DE-NOVO ASSEMBLY AND ANNOTATION OF MITOCHONDRIAL GENOME OF MULBERRY (MORUS INDICA L.) USING NGS DATA

Abstract

Morus, a genus of flowering plants in the family Moraceae, comprises 10–16 species of deciduous trees commonly known as mulberries growing wild and under cultivation in many temperate world regions. Mulberry is a very widespread and important crop for silkworm feed, fruit and timber as well as being an excellent amenity tree. Morus indica is a species of mulberry exclusively found in Eastern and Southern Asia and is of great importance to the Asian silk industry. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mitochondrial genomes in plants. In this study we have attempted to assemble and annotate the mitochondrial genome of Morus indica L using Roche derived 454 Next Generation Sequencing data. The Morus indica mt-genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA. Various Bioinformatics tools and in-house developed perl and shell scripts were used to assemble and annotate the quality-filtered 454 raw NGS reads. We report the first ever, near complete mt-genome of mulberry in terms of gene-content in closely related species with 27 high-quality, high read-coverage contigs comprising of 45 functional protein coding mt-genes, 2 rRNA genes and 25 tRNAs (transfer RNAs) that recognize 14 different amino-acids. The average coverage of reported mulberry mt-genome is 66x and the estimated mt-genome size is 380,529 nt. A 454 bp segment from plastid origin is incorporated in the 380,529 nt of mulberry mit-genome. We also report a procedure for efficient assembly and annotation of mitochondrial genomes of plants without physical separation of mitochondria. This procedure can be extended to other platforms with low coverage genome sequencing, such as the Illumina HiSeq platform for efficient and straight-forward organellar genome sequencing. The draft Mulberry Mit-genome assembled by our procedure could be an essential resource to biologists, geneticists, plant scientists, and plant breeders and can be used as a reference to assemble mt-genomes of closely related species.