http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.913164
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Poratrioza sinica (Insecta: Hemiptera: Psyllidae) Qi-Lin Zhang, Zhong-Long Guo, and Ming-Long Yuan
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People’s Republic of China Abstract
Keywords
The complete mitochondrial genome (mitogenome) of Poratrioza sinica (Hemiptera: Psyllidae) has been sequenced and annotated in this study. This mitogenome is 14,863 bp in length with an A + T content of 72.0%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the putative ancestral insect mitogenome. All proteincoding genes start with ATN codons except for nad5, which uses TTG as the initial codon. All the transfer RNA genes have the typical cloverleaf structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm. The control region is 700 bp in length with 82.4% A + T content. This is the second completely sequenced mitogenome from the family Psyllidae of Hemiptera.
Insecta, mitogenome, Poratrioza sinica, psyllids, Sternorrhyncha
Psyllids (Hemiptera: Psyllidae) consist of about 1139 described species (Ouvrard, 2014), many of which are economically important pests around the world. Up to date, the complete mitochondrial genome (mitogenome) of only one psyllid (Pachypsylla venusta) has been determined (Thao et al., 2004). In this study, we sequenced the complete mitogenome of Poratrioza sinica (Hemiptera: Psyllidae), an important pest of Lycium chinense in China. The specimens of P. sinica were collected from Jingyuan County, Gansu Province, China. The entire P. sinica mitogenome was amplified with eight overlapping fragments by a set of universal and specific primer pairs (available from corresponding author on request), and sequenced in both directions. The mitogenome of P. sinica is a typical circular DNA molecule of 14,863 bp in length (GenBank accession number KJ650081). This genome is slightly larger than that of the samefamily species P. venusta (14,711 bp) (Thao et al., 2004). The P. sinica mitogenome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), the large and small ribosomal
Correspondence: Ming-Long Yuan, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People’s Republic of China. Tel: +86 9318915310. Fax: +86 9318915310. E-mail: [email protected]
History Received 3 April 2014 Accepted 5 April 2014 Published online 8 May 2014
RNA unit genes (rrnL and rrnS), and a large non-coding region (putative control region; Table 1). The order and orientation of the mitochondrial genes is identical to that of the putative ancestral insect mitogenome (Boore, 1999). Gene overlaps have been found at seven gene junctions and have involved a total of 40 bp; the longest overlap (12 bp) exists between trnE and trnF. A total of 55 bp intergenic spacers are present in the P. sinica mitogenome and are spread over seven positions, ranging in size from 1 to 31 bp. The nucleotide composition of the P. sinica mitogenome is significantly biased toward A and T. The total A + T content of the major strand is 72.0%, with a positive AT-skew (0.047) and a negative GC-skew ( 0.249). Among the 13 PCGs, the lowest A + T content is 67.5% in cox1, while the highest is 76.8% in nad4L. Twelve of the 13 PCGs start with a typical ATN codon: one (atp8) with ATC, three (atp6, cox3 and nad4) with ATG, three (nad2, cox2 and nad3) with ATT, five (cox1, nad4L, nad6, cob and nad1) with ATA. The only exception is nad5, which uses TTG as a start codon. This atypical codon has also been reported for many hemipteran species (Li et al., 2013; Zhang et al., 2013, 2014). Six PCGs stop with the complete termination codons TAA or TAG, and the remaining seven have incomplete termination codons TA or T. All of the 22 tRNAs, ranging from 54 to 71 bp, have a typical cloverleaf structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm. The loss of the DHU arm in trnS1 is a typical feature of metazoan mitogenomes (Wolstenholme, 1992). The size of rrnL and rrnS are 1159 bp and 802 bp long, respectively, with an A + T content of 75.1%. The control region is located at the conserved position between rrnS and trnI-trnQ-trnM gene cluster, and is 700 bp long with an A + T content of 82.4%.
2
Q.-L. Zhang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Annotation and organization of the complete mitochondrial genome of P. sinica.
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
Gene
Strand
Position
Length (bp)
J N J J J N N J J J J J J J J J J J J J J J N N N N N J N J J J N N N N N J
1–66 64–129 129–191 192–1161 1162–1232 1225–1286 1287–1350 1357–2895 2896–2959 2960–3623 3624–3693 3692–3757 3758–3910 3904–4577 4578–5360 5364–5422 5423–5771 5772–5833 5835–5895 5896–5960 5961–6014 6015–6076 6065–6126 6127–7750 7751–7810 7811–9050 9044–9328 9333–9394 9395–9454 9457–9939 9948–11,073 11,074–11,135 11,167–12,081 12,082–12,143 12,144–13,301 13,302–13,361 13,362–14,163 14,164–14,863
66 66 63 970 71 62 64 1539 64 664 70 66 153 674 783 59 349 62 61 65 54 62 62 1624 60 1240 285 62 60 483 1126 62 915 61 1159 60 802 700
trnI trnQ trnM nad2 trnW trnC trnY cox1 trnL2(UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnS1(AGN) trnE trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2(UCN) nad1 trnL1(CUN) rrnL trnV rrnS Control region
Intergenic nucleotides
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The study was funded by the Specialized Research Fund for the Doctoral Program of Higher Education of China (20120211120043), and the Fundamental Research Funds for the Central Universities (lzujbky-2012-91).
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Li T, Gao C, Cui Y, Xie Q, Bu W. (2013). The complete mitochondrial genome of the stalk-eyed bug Chauliops fallax Scott, and the monophyly of Malcidae (Hemiptera: Heteroptera). PLoS One 8: e55381.
0 3 1 0 0 8 0 6 0 0 0 2 0 7 0 3 0 0 1 0 0 0 12 0 0 0 7 4 0 2 8 0 31 0 0 0 0 0
Start codon
Stop codon
Anticodon GAU UUG CAU
ATT
T UCA GCA GUA
ATA
TAA
ATT
T
UAA CUU GUC ATC ATG ATG
TAA TA TAA
ATT
T
UCC UGC UCG GUU GCU UUC GAA TTG
T
ATG ATA
T TAG
GUG UGU UGG ATA ATA
TAA T
ATA
TAA
UGA UAG UAC
Ouvrard D. (2014). Psyl’list – The world psylloidea database. Available at: http://www.hemiptera-databases.com/psyllist (Accessed 31 March 2014). Thao ML, Baumann L, Baumann P. (2004). Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evol Biol 4:25. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. Int Rev Cytol 141:173–216. Zhang KJ, Zhu WC, Rong X, Liu J, Ding XL, Hong XY. (2014). The complete mitochondrial genome sequence of Sogatella furcifera (Horva´th) and a comparative mitogenomic analysis of three predominant rice planthoppers. Gene 533:100–9. Zhang QL, Yuan ML, Shen YY. (2013). The complete mitochondrial genome of Dolycoris baccarum (Insecta: Hemiptera: Pentatomidae). Mitochondrial DNA 24:469–71.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Poratrioza sinica (Insecta: Hemiptera: Psyllidae) Qi-Lin Zhang, Zhong-Long Guo, and Ming-Long Yuan
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People’s Republic of China Abstract
Keywords
The complete mitochondrial genome (mitogenome) of Poratrioza sinica (Hemiptera: Psyllidae) has been sequenced and annotated in this study. This mitogenome is 14,863 bp in length with an A + T content of 72.0%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the putative ancestral insect mitogenome. All proteincoding genes start with ATN codons except for nad5, which uses TTG as the initial codon. All the transfer RNA genes have the typical cloverleaf structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm. The control region is 700 bp in length with 82.4% A + T content. This is the second completely sequenced mitogenome from the family Psyllidae of Hemiptera.
Insecta, mitogenome, Poratrioza sinica, psyllids, Sternorrhyncha
Psyllids (Hemiptera: Psyllidae) consist of about 1139 described species (Ouvrard, 2014), many of which are economically important pests around the world. Up to date, the complete mitochondrial genome (mitogenome) of only one psyllid (Pachypsylla venusta) has been determined (Thao et al., 2004). In this study, we sequenced the complete mitogenome of Poratrioza sinica (Hemiptera: Psyllidae), an important pest of Lycium chinense in China. The specimens of P. sinica were collected from Jingyuan County, Gansu Province, China. The entire P. sinica mitogenome was amplified with eight overlapping fragments by a set of universal and specific primer pairs (available from corresponding author on request), and sequenced in both directions. The mitogenome of P. sinica is a typical circular DNA molecule of 14,863 bp in length (GenBank accession number KJ650081). This genome is slightly larger than that of the samefamily species P. venusta (14,711 bp) (Thao et al., 2004). The P. sinica mitogenome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), the large and small ribosomal
Correspondence: Ming-Long Yuan, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People’s Republic of China. Tel: +86 9318915310. Fax: +86 9318915310. E-mail: [email protected]
History Received 3 April 2014 Accepted 5 April 2014 Published online 8 May 2014
RNA unit genes (rrnL and rrnS), and a large non-coding region (putative control region; Table 1). The order and orientation of the mitochondrial genes is identical to that of the putative ancestral insect mitogenome (Boore, 1999). Gene overlaps have been found at seven gene junctions and have involved a total of 40 bp; the longest overlap (12 bp) exists between trnE and trnF. A total of 55 bp intergenic spacers are present in the P. sinica mitogenome and are spread over seven positions, ranging in size from 1 to 31 bp. The nucleotide composition of the P. sinica mitogenome is significantly biased toward A and T. The total A + T content of the major strand is 72.0%, with a positive AT-skew (0.047) and a negative GC-skew ( 0.249). Among the 13 PCGs, the lowest A + T content is 67.5% in cox1, while the highest is 76.8% in nad4L. Twelve of the 13 PCGs start with a typical ATN codon: one (atp8) with ATC, three (atp6, cox3 and nad4) with ATG, three (nad2, cox2 and nad3) with ATT, five (cox1, nad4L, nad6, cob and nad1) with ATA. The only exception is nad5, which uses TTG as a start codon. This atypical codon has also been reported for many hemipteran species (Li et al., 2013; Zhang et al., 2013, 2014). Six PCGs stop with the complete termination codons TAA or TAG, and the remaining seven have incomplete termination codons TA or T. All of the 22 tRNAs, ranging from 54 to 71 bp, have a typical cloverleaf structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm. The loss of the DHU arm in trnS1 is a typical feature of metazoan mitogenomes (Wolstenholme, 1992). The size of rrnL and rrnS are 1159 bp and 802 bp long, respectively, with an A + T content of 75.1%. The control region is located at the conserved position between rrnS and trnI-trnQ-trnM gene cluster, and is 700 bp long with an A + T content of 82.4%.
2
Q.-L. Zhang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Annotation and organization of the complete mitochondrial genome of P. sinica.
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
Gene
Strand
Position
Length (bp)
J N J J J N N J J J J J J J J J J J J J J J N N N N N J N J J J N N N N N J
1–66 64–129 129–191 192–1161 1162–1232 1225–1286 1287–1350 1357–2895 2896–2959 2960–3623 3624–3693 3692–3757 3758–3910 3904–4577 4578–5360 5364–5422 5423–5771 5772–5833 5835–5895 5896–5960 5961–6014 6015–6076 6065–6126 6127–7750 7751–7810 7811–9050 9044–9328 9333–9394 9395–9454 9457–9939 9948–11,073 11,074–11,135 11,167–12,081 12,082–12,143 12,144–13,301 13,302–13,361 13,362–14,163 14,164–14,863
66 66 63 970 71 62 64 1539 64 664 70 66 153 674 783 59 349 62 61 65 54 62 62 1624 60 1240 285 62 60 483 1126 62 915 61 1159 60 802 700
trnI trnQ trnM nad2 trnW trnC trnY cox1 trnL2(UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnS1(AGN) trnE trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2(UCN) nad1 trnL1(CUN) rrnL trnV rrnS Control region
Intergenic nucleotides
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The study was funded by the Specialized Research Fund for the Doctoral Program of Higher Education of China (20120211120043), and the Fundamental Research Funds for the Central Universities (lzujbky-2012-91).
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Li T, Gao C, Cui Y, Xie Q, Bu W. (2013). The complete mitochondrial genome of the stalk-eyed bug Chauliops fallax Scott, and the monophyly of Malcidae (Hemiptera: Heteroptera). PLoS One 8: e55381.
0 3 1 0 0 8 0 6 0 0 0 2 0 7 0 3 0 0 1 0 0 0 12 0 0 0 7 4 0 2 8 0 31 0 0 0 0 0
Start codon
Stop codon
Anticodon GAU UUG CAU
ATT
T UCA GCA GUA
ATA
TAA
ATT
T
UAA CUU GUC ATC ATG ATG
TAA TA TAA
ATT
T
UCC UGC UCG GUU GCU UUC GAA TTG
T
ATG ATA
T TAG
GUG UGU UGG ATA ATA
TAA T
ATA
TAA
UGA UAG UAC
Ouvrard D. (2014). Psyl’list – The world psylloidea database. Available at: http://www.hemiptera-databases.com/psyllist (Accessed 31 March 2014). Thao ML, Baumann L, Baumann P. (2004). Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evol Biol 4:25. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. Int Rev Cytol 141:173–216. Zhang KJ, Zhu WC, Rong X, Liu J, Ding XL, Hong XY. (2014). The complete mitochondrial genome sequence of Sogatella furcifera (Horva´th) and a comparative mitogenomic analysis of three predominant rice planthoppers. Gene 533:100–9. Zhang QL, Yuan ML, Shen YY. (2013). The complete mitochondrial genome of Dolycoris baccarum (Insecta: Hemiptera: Pentatomidae). Mitochondrial DNA 24:469–71.
