Authors:
Mei-Yeh Jade Lu1, Luis B. Gómez-Luciano1, 2, Kevin J. Tsai1, 3, Mengyun Li1, Yuchuan Teng1, Shihmay Chen1, Maurice Ku4, Hitoshi Nakayashiki5, Wen-Hsiung Li1
1 Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11574
2 Biodiversity Research Program, Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11574
3 Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan 11574
4 Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600
5 Laboratory of Plant Pathology, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe 657-8501, Japan
De novo genome assembly is often challenged by factors such as large genome size, long and/or tandem repeat sequences, and high GC% content.
Currently the vast majority of the modern sequencing data are from 2nd-Gen platforms which are short reads of <300bps for Illumina (or <900bp for Roche 454). Despite of high resolution of local assembly owing to their large sequencing output and high base quality, they often fails to bridge repeats that occur tandemly or are too long (in kb ranges). In recent years the 3rd-Gen long read sequencing (10-15kb) has enabled reading through long repeats and also high GC regions which may be difficult for some 2nd-Gen platforms. Yet it also faces the challenge of sequencing cost effectiveness and high requirement of sample purity and amount.
Using a hybrid assembly approach can help to achieve sequencing through long repeats while maintain high assembly base accuracy. Here we present genome assembly effort for a rice blast fungus isolate and a millet cultivar in Taiwan by using hybrid approaches. We utilized various platforms as well as library types to meet each project’s need, including Roche 454, Illumina, and PacBio. These datasets bear distinct library structure and vary in read base quality, thus the bioinformatics pipelines are costumed to best fit the genome’s complexity and also the related data in public domains. Both genomes were assembled to scaffolds at chromosomal level.