Mo17 Genome Assembly and Identification of SNPs Between B73 and Mo17 (Xin et al., 2013) We performed a reference-guided assembly of the Mo17 genome based on the B73 genome (release 5b.60; http://MaizeSequence.org), using 650 Gb Illumina short reads obtained from the Joint Genomics Institute, Department of Energy (SRA accession: SRP003567). The sequence quality of the short reads was first examined by the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Then, the short reads were aligned to the B73 reference genome sequence using Bowtie2 with parameters --score-min L,-15,-0.4 -3 26 --very-sensitive. The alignment results were imported into the SHORE pipeline http://1001genomes.org/software/shore.html (Schneeberger et al., 2009) to identify the SNPs andINDELs (insertion and deletions) between the B73 and Mo17 genomes. We identified 6,557,611 SNPs, 157,994 insertions and 191,549 deletions between the B73 and Mo17 genome. Finally, we used a customized Perl script to generate the consensus sequences (contigs) based on the alignment of Mo17 reads to the B73 genome, and connect the Mo17 contigs to form pseudo-chromosome sequences based on their positions in the B73 genome. The chromosomal coordinates of the nucleotides in the Mo17 assembly were adjusted based on the sizes of deletions or insertions occurred between the two genomes. Moreover, if a relatively long genomic portion in the B73 genome was not covered by Mo17 reads, the same number of Ħ°NĦħ was filled in the Mo17 assembly to indicate the existence of a gap. The corresponding chromosomal coordinates of the SNPs and INDELs in the two genomes were correlated for the differentiation of allele-specific reads. REFERENCES Xin, M., Yang, R., Li, G., Chen, H., Laurie, J., Ma, C., Wang, D., Yao, Y., Larkins, B., Sun, Q., Yadegari, R., Wang, X., and Ni, Z. (2013). Dynamic Expression of Imprinted Genes Associates with Maternally Controlled Nutrient Allocation during Maize Endosperm Development Plant Cell, Accepted Schneeberger, K., Ossowski, S., Lanz, C., Juul, T., Petersen, A.H., Nielsen, K.L., Jorgensen, J.E., Weigel, D., and Andersen, S.U. (2009). SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nature methods 6, 550-551. ----- Descriptions of the files in this folder -------------- RefGen_Mo17_v1.fasta: The genome assemby of Zea mays Mo17, containing the ten pseudo- chromosome sequences. The Mo17 genome assembly comprised 2,058,527,894 bases containing a total of 117,847,390 bp short gaps. The coverage of the Mo17 genome was approximately 94.3%. 20120716_snp_all.txt: SNPs identified between the B73 and Mo17 genomes Col-1 Col-2 Col-3 Col-4 Col-5 Col-6 Col-7 Col-8 chr6 B73 14240 C Mo17 14240 T 21 Col-1: Chromosome ID Col-2: Inbred line B73 Col-3: Position of the SNP site in the B73 chromosome Col-4: Nucleotide on B73 Col-5: Inbred line Mo17 Col-6: Position of the SNP site in the Mo17 chromosome Col-7: Nucleotide on Mo17 Col-8: Number of Mo17 shotgun reads covering the SNP site 20120716_deletion_all.txt: Deletions identified in the Mo17 genome Col-1 Col-2 Col-3 Col-4 Col-5 Col-6 Col-7 Col-8 chr6 B73 474134 CGG Mo17 474162 - 25 Col-1: Chromosome ID Col-2: Inbred line B73 Col-3: Position of the deletion site in the B73 chromosome Col-4: Deleted nucleotide(s) in the Mo17 genome Col-5: Inbred line Mo17 Col-6: Position of the deletion site in the Mo17 chromosome Col-7: "-" indicates no nucleotide(s) in the Mo17 genome Col-8: Number of Mo17 shotgun reads covering the insertion site 20120716_insertion_all.txt Insertions identified in the Mo17 genome Col-1 Col-2 Col-3 Col-4 Col-5 Col-6 Col-7 Col-8 chr6 B73 126071 - Mo17 126071 AAC 10 Col-1: Chromosome ID Col-2: Inbred line B73 Col-3: Position of the insertion site in the B73 chromosome Col-4: "-" indicates no nucleotide(s) in the B73 genome Col-5: Inbred line Mo17 Col-6: Position of the insertion site in the Mo17 chromosome Col-7: Inserted nucleotide in the Mo17 genome Col-8: Number of Mo17 shotgun reads covering the insertion site