Computational protocol: Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer line

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Protocol publication

[…] The entire nucleotide sequences of Km3 mtDNA (accession number EU534409) and Ks3 mtDNA (accession number GU985444) were determined at the Beijing Institute of Genomics, Chinese Academy of Sciences, and DNA sequences were assembled using the software package phred/phrap/consed [,] on a PC/UNIX platform. Physical gaps were closed based on direct sequencing of selected clones. The final assembly of Ks3 mtDNA and Km3 mtDNA included 11,200 and 9931 sequences, respectively. Both genome sequences have nine-fold coverage on average, with a quality value Q20. The final master circle (MC) molecules were obtained with manual editing.The mitochondrial sequences were annotated with Glimmer 3.0 and BLAST tools, and tRNA genes and their secondary structures were identified according to tRNA scan-SE []. The Pairwise BLAST program on our local server was used for comparison between Ks3 mtDNA and Km3 mtDNA and Ks3 mtDNA and the mitochondrial genomes of other plants, with an E-value cutoff at 0.001. A database search was executed using the BLAST network service http://blast.ncbi.nlm.nih.gov/Blast.cgi with default parameters.Alignments were obtained using MultiPipMaker, a web-based tool for genomic sequence alignments http://bio.cse.psu.edu/pipmaker[,]. The annotated Ks3 mtDNA genomic sequence was used as a reference genome and compared with mtDNA sequences from Km3 (Triticum aestivum cv. Yumai 3; EU534409), rice (AB076665, AB076666), maize NB (Zea mays ssp. Mays cytotype NB; AY506529), Arabidopsis (Arabidopsis thaliana; NC001284), and rapeseed (Brassica napus L.; AP006444) […]

Pipeline specifications

Software tools Consed, Glimmer, tRNAscan-SE, MultiPipMaker
Applications Miscellaneous, Genome annotation
Organisms Triticum aestivum, Oryza sativa, Aegilops kotschyi, Zea mays, Arabidopsis thaliana
Diseases Infertility, Male
Chemicals Adenosine Triphosphate