http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.880898
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of the plant bug Adelphocoris fasciaticollis (Hemiptera: Heteroptera: Miridae) Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 01/16/15 For personal use only.
Ying Wang1, Hu Li1,2, Huaizhu Xun1, and Wanzhi Cai1 1
Department of Entomology and 2Department of Ornamental Horticulture, China Agricultural University, Beijing, China
Abstract
Keywords
The mitochondrial genome of Adelphocoris fasciaticollis Reuter, an important pest plant bug, is a typical circular DNA molecule of 15,434 bp with 37 genes and 77.4% A + T content. Twentythree genes are located on the J-strand, the remaining being oriented on the N-strand. Gene order is identical to that of the typical arrangement of insects and other plant bugs. This genome is highly economized with 54 overlapped nucleotides between neighboring genes in 12 locations. All protein-coding genes initiate with ATN codons. All of the 22 tRNAs, ranging from 62 to 71 bp, have the clover-leaf structure. Two tRNAs, trnK and trnS1, use the non-standard anticodons TTT and TCT. The sizes of the large and small ribosomal RNA genes are 1229 and 793 bp, respectively. The control region is 922 bp in length with 78.2% A + T content and includes two 30-bp repeat units and two 35-bp repeat units.
Hemiptera, Miridae, mitochondrial genome, plant bug
Miridae, the plant bugs, are the largest family of true bugs belonging to the suborder Heteroptera, with over 10,500 described species in 1200 genera and a worldwide distribution (Jung & Lee, 2012; Schuh, 1995; Schuh & Slater, 1995). Members in this family exhibit great morphological diversity and play a key role in agroecosystems (Schuh & Slater, 1995; Wheeler, 2001). Most of the well-known plant bugs are agricultural pests. To date, only three mitochondrial genomes of plant bugs have been sequenced from two subfamilies, Apolygus lucorum (Wang et al., 2013) and Lygus lineolaris from the subfamily Mirinae, and Nesidiocoris tenuis from the subfamily Bryocorinae (Dai et al., 2012). In this study, we present the complete mitochondrial genome of Adelphocoris fasciaticollis, the third species from the plant bug subfamily Mirinae. This mitochondrial genome is 15,434 bp long (GenBank accession number KJ001714). It includes the entire set of 37 genes (i.e. 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes) usually present in animal mitochondrial genomes and a control region (Figure 1). Twenty-three genes are located on the J-strand (major strand), the remaining being oriented on the N-strand (minor strand). Gene order is identical to that of the putative ancestral arrangement of insects and other plant bugs (Boore, 1999; Dai et al., 2012; Wang et al., 2013). This mitochondrial genome is highly economized and has 54 overlapped nucleotides between neighboring genes in 12 locations, ranging from 1 to 14 bp in length; while there are totally 29 bp intergenic nucleotides in eight locations, ranging from 1 to 10 bp in length. The A + T content is 77.4% with obvious positive AT-skew (0.16) and negative GC-skew ( 0.22). There is a strong bias
Correspondence: Dr. Wanzhi Cai, Department of Entomology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China. Tel: 86-10-62732885. Fax: 86-10-62732885. E-mail: [email protected]
History Received 2 January 2014 Accepted 5 January 2014 Published online 4 February 2014
toward AT-rich codons with the five most prevalent codons, ATA (Met), ATT (Ile), TTA (Leu), TTT (Phe) and TAT (Tyr). The overall pattern is very similar among plant bugs and other true bugs, with similar frequency of occurrences of various codons within a single codon family (Dai et al., 2012; Li et al., 2011, 2012a,b,c). All protein-coding genes initiate with ATN as the start codon (five with ATG, five with ATT, two with ATA and one with ATC). Conventional stop codons (TAA or TAG) have been assigned to majority of the protein-coding genes. COII, COIII, ND3, ND4 and ND5, however, terminate with a single T residue. All of the 22 tRNA genes, ranging from 62 to 71 bp, have a typically cloverleaf structure. This is different from most other true bugs that the dihydrouridine arm of trnS1 always forms a simple loop (Dai et al., 2012; Hua et al., 2008; Li et al., 2011, 2012a,b,c; Shi et al., 2012). Two tRNAs, trnK and trnS1, use the non-standard anticodons TTT and TCT. The lengths and AT content of lrRNA and srRNA were determined to be 1229 and 793 bp and 81.0% and 81.2%, respectively. The control region is located between srRNA and trnI and is 922 bp long with 78.2% A + T content. Two 30-bp repeat sequences and two 35-bp repeat sequences are detected in this region.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. Funding for this study was supported by grants from the Special Fund for Agroscientific Research in the Public Interest (No. 201103012), the National Basic Research Program of China (No. 2013CB127600), the National Natural Science Foundation of China (No. 31372229), and the Special Fund for Scientific Research (No. 2012FY111100) for WZC; and the China Postdoctoral Science Foundation (No. 2013M540167) and the Fundamental Research Funds for the Central Universities (2014BH021) for HL. All authors have read and approved the final manuscript.
Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 01/16/15 For personal use only.
2
Y. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Map of the mitochondrial genome of A. fasciaticollis. Direction of gene transcription is indicated by arrows. PCGs are shown as blue arrows, rRNAs as purple arrows, tRNAs as red arrows and large NC regions (4100 bp) as grey arrows. tRNAs are labeled according to single-letter IUPACIUB abbreviations (L1: CUN; L2: UUR; S1: AGN; and S2: UCN). The GC content is plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC-skew is plotted as the deviation from the average GC-skew of the entire sequence (inner sliding window). GC skew+ is shown as the external sliding window with green color. GC skew is shown as the internal sliding window with dark purple color. Ticks in the inner cycle indicate the sequence length.
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Dai X, Xun HZ, Chang J, Zhang JH, Hu BW, Li H, Yuan XQ, Cai W. (2012). The complete mitochondrial genome of the plant bug Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae: Bryocorinae: Dicyphini). Zootaxa 3554:30–44. Hua JM, Li M, Dong PZ, Cui Y, Xie Q, Bu WJ. (2008). Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera). BMC Genomics 9:610. Jung S, Lee S. (2012). Molecular phylogeny of the plant bugs (Heteroptera: Miridae) and the evolution of feeding habits. Cladistics 28:50–79. Li H, Gao JY, Liu HY, Liu H, Liang AP, Zhou XG, Cai W. (2011). The architecture and complete sequence of mitochondrial genome of an assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae). Int J Biol Sci 7:792–804. Li H, Liu H, Shi AM, Sˇtys P, Zhou XG, Cai W. (2012a). The complete mitochondrial genome and novel gene arrangement of the uniqueheaded bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS One 7:e29419.
Li H, Liu H, Song F, Shi AM, Zhou XG, Cai W. (2012b). Comparative mitogenomic analysis of damsel bugs representing three tribes in the family Nabidae (Insecta: Hemiptera). PLoS One 7:e45925. Li H, Liu HY, Cao LM, Shi AM, Yang HL, Cai W. (2012c). The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). Int J Bio Sci 8:93–107. Schuh RT. (1995). Plant bugs of the world (Insecta: Heteroptera: Miridae): Systematic catalogue, distributions, host list, and bibliography. New York: New York Entomological Society. Schuh RT, Slater JA. (1995). True bugs of the world (Hemiptera: Heteroptera): Classification and natural history. Ithaca: Cornell University Press. Shi AM, Li H, Bai XS, Dai X, Chang J, Guilbert E, Cai W. (2012). The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae). Zootaxa 3238:23–38. Wang P, Li H, Wang Y, Zhang JH, Dai X, Chang J, Hu BW, Cai W. (2013). The mitochondrial genome of the plant bug Apolygus lucorum (Hemiptera: Miridae): Presently known as the smallest in Heteroptera. Insect Sci. [Epub ahead of print]. doi: 10.1111/17447917.12029. Wheeler AG. (2001). Biology of the plant bugs (Hemiptera: Miridae): pests, predators, opportunists. Ithaca: Cornell University Press.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of the plant bug Adelphocoris fasciaticollis (Hemiptera: Heteroptera: Miridae) Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 01/16/15 For personal use only.
Ying Wang1, Hu Li1,2, Huaizhu Xun1, and Wanzhi Cai1 1
Department of Entomology and 2Department of Ornamental Horticulture, China Agricultural University, Beijing, China
Abstract
Keywords
The mitochondrial genome of Adelphocoris fasciaticollis Reuter, an important pest plant bug, is a typical circular DNA molecule of 15,434 bp with 37 genes and 77.4% A + T content. Twentythree genes are located on the J-strand, the remaining being oriented on the N-strand. Gene order is identical to that of the typical arrangement of insects and other plant bugs. This genome is highly economized with 54 overlapped nucleotides between neighboring genes in 12 locations. All protein-coding genes initiate with ATN codons. All of the 22 tRNAs, ranging from 62 to 71 bp, have the clover-leaf structure. Two tRNAs, trnK and trnS1, use the non-standard anticodons TTT and TCT. The sizes of the large and small ribosomal RNA genes are 1229 and 793 bp, respectively. The control region is 922 bp in length with 78.2% A + T content and includes two 30-bp repeat units and two 35-bp repeat units.
Hemiptera, Miridae, mitochondrial genome, plant bug
Miridae, the plant bugs, are the largest family of true bugs belonging to the suborder Heteroptera, with over 10,500 described species in 1200 genera and a worldwide distribution (Jung & Lee, 2012; Schuh, 1995; Schuh & Slater, 1995). Members in this family exhibit great morphological diversity and play a key role in agroecosystems (Schuh & Slater, 1995; Wheeler, 2001). Most of the well-known plant bugs are agricultural pests. To date, only three mitochondrial genomes of plant bugs have been sequenced from two subfamilies, Apolygus lucorum (Wang et al., 2013) and Lygus lineolaris from the subfamily Mirinae, and Nesidiocoris tenuis from the subfamily Bryocorinae (Dai et al., 2012). In this study, we present the complete mitochondrial genome of Adelphocoris fasciaticollis, the third species from the plant bug subfamily Mirinae. This mitochondrial genome is 15,434 bp long (GenBank accession number KJ001714). It includes the entire set of 37 genes (i.e. 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes) usually present in animal mitochondrial genomes and a control region (Figure 1). Twenty-three genes are located on the J-strand (major strand), the remaining being oriented on the N-strand (minor strand). Gene order is identical to that of the putative ancestral arrangement of insects and other plant bugs (Boore, 1999; Dai et al., 2012; Wang et al., 2013). This mitochondrial genome is highly economized and has 54 overlapped nucleotides between neighboring genes in 12 locations, ranging from 1 to 14 bp in length; while there are totally 29 bp intergenic nucleotides in eight locations, ranging from 1 to 10 bp in length. The A + T content is 77.4% with obvious positive AT-skew (0.16) and negative GC-skew ( 0.22). There is a strong bias
Correspondence: Dr. Wanzhi Cai, Department of Entomology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China. Tel: 86-10-62732885. Fax: 86-10-62732885. E-mail: [email protected]
History Received 2 January 2014 Accepted 5 January 2014 Published online 4 February 2014
toward AT-rich codons with the five most prevalent codons, ATA (Met), ATT (Ile), TTA (Leu), TTT (Phe) and TAT (Tyr). The overall pattern is very similar among plant bugs and other true bugs, with similar frequency of occurrences of various codons within a single codon family (Dai et al., 2012; Li et al., 2011, 2012a,b,c). All protein-coding genes initiate with ATN as the start codon (five with ATG, five with ATT, two with ATA and one with ATC). Conventional stop codons (TAA or TAG) have been assigned to majority of the protein-coding genes. COII, COIII, ND3, ND4 and ND5, however, terminate with a single T residue. All of the 22 tRNA genes, ranging from 62 to 71 bp, have a typically cloverleaf structure. This is different from most other true bugs that the dihydrouridine arm of trnS1 always forms a simple loop (Dai et al., 2012; Hua et al., 2008; Li et al., 2011, 2012a,b,c; Shi et al., 2012). Two tRNAs, trnK and trnS1, use the non-standard anticodons TTT and TCT. The lengths and AT content of lrRNA and srRNA were determined to be 1229 and 793 bp and 81.0% and 81.2%, respectively. The control region is located between srRNA and trnI and is 922 bp long with 78.2% A + T content. Two 30-bp repeat sequences and two 35-bp repeat sequences are detected in this region.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. Funding for this study was supported by grants from the Special Fund for Agroscientific Research in the Public Interest (No. 201103012), the National Basic Research Program of China (No. 2013CB127600), the National Natural Science Foundation of China (No. 31372229), and the Special Fund for Scientific Research (No. 2012FY111100) for WZC; and the China Postdoctoral Science Foundation (No. 2013M540167) and the Fundamental Research Funds for the Central Universities (2014BH021) for HL. All authors have read and approved the final manuscript.
Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 01/16/15 For personal use only.
2
Y. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Map of the mitochondrial genome of A. fasciaticollis. Direction of gene transcription is indicated by arrows. PCGs are shown as blue arrows, rRNAs as purple arrows, tRNAs as red arrows and large NC regions (4100 bp) as grey arrows. tRNAs are labeled according to single-letter IUPACIUB abbreviations (L1: CUN; L2: UUR; S1: AGN; and S2: UCN). The GC content is plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC-skew is plotted as the deviation from the average GC-skew of the entire sequence (inner sliding window). GC skew+ is shown as the external sliding window with green color. GC skew is shown as the internal sliding window with dark purple color. Ticks in the inner cycle indicate the sequence length.
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Dai X, Xun HZ, Chang J, Zhang JH, Hu BW, Li H, Yuan XQ, Cai W. (2012). The complete mitochondrial genome of the plant bug Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae: Bryocorinae: Dicyphini). Zootaxa 3554:30–44. Hua JM, Li M, Dong PZ, Cui Y, Xie Q, Bu WJ. (2008). Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera). BMC Genomics 9:610. Jung S, Lee S. (2012). Molecular phylogeny of the plant bugs (Heteroptera: Miridae) and the evolution of feeding habits. Cladistics 28:50–79. Li H, Gao JY, Liu HY, Liu H, Liang AP, Zhou XG, Cai W. (2011). The architecture and complete sequence of mitochondrial genome of an assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae). Int J Biol Sci 7:792–804. Li H, Liu H, Shi AM, Sˇtys P, Zhou XG, Cai W. (2012a). The complete mitochondrial genome and novel gene arrangement of the uniqueheaded bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS One 7:e29419.
Li H, Liu H, Song F, Shi AM, Zhou XG, Cai W. (2012b). Comparative mitogenomic analysis of damsel bugs representing three tribes in the family Nabidae (Insecta: Hemiptera). PLoS One 7:e45925. Li H, Liu HY, Cao LM, Shi AM, Yang HL, Cai W. (2012c). The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). Int J Bio Sci 8:93–107. Schuh RT. (1995). Plant bugs of the world (Insecta: Heteroptera: Miridae): Systematic catalogue, distributions, host list, and bibliography. New York: New York Entomological Society. Schuh RT, Slater JA. (1995). True bugs of the world (Hemiptera: Heteroptera): Classification and natural history. Ithaca: Cornell University Press. Shi AM, Li H, Bai XS, Dai X, Chang J, Guilbert E, Cai W. (2012). The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae). Zootaxa 3238:23–38. Wang P, Li H, Wang Y, Zhang JH, Dai X, Chang J, Hu BW, Cai W. (2013). The mitochondrial genome of the plant bug Apolygus lucorum (Hemiptera: Miridae): Presently known as the smallest in Heteroptera. Insect Sci. [Epub ahead of print]. doi: 10.1111/17447917.12029. Wheeler AG. (2001). Biology of the plant bugs (Hemiptera: Miridae): pests, predators, opportunists. Ithaca: Cornell University Press.
