http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.982556
MITOGENOME ANNOUNCEMENT
The complete mitogenome of Eucryptorrhynchus brandti (Harold) (Insecta: Coleoptera: Curculionidae) Xiaoning Nan1, Cong Wei2, and Hong He1
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 01/03/15 For personal use only.
1
College of Forestry, Northwest A&F University, Yangling, P.R. China and 2College of Plant Protection, Northwest A&F University, Yangling, P.R. China Abstract
Keywords
The complete mitochondrial genome of Eucryptorrhynchus brandti (Harold) (Insecta: Coleoptera: Curculionidae) were reconstructed from whole-genome Illumina Hiseq 2000 sequencing data with an average coverage of 1406.7X. The circular genome is 15,122 bp in length, consisting of 13 protein-coding genes (PCGs), 21 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and one D-loop or control region. The tRNA-Ile gene was not found in the mitochondrial genome, as is identical to two other curculionidae species, i.e. Sphenophorus sp. (GU176342) and Naupactus xanthographus (GU176345). All PCGs initiated with ATN codons, except for the ND1 started with TTG. Two PCGs (COI and ND4) have an incomplete stop codon T. Two PCGs (ND4L and ND1) harbor the stop codon TAG, while all other PCGs terminated with the TAA codon. The nucleotide composition is highly asymmetric (38.7% A, 14.4% C, 9.2% G and 37.8% T) with an overall AT content of 76.5%.
Cryptorrhychinae, curculionidae, Eucryptorrhynchus brandti, mitochondrial genome
The weevil genus Eucryptorrhynchus belongs to the subfamily Cryptorrhychinae of the family Curculionidae, among which E. brandti (Harold) is widely distributed in China and is considered one of the potential biological control agents for tree-of-heaven (Ailanthus altissima (Mill.) Swingle) in North America (Yu et al., 2013). We reconstructed the complete mitochondrial genome of the E. brandti (Harold) from the
History Received 23 September 2014 Revised 6 October 2014 Accepted 18 October 2014 Published online 27 November 2014
whole-genome Illumina sequencing data (Novogene Bioinformatics Technology Co., Ltd, Beijing, China) (GeneBank accession number: KM593905). In total, 76.4M 100-bp raw reads were retrieved and qualitytrimmed with default parameters using CLC Genomics Workbench v7.0.4 (CLC Bio, Aarhus, Denmark), which resulted in 76.1M clean reads. These reads were then used for
Table 1. Characterization of the complete mitochondrial genome of Eucryptorrhynchus brandti. Position Gene tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Cys tRNA-Tyr COI tRNA-Leu(UUR) COII tRNA-Lys tRNA-Asp ATP8 ATP6 COIII tRNA-Gly
Codons
Size (bp)
Start
Stop
IGS (bp)
Anticodon
68 69 1,014 69 66 65 1,540 65 684 72 66 156 672 783 64
1 78 147 1,160 1,228 1,307 1,364 2,904 2,969 3,654 3,725 3,791 3,943 4,614 5,402
68 146 1,160 1,228 1,293 1,371 2,903 2,968 3,652 3,725 3,790 3,946 4,614 5,396 5,465
0 9 0 1 1 13 8 0 0 1 1 0 4 1 5
TTG CAT
Start
Stop
ATC
TAA
ATT
T(aa)
ATC
TAA
ATT ATA ATG
TAA TAA TAA
TCA GCA GTA TAA CTT GTC
TCC
Coding strand L H H H L L H H H H H H H H H (continued )
Correspondence: Hong He, College of Forestry, Northwest A&F University, Yangling, P.R. China. Tel: +86 29 87082688. E-mail: [email protected]
2
X. Nan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 01/03/15 For personal use only.
Gene ND3 tRNA-Ala tRNA-Arg tRNA-Asn tRNA-Ser(AGN) tRNA-Glu tRNA-Phe ND5 tRNA-His ND4 ND4L tRNA-Thr tRNA-Pro ND6 Cytb tRNA-Ser(UCN) ND1 tRNA-Leu(CUN) 16S rRNA tRNA-Val 12S rRNA D-loop
Codons
Size (bp)
Start
Stop
IGS (bp)
354 69 63 63 66 63 66 1,722 65 1,330 294 64 67 507 1,137 68 951 67 1,306 65 779 465
5,466 5,819 5,888 5,950 6,013 6,078 6,141 6,206 7,928 7,993 9,319 9,619 9,683 9,752 10,262 11,399 11,485 12,437 12,508 13,814 13,879 14,658
5,819 5,887 5,950 6,012 6,078 6,140 6,206 7,927 7,992 9,322 9,612 9,682 9,749 10,258 11,398 11,466 12,435 12,503 13,813 13,878 14,657 15,122
0 1 0 1 0 1 0 1 0 0 4 6 0 2 3 0 18 1 4 0 0 0
Anticodon
Start
Stop
Coding strand
ATT
TAA
ATT
TAA
ATA ATG
T(aa) TAG
ATT ATA
TAA TAA
TTG
TAG
H H H H H H L L L L L H L H H H L L L L L –
TGC TCG GTT TCT TTC GAA GTG TGT TGG TGA TAG TAC
IGS denotes the length of the intergenic spacer region, for which negative numbers indicate nucleotide overlapping between adjacent genes. T(aa) denotes that the TAA stop codon is presumed to be completed by the addition of 30 A residues to the mRNA. H and L denote heavy and light strands, respectively. Table 2. Length of each genomic region and the percentage of the total genomic size.
Genomic regions Protein coding genes (PCGs) Transport RNA (tRNAs) ribosomal RNA (rRNAs) Control region (D-loop) Others
Total length (bp)
Percentage of the total genomic size (%)
11,144 1390 2085 465 38
73.69 9.19 13.79 3.08 0.25
reconstructing the mitochondrial genome with MITObim v1.7 (Hahn et al., 2013), with that of Naupactus xanthographus (GenBank accession number: HE579083) as the initial reference. A total of 162,157 individual mitochondrial reads generated an average coverage of 1406.7X. The genome was annotated with GENEIOUS R7 (Biomatters Ltd., Auckland, New Zealand) by using the MITOS (Bernt et al., 2013) and the tRNAscan-SE web servers (http://lowelab.ucsc.edu/tRNAscan-SE/) (Lowe & Eddy, 1997; Schattner et al., 2005). The 15,122-bp-long mitochondrial genome of Eucryptorrhynchus brandti consists of 13 protein coding genes (PCGs), 21 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one D-loop or control region (Table 1). The tRNA-Ile gene was not found in the mitochondrial genome, which is identical to two other Curculionidae species: Sphenophorus sp. (GenBank accession number: GU176342) and Naupactus xanthographus (GenBank accession number: GU176345). All the 36 genes were arranged in the same orientation as in most previously reported mitochondrial genomes of Coleopteran species, e.g. Sphenophorus sp. and Naupactus xanthographus (Song et al., 2010). Four PCGs (ND1, ND4, ND4L and ND5), eight tRNAs (tRNA-Gln, -Cys, -Tyr -His, -Phe, -Pro, -Leu (CUN) and -Val), and two rRNAs (12S and 16S) were encoded on the minority strand, while all the other genes were encoded on the majority strand. The nucleotide composition is highly asymmetric (38.7% A, 14.4% C, 9.2% G and 37.8% T), with an overall AT content of 76.5% (Table 1).
The total length of protein-coding genes (PCGs, tRNAs and rRNAs) is 14,619 bp, accounting to 96.67% of the complete mitochondrial genome (Table 2). All PCGs initiated with ATN codons, except for ND1 started with TTG. COI and ND4 have an incomplete stop codon T. ND4L and ND1 harbor the stop codon TAG. All other PCGs terminated with TAA codon. Twenty-one tRNAs with a total length of 1,390 bp ranged in size from 63 to 72 bp. The 12S rRNA was 779 bp in length with an AT content of 85.0%; the 16S rRNA was 1306 bp in length, with an AT content of 85.2%. The D-loop or control region was 465 bp in length with an AT content of 95.5%, located between 12S rRNA and tRNA-Gln. Nine instances of intergenic overlapping regions ranged from 1 to 7 bp, and 14 instances of intergenic spacer regions ranged from 1 to 48 bp.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of this article.
References Bernt M, Donath A, Ju¨hling F, Externbrink F, Florentz C, Fritzsch G, Pu¨tz J, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucl Acids Res 41:e129. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955–64. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl Acids Res 33:W686–9. Song H, Sheffield NC, Cameron SL, Miller KB, Whiting MF. (2010). When phylogenetic assumptions are violated: Base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Syst Entomol 35:429–48. Yu Q, Liu Z, Chen C, Wen J. (2013). Antennal sensilla of Eucryptorrhynchus chinensis (Olivier) and Eucryptorrhynchus brandti (Harold) (Coleoptera: Curculionidae). Microsc Res Tech 76:968–78.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of Eucryptorrhynchus brandti (Harold) (Insecta: Coleoptera: Curculionidae) Xiaoning Nan1, Cong Wei2, and Hong He1
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 01/03/15 For personal use only.
1
College of Forestry, Northwest A&F University, Yangling, P.R. China and 2College of Plant Protection, Northwest A&F University, Yangling, P.R. China Abstract
Keywords
The complete mitochondrial genome of Eucryptorrhynchus brandti (Harold) (Insecta: Coleoptera: Curculionidae) were reconstructed from whole-genome Illumina Hiseq 2000 sequencing data with an average coverage of 1406.7X. The circular genome is 15,122 bp in length, consisting of 13 protein-coding genes (PCGs), 21 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and one D-loop or control region. The tRNA-Ile gene was not found in the mitochondrial genome, as is identical to two other curculionidae species, i.e. Sphenophorus sp. (GU176342) and Naupactus xanthographus (GU176345). All PCGs initiated with ATN codons, except for the ND1 started with TTG. Two PCGs (COI and ND4) have an incomplete stop codon T. Two PCGs (ND4L and ND1) harbor the stop codon TAG, while all other PCGs terminated with the TAA codon. The nucleotide composition is highly asymmetric (38.7% A, 14.4% C, 9.2% G and 37.8% T) with an overall AT content of 76.5%.
Cryptorrhychinae, curculionidae, Eucryptorrhynchus brandti, mitochondrial genome
The weevil genus Eucryptorrhynchus belongs to the subfamily Cryptorrhychinae of the family Curculionidae, among which E. brandti (Harold) is widely distributed in China and is considered one of the potential biological control agents for tree-of-heaven (Ailanthus altissima (Mill.) Swingle) in North America (Yu et al., 2013). We reconstructed the complete mitochondrial genome of the E. brandti (Harold) from the
History Received 23 September 2014 Revised 6 October 2014 Accepted 18 October 2014 Published online 27 November 2014
whole-genome Illumina sequencing data (Novogene Bioinformatics Technology Co., Ltd, Beijing, China) (GeneBank accession number: KM593905). In total, 76.4M 100-bp raw reads were retrieved and qualitytrimmed with default parameters using CLC Genomics Workbench v7.0.4 (CLC Bio, Aarhus, Denmark), which resulted in 76.1M clean reads. These reads were then used for
Table 1. Characterization of the complete mitochondrial genome of Eucryptorrhynchus brandti. Position Gene tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Cys tRNA-Tyr COI tRNA-Leu(UUR) COII tRNA-Lys tRNA-Asp ATP8 ATP6 COIII tRNA-Gly
Codons
Size (bp)
Start
Stop
IGS (bp)
Anticodon
68 69 1,014 69 66 65 1,540 65 684 72 66 156 672 783 64
1 78 147 1,160 1,228 1,307 1,364 2,904 2,969 3,654 3,725 3,791 3,943 4,614 5,402
68 146 1,160 1,228 1,293 1,371 2,903 2,968 3,652 3,725 3,790 3,946 4,614 5,396 5,465
0 9 0 1 1 13 8 0 0 1 1 0 4 1 5
TTG CAT
Start
Stop
ATC
TAA
ATT
T(aa)
ATC
TAA
ATT ATA ATG
TAA TAA TAA
TCA GCA GTA TAA CTT GTC
TCC
Coding strand L H H H L L H H H H H H H H H (continued )
Correspondence: Hong He, College of Forestry, Northwest A&F University, Yangling, P.R. China. Tel: +86 29 87082688. E-mail: [email protected]
2
X. Nan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 01/03/15 For personal use only.
Gene ND3 tRNA-Ala tRNA-Arg tRNA-Asn tRNA-Ser(AGN) tRNA-Glu tRNA-Phe ND5 tRNA-His ND4 ND4L tRNA-Thr tRNA-Pro ND6 Cytb tRNA-Ser(UCN) ND1 tRNA-Leu(CUN) 16S rRNA tRNA-Val 12S rRNA D-loop
Codons
Size (bp)
Start
Stop
IGS (bp)
354 69 63 63 66 63 66 1,722 65 1,330 294 64 67 507 1,137 68 951 67 1,306 65 779 465
5,466 5,819 5,888 5,950 6,013 6,078 6,141 6,206 7,928 7,993 9,319 9,619 9,683 9,752 10,262 11,399 11,485 12,437 12,508 13,814 13,879 14,658
5,819 5,887 5,950 6,012 6,078 6,140 6,206 7,927 7,992 9,322 9,612 9,682 9,749 10,258 11,398 11,466 12,435 12,503 13,813 13,878 14,657 15,122
0 1 0 1 0 1 0 1 0 0 4 6 0 2 3 0 18 1 4 0 0 0
Anticodon
Start
Stop
Coding strand
ATT
TAA
ATT
TAA
ATA ATG
T(aa) TAG
ATT ATA
TAA TAA
TTG
TAG
H H H H H H L L L L L H L H H H L L L L L –
TGC TCG GTT TCT TTC GAA GTG TGT TGG TGA TAG TAC
IGS denotes the length of the intergenic spacer region, for which negative numbers indicate nucleotide overlapping between adjacent genes. T(aa) denotes that the TAA stop codon is presumed to be completed by the addition of 30 A residues to the mRNA. H and L denote heavy and light strands, respectively. Table 2. Length of each genomic region and the percentage of the total genomic size.
Genomic regions Protein coding genes (PCGs) Transport RNA (tRNAs) ribosomal RNA (rRNAs) Control region (D-loop) Others
Total length (bp)
Percentage of the total genomic size (%)
11,144 1390 2085 465 38
73.69 9.19 13.79 3.08 0.25
reconstructing the mitochondrial genome with MITObim v1.7 (Hahn et al., 2013), with that of Naupactus xanthographus (GenBank accession number: HE579083) as the initial reference. A total of 162,157 individual mitochondrial reads generated an average coverage of 1406.7X. The genome was annotated with GENEIOUS R7 (Biomatters Ltd., Auckland, New Zealand) by using the MITOS (Bernt et al., 2013) and the tRNAscan-SE web servers (http://lowelab.ucsc.edu/tRNAscan-SE/) (Lowe & Eddy, 1997; Schattner et al., 2005). The 15,122-bp-long mitochondrial genome of Eucryptorrhynchus brandti consists of 13 protein coding genes (PCGs), 21 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one D-loop or control region (Table 1). The tRNA-Ile gene was not found in the mitochondrial genome, which is identical to two other Curculionidae species: Sphenophorus sp. (GenBank accession number: GU176342) and Naupactus xanthographus (GenBank accession number: GU176345). All the 36 genes were arranged in the same orientation as in most previously reported mitochondrial genomes of Coleopteran species, e.g. Sphenophorus sp. and Naupactus xanthographus (Song et al., 2010). Four PCGs (ND1, ND4, ND4L and ND5), eight tRNAs (tRNA-Gln, -Cys, -Tyr -His, -Phe, -Pro, -Leu (CUN) and -Val), and two rRNAs (12S and 16S) were encoded on the minority strand, while all the other genes were encoded on the majority strand. The nucleotide composition is highly asymmetric (38.7% A, 14.4% C, 9.2% G and 37.8% T), with an overall AT content of 76.5% (Table 1).
The total length of protein-coding genes (PCGs, tRNAs and rRNAs) is 14,619 bp, accounting to 96.67% of the complete mitochondrial genome (Table 2). All PCGs initiated with ATN codons, except for ND1 started with TTG. COI and ND4 have an incomplete stop codon T. ND4L and ND1 harbor the stop codon TAG. All other PCGs terminated with TAA codon. Twenty-one tRNAs with a total length of 1,390 bp ranged in size from 63 to 72 bp. The 12S rRNA was 779 bp in length with an AT content of 85.0%; the 16S rRNA was 1306 bp in length, with an AT content of 85.2%. The D-loop or control region was 465 bp in length with an AT content of 95.5%, located between 12S rRNA and tRNA-Gln. Nine instances of intergenic overlapping regions ranged from 1 to 7 bp, and 14 instances of intergenic spacer regions ranged from 1 to 48 bp.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of this article.
References Bernt M, Donath A, Ju¨hling F, Externbrink F, Florentz C, Fritzsch G, Pu¨tz J, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucl Acids Res 41:e129. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955–64. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl Acids Res 33:W686–9. Song H, Sheffield NC, Cameron SL, Miller KB, Whiting MF. (2010). When phylogenetic assumptions are violated: Base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Syst Entomol 35:429–48. Yu Q, Liu Z, Chen C, Wen J. (2013). Antennal sensilla of Eucryptorrhynchus chinensis (Olivier) and Eucryptorrhynchus brandti (Harold) (Coleoptera: Curculionidae). Microsc Res Tech 76:968–78.
