast-specific reads from leaf transcriptome data of using bowtie2 aligner program.

Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance.

The genus Eucalyptus with over 747 species occurs in wide ecological range and is preferred for bioenergy plantations due to their short rotation, rapid growth and superior wood properties. They are planted in 22 million ha area and India is third largest planter of Eucalyptus. In the present study, the bacterial endophyte community in leaves of six Eucalyptus clones belonging to E.

Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls.

Leifsonia sp. ku-ls is an endophytic bacterial strain colonizing in high numbers the stem and leaf of the high-yielding and widely grown indica rice cultivar RP Bio-226. Whole genome sequencing of this strain using Illumina Hiseq-2500 system resulted in generation of 10,103,994 paired-end reads of 150 nucleotides length.

Marker-Assisted Improvement of the Elite Maintainer Line of Rice, IR 58025B for Wide Compatibility ( ) Gene.

The degree of heterosis in different hybrid rice varieties is reported to be at the highest in / cross combination, however, there is a problem of sterility and semi-sterility in such inter sub specific hybrids. To overcome this problem, it is essential to develop parental lines having wide compatibility ( ) gene. In this study, a functional marker S5-InDel was used for marker-assisted backcrossing (MABB) to introgress gene from Dular into the genetic background of a widely grown recurrent parent IR 58025B, a maintainer line of wild-abortive (WA) cytoplasmic male sterile line, IR 58025A.

RNA-seq data of control and powdery mildew pathogen ( treated transcriptomes of .

Identification of genes expressed during the infection process in assumes importance for incorporation of resistance to powdery mildew in cultivated sunflower ( L.) from this donor species. RNA-seq analysis of control (uninfected) and infected samples of resulted in identification of 231,754 transcripts.

Assembly of genomic reads of elite indica rice cultivar onto 2101 reference bacterial genomes for identification of co-sequenced endophytic bacteria.

Reference based assembly of genomic reads of the elite indica rice cultivar RP Bio-226 was carried out against 2101 reference bacterial genomes using Bowtie-2 genome assembly tool. Five types of data: Number of paired end reads concordantly aligned exactly only once, number of paired end reads concordantly aligned more than once, number of mates that make the pairs aligned exactly only once, number of mates that make the pairs aligned more than once and overall percentage of alignment were collected. Interpretation of the results and identification of endophytes based on these alignment statistics are described in detail in our research article "L.

Genome inside genome: NGS based identification and assembly of endophytic Sphingopyxis granuli and Pseudomonas aeruginosa genomes from rice genomic reads.

The interactions between crop plants and the endophytic bacteria colonizing them are poorly understood and experimental methods were found to be inadequate to meet the complexities associated with the interaction. Moreover, research on endophytic bacteria was focused at host plant species level and not at cultivar level which is essential for understanding the role played by them on the productivity of specific crop genotype. High throughput genomics offers valuable tools for identification, characterization of endophytic bacteria and understand their interaction with host plants.

RNA-Seq analysis of urea nutrition responsive transcriptome of Oryza sativa elite indica cultivar RP Bio 226.

Rice yield is greatly influenced by the nitrogen and rice varieties show variation in yield. For understanding the role of urea nutrition in the yield of elite indica rice cultivar RPBio-226, the urea responsive transcriptome was sequenced and analyzed. The raw reads and the Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GDKM00000000.

Draft Genome Sequence of Saccharomyces cerevisiae Strain NCIM3186 Used in the Production of Bioethanol from Sweet Sorghum.

Here, we report the draft genome sequence of Saccharomyces cerevisiae strain NCIM3186 used in bioethanol production from sweet sorghum. The size of the genome is approximately 11.9 Mb and contains 5,347 protein-coding genes.

Proteins for breaking barriers in lignocellulosic bioethanol production.

Reduction in fossil fuel consumption by using alternate sources of energy is a major challenge facing mankind in the coming decades. Bioethanol production using lignocellulosic biomass is the most viable option for addressing this challenge. Industrial bioconversion of lignocellulosic biomass, though possible now, is not economically viable due to presence of barriers that escalate the cost of production.

Genome Sequence of Saccharomyces cerevisiae NCIM3107, Used in Bioethanol Production.

Here, we report the genome of Saccharomyces cerevisiae strain NCIM3107, used in bioethanol production. The genome size is approximately 11.8 Mb and contains 5,435 protein-coding genes.

Genome-wide analyses of rice root development QTLs and development of an online resource, Rootbrowse.

Unlabelled: Genetic control of root development in rice is complex and the underlying mechanisms (constitutive and adaptive) are poorly understood. Lowland and upland varieties of indica and japonica rice with contrasting root development characteristics have been crossed, mapping populations developed and a number of QTLs in different chromosomes were identified. As these studies have used different sets of markers and many of the QTLs identified are long, it is difficult to exploit the varietal difference for improved root traits by marker assisted selection and for identification of concerned alleles.