Open Access Highly Accessed Database

KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella

Akiya Jouraku*, Kimiko Yamamoto, Seigo Kuwazaki, Masahiro Urio, Yoshitaka Suetsugu, Junko Narukawa, Kazuhisa Miyamoto, Kanako Kurita, Hiroyuki Kanamori, Yuichi Katayose, Takashi Matsumoto and Hiroaki Noda

Author Affiliations

National Institute of Agrobiological Sciences, Tsukuba 305-8634, Japan

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BMC Genomics 2013, 14:464  doi:10.1186/1471-2164-14-464

Published: 9 July 2013

Additional files

Additional file 1: Figure S1:

Phylogenetic tree of DBM, Bombyx mori and other insects P450 genes. The amino acid sequences (232 aa or longer) of p450 domain (Pfam ID: PF00067) were extracted (61 domains in DBM; 79 domains in B. mori; 1 domain (CYP321A1) in Helicoverpa zea; 1 domain (CYP6BD6) in Manduca sexta; 1 domain (CYP347A1) in Tribolium castaenum; 1 domain (CYP304F2) in Zygaena filipendulae) and aligned using ClustalW. Phylogenetic tree was built using neighbor-joining method in MEGA5 with a bootstrap of 1,000 replicates, Poisson model for amino acid substitution, and pairwise deletion of gaps. Bootstrap values resulting from 1,000 replicates are shown at the branch points. Each DBM gene ID (PxCYP-XXXXXX) corresponds to PXGS_V2_XXXXXX in KONAGAbase.

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Additional file 2: Figure S2:

Phylogenetic tree of DBM and Bombyx mori GST genes. The amino acid sequences (38 aa or longer) of Glutathione S-transferase, N-terminal (GST_N) domain (Pfam ID: PF02798) were extracted (20 domains in DBM; 23 domains in B. mori) and aligned using ClustalW. Phylogenetic tree was built using neighbor-joining method in MEGA5 with a bootstrap of 1,000 replicates, Poisson model for amino acid substitution, and pairwise deletion of gaps. Bootstrap values resulting from 1,000 replicates are shown at the branch points. Each DBM gene ID (PxGST-XXXXXX) corresponds to PXGS_V2_XXXXXX in KONAGAbase.

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Additional file 3: Figure S3:

Phylogenetic tree of DBM and Bombyx mori ABC transporter genes. The amino acid sequences (60 aa or longer) of nucleotide-binding domains (NBDs) (Pfam ID: PF00005) were extracted (57 NBDs from 54 ABC transporter genes in DBM; 70 NBDs from 52 ABC transporter genes in B. mori) and aligned using ClustalW. To avoid “No common sites” error in MEGA5, 6 NBDs (3 genes) of B. mori were removed, resulting in 64 NBDs from 49 ABC transporter genes. Phylogenetic tree was built using neighbor-joining method in MEGA5 with a bootstrap of 1,000 replicates, Poisson model for amino acid substitution, and pairwise deletion of gaps. Bootstrap values resulting from 1,000 replicates are shown at the branch points. The number (1 or 2) in parentheses is added to ID of each ABC transporter gene containing two NBDs. Each DBM gene ID (PxABC-XXXXXX) corresponds to PXGS_V2_XXXXXX in KONAGAbase.

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Additional file 4: Figure S4:

Phylogenetic subtree of DBM, Bombyx mori and other insects P450 genes in CYP2 clan.

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Additional file 5: Figure S5:

Phylogenetic subtree of DBM, Bombyx mori and other insects P450 genes of CYP3 clan.

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Additional file 6: Figure S6:

Phylogenetic subtree of DBM, Bombyx mori and other insects P450 genes of CYP4 clan.

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Additional file 7: Figure S7:

Phylogenetic subtree of DBM, Bombyx mori and other insects P450 genes of Mito. clan.

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