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.

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.