http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007319
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Cacopsylla coccinae (Hemiptera: Psyllidae) Shengquan Que1,2*, Liping Yu1*, Tianrong Xin1,2, Zhiwen Zou1, Liangxiong Hu3, and Bin Xia1,2 School of Life Sciences, Nanchang University, Nanchang, China, 2Center for Watershed Ecology, Institute of Life Sciences, Nanchang University, Nanchang, China, and 3School of Life Sciences, Jiujiang University, Jiujiang, China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 03/13/15 For personal use only.
1
Abstract
Keywords
In this study, the first complete mitochondrial genome (mitogenome) sequence of Cacopsylla coccinae was determined by long PCR and primer walking methods. The complete mitochondrial genome is 14,832 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes as well as a control region. The overall base composition of the genome is A (38.16%), T (33.88%), C (17.95%) and G (10.01%). Stop codon was incomplete for coxII gene and ND1 gene. The gene overlaps were suggested between 13 pairs of the contiguous genes in C. coccinae. The mitogenome would contribute to resolving phylogenetic position and interrelationships of Cacopsylla.
Cacopsylla coccinae, complete mitogenome, control region, Psyllidae
Cacopsylla coccinae Kuwayama (Hemiptera: Psyllidae) is an important kebia quinata pest, which distributes in China, Japan and Korea. Former studies were mainly focused on the characteristics of its morphological structure (Drohojowska et al., 2013). However, few researches were conducted on its genetic characteristics. Therefore, it is very important to obtain the complete mitogenome sequence for resolving phylogenetic position and interrelationships of Cacopsylla. The sampled specimens of C. coccinae were collected from Jiujiang, Jiangxi Province, China, in August 2014. Total DNA was extracted using the QIAamp DNA Micro Kit (Qiagen, Hilden, Germany). Initially, four short fragments were amplified using the universal primers from the previous work (Simon et al., 2006). Four perfectly matching primers were then designed on the basis of these short fragments for secondary PCRs. The PCR products were purified, cloned and last sequenced by Sangon Biotech in Shanghai, China. The complete mitochondrial genome sequence of C. coccinae was determined by long PCR and primer-walking methods (Li et al., 2012a). The mitogenome data of C. coccinae were submitted to GenBank with accession number Kp245955. In this study, we determined the first complete mitochondrial genome of C. coccinae. Its genome is 14,832 bp in length and consists of 13 protein-coding, 22 tRNA genes, 2 rRNA genes and 1 control region designated as the A + T-rich region in insects (Table 1). In the genome, the 671-bp A + T-rich region without any repeat, which has putative termination associated sequences, is located between rrnS and tRNAIle. The gene order and orientation of C. coccinae were identical to those of most Psyllidae insects that have been regarded as a synapomorphy for Hemiptera (Li et al., 2012b, 2014; Wang et al., 2013). The overall *These authors contributed equally to this study. Correspondence: Bin Xia, School of Life Sciences and Food Engineering, Nanchang University, Nanchang 330031 China. Tel: +86 0791 83969530. E-mail: [email protected]
History Received 26 December 2014 Accepted 30 December 2014 Published online 19 February 2015
Table 1. Characteristics of the mitochondrial genome of the mold, C. coccinae. Gene
CoxI tRNALeu CoxII tRNALys tRNAAsp ATP8 ATP6 CoxIII tRNAGly ND3 tRNAAla tRNAArg tRNAAsn tRNASer tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cob tRNASer ND1 tRNALeu rrnL tRNAVal rrnS CR
Position From
To
1 1533 1601 2265 2338 2412 2549 3223 4002 4058 4110 4474 4534 4599 4653 4701 4764 6382 6438 7676 7965 8024 8088 8567 9711 9801 10,716 10,779 11,933 11,996 12,769
1533 1600 2264 2334 2402 2555 3223 4002 4060 4411 4472 4534 4598 4652 4712 4763 6384 6442 7724 7936 8023 8085 8573 9712 9772 10,721 10,778 11,932 11,994 12,768 13,439
Codon Length (bp) Start 1533 68 664 70 65 144 675 780 59 354 63 61 65 54 60 63 1621 61 1287 261 59 62 486 1146 72 921 63 1153 62 806 671
Intergenic Stop nucleotidesa Strandb
ATG TAA ATA
T– –
ATA TAA ATG TAA ATA TAA ATA TAG
ATT
T– –
ATG TAG ATA TAG ATA TAA ATA TAG ATA TAG
1 0 0 3 9 7 1 1 3 2 1 1 0 0 13 0 3 5 51 18 28 0 2 7 2 28 6 0 0 1 0
H H H H H H H H H H H H H H H L L L L L H L H H H L L L L L (continued )
2
S. Que et al.
Mitochondrial DNA, Early Online: 1–2
Declaration of interest
Table 1. Continued.
Gene
tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNACys tRNATyr
Position From
To
13,440 13,510 13,581 13,648 14,642 14,707 14,770
13,505 13,575 13,647 14,619 14,703 14,769 14,831
Codon Length (bp) Start 66 66 67 972 62 63 62
Intergenic Stop nucleotidesa Strandb
ATT TAA
0 4 5 0 22 3 0
H L H H H L L
a
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 03/13/15 For personal use only.
Numbers correspond to the nucleotides separating different genes. Positive numbers indicate the number of nucleotides found in intergenic spaces, and negative numbers indicate overlapping nucleotides between adjacent genes. b H and L indicate heavy and light strands, respectively.
base composition of the entire genome is as follows: A (38.16%), T (38.88%), C (17.95%) and G (10.01%), respectively. Except for ND5, ND4, ND4l, ND1, 6 tRNA genes and 2 rRNA, all the other mitochondrial genes are encoded on the heavy strand. The sequence alignment by Clustal W 2.0 showed that the insect shared 72 and 70% sequence identity with Paratrioza sinica (AC: KJ650081) and Pachypsylla venusta (AC: AY278317). Among the tRNAs ranging from 54 to 72 bp in size, the longest and the shortest were both the tRNASer. The start codon was mainly ATA in most of the mitochondrial protein-coding genes except COI, ATP6 and ND4 genes employing ATG and ND5 gene with ATT; the stop codon was either complete, such as TAA or TAG, or incomplete, such as T– – for COII and ND5 genes, which was also observed in many other insect species (e.g. Song et al., 2010; Wei et al., 2012; Wu et al., 2014). The gene overlaps could also be observed between 13 pairs of the contiguous genes in C. coccinae.
The authors alone are responsible for the content and writing of this article. This study was supported by Natural Science Foundation of China (30860041, 31160418 and 31160081), Natural Science Foundation of Jiangxi (20132BAB and 2013BAB204005), Science & Technology Foundations of Education Department of Jiangxi (GJJ13097 and GJJ13104) and Foundations from the Administration of Science & Technology in Nanchang (2010NYZZ037 and 2013HZCG008).
References Drohojowska J, Kalandyk-Kołodziejczyk M, Simon E. (2013). Thorax morphology of selected species of the genus Cacopsylla (Hemiptera, Psylloidea). ZooKeys 319:27–35. Li H, Liu H, Cao L, Shi A, Yang H, Cai W. (2012a). The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). Int J Bio Sci 8:93–107. Li H, Liu H, Shi A, Sˇtys P, Zhou X, Cai W. (2012b). The complete mitochondrial genome and novel gene arrangement of the uniqueheaded bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS One 7:e29419. Li T, Hua J, Wright AM, Cui Y, Xie Q, Bu W, Hillis DM. (2014). Longbranch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes. BMC Evol Biol 14:99. Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT. (2006). Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu Rev Ecol Evol Syst 7:545–79. Song N, Liang AP, Ma C. (2010). The complete mitochondrial genome sequence of the planthopper, Sivaloka damnosus. J Insect Sci 10:76. Wang HL, Yang J, Boykin LM, Zhao QY, Li Q, Wang XW, Liu SS. (2013). The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex. BMC Genomics 14:401. Wei SJ, Ni JF, Yu ML, Shi BC. (2012). The complete mitochondrial genome of Macrotermes barneyi light (Isoptera: Termitidae). Mitochrodial DNA 23:426–8. Wu LW, Lin LH, Lees DC, Hsu YF. (2014). Mitogenomic sequences effectively recover relationships within brush-footed butterflies (Lepidoptera: Nymphalidae). BMC Genomics 15:468.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Cacopsylla coccinae (Hemiptera: Psyllidae) Shengquan Que1,2*, Liping Yu1*, Tianrong Xin1,2, Zhiwen Zou1, Liangxiong Hu3, and Bin Xia1,2 School of Life Sciences, Nanchang University, Nanchang, China, 2Center for Watershed Ecology, Institute of Life Sciences, Nanchang University, Nanchang, China, and 3School of Life Sciences, Jiujiang University, Jiujiang, China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 03/13/15 For personal use only.
1
Abstract
Keywords
In this study, the first complete mitochondrial genome (mitogenome) sequence of Cacopsylla coccinae was determined by long PCR and primer walking methods. The complete mitochondrial genome is 14,832 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes as well as a control region. The overall base composition of the genome is A (38.16%), T (33.88%), C (17.95%) and G (10.01%). Stop codon was incomplete for coxII gene and ND1 gene. The gene overlaps were suggested between 13 pairs of the contiguous genes in C. coccinae. The mitogenome would contribute to resolving phylogenetic position and interrelationships of Cacopsylla.
Cacopsylla coccinae, complete mitogenome, control region, Psyllidae
Cacopsylla coccinae Kuwayama (Hemiptera: Psyllidae) is an important kebia quinata pest, which distributes in China, Japan and Korea. Former studies were mainly focused on the characteristics of its morphological structure (Drohojowska et al., 2013). However, few researches were conducted on its genetic characteristics. Therefore, it is very important to obtain the complete mitogenome sequence for resolving phylogenetic position and interrelationships of Cacopsylla. The sampled specimens of C. coccinae were collected from Jiujiang, Jiangxi Province, China, in August 2014. Total DNA was extracted using the QIAamp DNA Micro Kit (Qiagen, Hilden, Germany). Initially, four short fragments were amplified using the universal primers from the previous work (Simon et al., 2006). Four perfectly matching primers were then designed on the basis of these short fragments for secondary PCRs. The PCR products were purified, cloned and last sequenced by Sangon Biotech in Shanghai, China. The complete mitochondrial genome sequence of C. coccinae was determined by long PCR and primer-walking methods (Li et al., 2012a). The mitogenome data of C. coccinae were submitted to GenBank with accession number Kp245955. In this study, we determined the first complete mitochondrial genome of C. coccinae. Its genome is 14,832 bp in length and consists of 13 protein-coding, 22 tRNA genes, 2 rRNA genes and 1 control region designated as the A + T-rich region in insects (Table 1). In the genome, the 671-bp A + T-rich region without any repeat, which has putative termination associated sequences, is located between rrnS and tRNAIle. The gene order and orientation of C. coccinae were identical to those of most Psyllidae insects that have been regarded as a synapomorphy for Hemiptera (Li et al., 2012b, 2014; Wang et al., 2013). The overall *These authors contributed equally to this study. Correspondence: Bin Xia, School of Life Sciences and Food Engineering, Nanchang University, Nanchang 330031 China. Tel: +86 0791 83969530. E-mail: [email protected]
History Received 26 December 2014 Accepted 30 December 2014 Published online 19 February 2015
Table 1. Characteristics of the mitochondrial genome of the mold, C. coccinae. Gene
CoxI tRNALeu CoxII tRNALys tRNAAsp ATP8 ATP6 CoxIII tRNAGly ND3 tRNAAla tRNAArg tRNAAsn tRNASer tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cob tRNASer ND1 tRNALeu rrnL tRNAVal rrnS CR
Position From
To
1 1533 1601 2265 2338 2412 2549 3223 4002 4058 4110 4474 4534 4599 4653 4701 4764 6382 6438 7676 7965 8024 8088 8567 9711 9801 10,716 10,779 11,933 11,996 12,769
1533 1600 2264 2334 2402 2555 3223 4002 4060 4411 4472 4534 4598 4652 4712 4763 6384 6442 7724 7936 8023 8085 8573 9712 9772 10,721 10,778 11,932 11,994 12,768 13,439
Codon Length (bp) Start 1533 68 664 70 65 144 675 780 59 354 63 61 65 54 60 63 1621 61 1287 261 59 62 486 1146 72 921 63 1153 62 806 671
Intergenic Stop nucleotidesa Strandb
ATG TAA ATA
T– –
ATA TAA ATG TAA ATA TAA ATA TAG
ATT
T– –
ATG TAG ATA TAG ATA TAA ATA TAG ATA TAG
1 0 0 3 9 7 1 1 3 2 1 1 0 0 13 0 3 5 51 18 28 0 2 7 2 28 6 0 0 1 0
H H H H H H H H H H H H H H H L L L L L H L H H H L L L L L (continued )
2
S. Que et al.
Mitochondrial DNA, Early Online: 1–2
Declaration of interest
Table 1. Continued.
Gene
tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNACys tRNATyr
Position From
To
13,440 13,510 13,581 13,648 14,642 14,707 14,770
13,505 13,575 13,647 14,619 14,703 14,769 14,831
Codon Length (bp) Start 66 66 67 972 62 63 62
Intergenic Stop nucleotidesa Strandb
ATT TAA
0 4 5 0 22 3 0
H L H H H L L
a
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 03/13/15 For personal use only.
Numbers correspond to the nucleotides separating different genes. Positive numbers indicate the number of nucleotides found in intergenic spaces, and negative numbers indicate overlapping nucleotides between adjacent genes. b H and L indicate heavy and light strands, respectively.
base composition of the entire genome is as follows: A (38.16%), T (38.88%), C (17.95%) and G (10.01%), respectively. Except for ND5, ND4, ND4l, ND1, 6 tRNA genes and 2 rRNA, all the other mitochondrial genes are encoded on the heavy strand. The sequence alignment by Clustal W 2.0 showed that the insect shared 72 and 70% sequence identity with Paratrioza sinica (AC: KJ650081) and Pachypsylla venusta (AC: AY278317). Among the tRNAs ranging from 54 to 72 bp in size, the longest and the shortest were both the tRNASer. The start codon was mainly ATA in most of the mitochondrial protein-coding genes except COI, ATP6 and ND4 genes employing ATG and ND5 gene with ATT; the stop codon was either complete, such as TAA or TAG, or incomplete, such as T– – for COII and ND5 genes, which was also observed in many other insect species (e.g. Song et al., 2010; Wei et al., 2012; Wu et al., 2014). The gene overlaps could also be observed between 13 pairs of the contiguous genes in C. coccinae.
The authors alone are responsible for the content and writing of this article. This study was supported by Natural Science Foundation of China (30860041, 31160418 and 31160081), Natural Science Foundation of Jiangxi (20132BAB and 2013BAB204005), Science & Technology Foundations of Education Department of Jiangxi (GJJ13097 and GJJ13104) and Foundations from the Administration of Science & Technology in Nanchang (2010NYZZ037 and 2013HZCG008).
References Drohojowska J, Kalandyk-Kołodziejczyk M, Simon E. (2013). Thorax morphology of selected species of the genus Cacopsylla (Hemiptera, Psylloidea). ZooKeys 319:27–35. Li H, Liu H, Cao L, Shi A, Yang H, Cai W. (2012a). The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). Int J Bio Sci 8:93–107. Li H, Liu H, Shi A, Sˇtys P, Zhou X, Cai W. (2012b). The complete mitochondrial genome and novel gene arrangement of the uniqueheaded bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS One 7:e29419. Li T, Hua J, Wright AM, Cui Y, Xie Q, Bu W, Hillis DM. (2014). Longbranch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes. BMC Evol Biol 14:99. Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT. (2006). Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu Rev Ecol Evol Syst 7:545–79. Song N, Liang AP, Ma C. (2010). The complete mitochondrial genome sequence of the planthopper, Sivaloka damnosus. J Insect Sci 10:76. Wang HL, Yang J, Boykin LM, Zhao QY, Li Q, Wang XW, Liu SS. (2013). The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex. BMC Genomics 14:401. Wei SJ, Ni JF, Yu ML, Shi BC. (2012). The complete mitochondrial genome of Macrotermes barneyi light (Isoptera: Termitidae). Mitochrodial DNA 23:426–8. Wu LW, Lin LH, Lees DC, Hsu YF. (2014). Mitogenomic sequences effectively recover relationships within brush-footed butterflies (Lepidoptera: Nymphalidae). BMC Genomics 15:468.
