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Open Access Research article

Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

Wang Minxiao12, Sun Song1*, Li Chaolun1 and Shen Xin3

Author Affiliations

1 KLMEES and JBMERS, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China

2 Graduate University, Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, China

3 Huaihai Institute of Technology, 59 Cangwu Road, Lianyungang 222005, China

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BMC Genomics 2011, 12:73  doi:10.1186/1471-2164-12-73

Published: 27 January 2011

Additional files

Additional file 1:

Comparison of the length, A + T-content and nucleotide compositional bias of mitochondrial genomes among copepods. Values were obtained from the corresponding GenBank files. Detailed values are present for the complete genomes, overall PCGs, separate codon of PCGs and structural rRNA genes. NA missing data due to incomplete sequencing of the mitogenome.

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Open Data

Additional file 2:

Codon usage for the protein-coding genes in the mitogenome of C. sinicus. n indicates the total number of codons used in all 13 mitochondrial protein-coding genes.

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Additional file 3:

Stem-loop structures in the putative control region of C. sinicus. Potential hairpin structures within the LNR3 between trnH and trnA were constructed using UNAfold. Conserved motifs in 3' and 5' flanking sequences are underlined. The depicted region corresponds to the complementary strand of 11522 -11708 bp in the submitted sequence.

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Open Data

Additional file 4:

Pairwise comparison of mitochondrial gene orders among copepods. tRNA genes were not included. Common intervals (above), defined as the number of shared gene blocks inside a block independent of their gene orders, were calculated for comparison.

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Additional file 5:

Phylogenetic tree presenting the monophyly of Copepoda and its position within arthropods inferred from concatenated amino acids of 12 mitochondrial protein coding genes. Tree topologies produced by ML (mtArt model under PHYML) and BI (mtArt model under MrBayes) were compactable. Numbers at the branch nodes refer to Bayesian posterior probabilities and bootstrap support values from left to right.

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Additional file 6:

List of primers used to determine the mitogenome of C. sinicus. Numbers refer to the nucleotide positions of 5' end of primers.

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Additional file 7:

Perl scripts to extract mitochondrial genomic information from GenBank files. Bioperl modules are required.

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Open Data

Additional file 8:

Nucleotide compositional properties of the candidates for phylogenetic analysis illustrated by principal components analysis (PCA). PCA ordination was based on the proportion of separate nucleotides. PC1 (principal component 1) explained 87% of the total variations and PC2 explained 10% of the total variations. Species were sampled predominantly inside the red ellipse.

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Open Data