http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.926498
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Sitobion avenae (Hemiptera: Aphididae) Bo Zhang1, Jincheng Zheng1, Lina Liang1, Susan Fuller2, and Chun-Sen Ma1 1
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/17/15 For personal use only.
Group of Climate Change Biology, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China and 2Science & Engineering Faculty, Queensland University of Technology, Brisbane, Qld, Australia
Abstract
Keywords
In this paper, we sequenced the complete mitogenome of the English grain aphid, Sitobion avenae. The mitogenome was mainly consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 large noncoding regions. The 15,180-bp mitogenome with a high A + T content (84.22%) was arranged in the same gene order as that of the ancestral insect. The repeat region between trnE and trnF included 1.29 copies of a 202 bp repeat unit. Characterization of the S. avenae mitogenome revealed architecture of one of important worldwide agricultural pests, thus advancing our understanding of insect mitogenomic diversities and further utilization in phylogenetic analysis.
Aphididae, mitochondrial genome, Sitobion avenae
The English grain aphid (Sitobion avenae) is a worldwide destructive aphid species in cereal production. It could cause a severe yield loss from 20–80% by direct sucking and transmitting virus diseases (Fereres et al., 1988; Trdan & Milevoj, 1999). The wide distribution and economic importance of this cereal pest has triggered the attention to its population genetic studies, efficient genetic markers however still remain limited (Llewellyn et al., 2003; Xu et al., 2011). In this study, we sequenced the complete mitochondrial genome of S. avenae to provide candidate markers for further population genetics and phylogenetic analysis. The full-length mitogenome of S. avenae was 15,180 bp in size (GenBank accession No. KJ742384), representing the shortest aphid mitogenome available to date. This mitogenome contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, a control region, and a repeat region (Table 1). These genes/regions were arranged in the same order as the inferred insect ancestral mitogenome (Boore, 1999), with the exception of the repeat region, which was reported exclusively in mitogenomes of the subfamily Aphidinae (Thao et al., 2004; Wang et al., 2014; Zhang et al., 2014). The overall nucleotide composition of S. avenae was highly A + T biased (84.22%). Six overlaps, totaling 34 bp, between adjacent genes were detected with the largest (14 bp) located between atp8 and atp6. A total of 14 non-coding regions involving 786 bp were present in S. avenae mitogenome. The largest non-coding region, i.e. the control region, was 430 bp in size with an A + T content of 93.02%. No tandem repeats larger than 50 bp were found in the control region. In the repeat region between trnE and trnF, a 202 bp repeat unit repeated 1.29 times, representing the lowest copy number in Aphidinae mitogenomes sequenced so far. All PCGs started with typical ATN codons,
Correspondence: Chun-Sen Ma, Group of Climate Change Biology, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China. Tel: +86 1062811430. E-mail: [email protected]
History Received 29 April 2014 Accepted 9 May 2014 Published online 12 June 2014
Table 1. The organization and annotation of S. avenae mitogenome.
Feature trnI trnQ trnM nad2 trnW trnC trnY cox1 trnL(UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnS (AGN) trnE repeat region trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS (UCN) nad1 trnL (CUN) rrnL trnV rrnS control region
Strand
Position
J N J J J N N J 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
1–64 62–127 135–201 202–1177 1178–1243 1236–1303 1307–1372 1374–2904 2905–2972 2973–3647 3650–3722 3723–3785 3786–3944 3931–4577 4578–5362 5363–5427 5428–5781 5782–5845 5845–5910 5911–5974 5974–6035 6039–6102 6101–6361 6362–6429 6430–8100 8151–8213 8214–9537 9531–9821 9823–9885 9888–9953 9955–10,448 10,449–11,567 11,572–11,636 11,647–12,582 12,583–12,647 12,648–13,910 13,911–13,972 13,986–14,750 14,751–15,180
Length Initiation Stop Intergenic (bp) codon codon Anticodon nucleotide 64 66 67 976 66 68 66 1531 68 675 73 63 159 647 785 65 354 64 66 64 62 64 261 68 1671 63 1324 291 63 66 494 1119 65 936 65 1263 62 765 430
GAT TTG CAT ATA
T– – TCA GCA GTA
ATA
T– –
ATC
TAA
TAA CTT GTC ATT ATA ATG
TAA TA– TA–
ATT
TAA
TCC TGC TCG GTT GCT TTC GAA ATT
TAA
ATA ATA
T– – TAA
GTG
TGT TGG ATT ATG
TA– TAA
ATT
TAA
TGA TAG TAC
– –3 7 0 0 –8 3 1 0 0 2 0 0 –14 0 0 0 0 –1 0 –1 3 –2 0 0 50 0 –7 1 2 1 0 4 10 0 0 0 13 0
2
B. Zhang et al.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/17/15 For personal use only.
while 6 out of the 13 PCGs terminated with incomplete stop codons (TA or T). The third codon positions (95.1%) exhibited a higher A + T content compared with the first (79.6%) and second (75%) codon positions. The large and small rRNA subunits (rrnL and rrnS) were located at trnL(CUN) to trnV and trnV to the control region, respectively. The rrnL gene was 1263 bp long with an A + T content of 85.59%; the corresponding values were 766 bp and 82.62% for rrnS. All the 22 tRNA genes, ranging in size from 62 bp [trnV and trnS (AGN)] to 73 bp (trnK), could be folded into typical clover-leaf secondary structures with the exception of trnS(AGN), of which the dihydrouridine arm formed a 8 bp loop rather than a stem. Six mismatched base pairs (1 A–A and 5 U–U) were present in the tRNA secondary structures in the T C stems of trnQ (1), trnW (2), trnE (1), and acceptor stem of trnL(UUR) (1) and trnD (1). Nineteen G–U wobble pairs were found in all four stems, including acceptor stem (4), T C stem (3), anticodon stem (3), DHU stem (9).
Declaration of interest The authors declare no conflicts of interests. The authors are responsible for the contents of the manuscript. This work was funded by the National Natural Science Foundation of China (31272035) and Beijing Natural Science Foundation (5144032).
Mitochondrial DNA, Early Online: 1–2
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Fereres A, Gutierrez C, Del Estal P, Castanera P. (1988). Impact of the english grain aphid, Sitobion avenae (F.) (Homoptera: Aphididae), on the yield of wheat plants subjected to water deficits. Environ Entomol 17:596–602. Llewellyn KS, Loxdale HD, Harrington R, Brookes CP, Clark SJ, Sunnucks P. (2003). Migration and genetic structure of the grain aphid (Sitobion avenae) in Britain related to climate and clonal fluctuation as revealed using microsatellites. Mol Ecol 12:21–34. Thao ML, Baumann L, Baumann P. (2004). Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evol Biol 4:25. Trdan A, Milevoj L. (1999). The cereal aphid as a wheat pest. SodobonoKmetijstro 32:119–28. Wang Y, Huang XL, Qiao GX. (2014). The complete mitochondrial genome of Cervaphis quercus (Insecta: Hemiptera: Aphididae: Greenideinae). Insect Sci 21:278–90. Xu ZH, Chen J, Cheng DF, Liu Y, Fre´de´ric, F. (2011). Genetic variation among the geographic population of the grain aphid, Sitobion avenae (Hemiptera: Aphididae) in China inferred from mitochondrial COI gene sequence. Agric Sci China 10:1041–8. Zhang B, Ma C, Edwards O, Fuller S, Kang L. (2014). The mitochondrial genome of the Russian wheat aphid Diuraphis noxia: Large repetitive sequences between trnE and trnF in aphids. Gene 533:253–60.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Sitobion avenae (Hemiptera: Aphididae) Bo Zhang1, Jincheng Zheng1, Lina Liang1, Susan Fuller2, and Chun-Sen Ma1 1
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/17/15 For personal use only.
Group of Climate Change Biology, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China and 2Science & Engineering Faculty, Queensland University of Technology, Brisbane, Qld, Australia
Abstract
Keywords
In this paper, we sequenced the complete mitogenome of the English grain aphid, Sitobion avenae. The mitogenome was mainly consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 large noncoding regions. The 15,180-bp mitogenome with a high A + T content (84.22%) was arranged in the same gene order as that of the ancestral insect. The repeat region between trnE and trnF included 1.29 copies of a 202 bp repeat unit. Characterization of the S. avenae mitogenome revealed architecture of one of important worldwide agricultural pests, thus advancing our understanding of insect mitogenomic diversities and further utilization in phylogenetic analysis.
Aphididae, mitochondrial genome, Sitobion avenae
The English grain aphid (Sitobion avenae) is a worldwide destructive aphid species in cereal production. It could cause a severe yield loss from 20–80% by direct sucking and transmitting virus diseases (Fereres et al., 1988; Trdan & Milevoj, 1999). The wide distribution and economic importance of this cereal pest has triggered the attention to its population genetic studies, efficient genetic markers however still remain limited (Llewellyn et al., 2003; Xu et al., 2011). In this study, we sequenced the complete mitochondrial genome of S. avenae to provide candidate markers for further population genetics and phylogenetic analysis. The full-length mitogenome of S. avenae was 15,180 bp in size (GenBank accession No. KJ742384), representing the shortest aphid mitogenome available to date. This mitogenome contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, a control region, and a repeat region (Table 1). These genes/regions were arranged in the same order as the inferred insect ancestral mitogenome (Boore, 1999), with the exception of the repeat region, which was reported exclusively in mitogenomes of the subfamily Aphidinae (Thao et al., 2004; Wang et al., 2014; Zhang et al., 2014). The overall nucleotide composition of S. avenae was highly A + T biased (84.22%). Six overlaps, totaling 34 bp, between adjacent genes were detected with the largest (14 bp) located between atp8 and atp6. A total of 14 non-coding regions involving 786 bp were present in S. avenae mitogenome. The largest non-coding region, i.e. the control region, was 430 bp in size with an A + T content of 93.02%. No tandem repeats larger than 50 bp were found in the control region. In the repeat region between trnE and trnF, a 202 bp repeat unit repeated 1.29 times, representing the lowest copy number in Aphidinae mitogenomes sequenced so far. All PCGs started with typical ATN codons,
Correspondence: Chun-Sen Ma, Group of Climate Change Biology, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China. Tel: +86 1062811430. E-mail: [email protected]
History Received 29 April 2014 Accepted 9 May 2014 Published online 12 June 2014
Table 1. The organization and annotation of S. avenae mitogenome.
Feature trnI trnQ trnM nad2 trnW trnC trnY cox1 trnL(UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnS (AGN) trnE repeat region trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS (UCN) nad1 trnL (CUN) rrnL trnV rrnS control region
Strand
Position
J N J J J N N J 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
1–64 62–127 135–201 202–1177 1178–1243 1236–1303 1307–1372 1374–2904 2905–2972 2973–3647 3650–3722 3723–3785 3786–3944 3931–4577 4578–5362 5363–5427 5428–5781 5782–5845 5845–5910 5911–5974 5974–6035 6039–6102 6101–6361 6362–6429 6430–8100 8151–8213 8214–9537 9531–9821 9823–9885 9888–9953 9955–10,448 10,449–11,567 11,572–11,636 11,647–12,582 12,583–12,647 12,648–13,910 13,911–13,972 13,986–14,750 14,751–15,180
Length Initiation Stop Intergenic (bp) codon codon Anticodon nucleotide 64 66 67 976 66 68 66 1531 68 675 73 63 159 647 785 65 354 64 66 64 62 64 261 68 1671 63 1324 291 63 66 494 1119 65 936 65 1263 62 765 430
GAT TTG CAT ATA
T– – TCA GCA GTA
ATA
T– –
ATC
TAA
TAA CTT GTC ATT ATA ATG
TAA TA– TA–
ATT
TAA
TCC TGC TCG GTT GCT TTC GAA ATT
TAA
ATA ATA
T– – TAA
GTG
TGT TGG ATT ATG
TA– TAA
ATT
TAA
TGA TAG TAC
– –3 7 0 0 –8 3 1 0 0 2 0 0 –14 0 0 0 0 –1 0 –1 3 –2 0 0 50 0 –7 1 2 1 0 4 10 0 0 0 13 0
2
B. Zhang et al.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/17/15 For personal use only.
while 6 out of the 13 PCGs terminated with incomplete stop codons (TA or T). The third codon positions (95.1%) exhibited a higher A + T content compared with the first (79.6%) and second (75%) codon positions. The large and small rRNA subunits (rrnL and rrnS) were located at trnL(CUN) to trnV and trnV to the control region, respectively. The rrnL gene was 1263 bp long with an A + T content of 85.59%; the corresponding values were 766 bp and 82.62% for rrnS. All the 22 tRNA genes, ranging in size from 62 bp [trnV and trnS (AGN)] to 73 bp (trnK), could be folded into typical clover-leaf secondary structures with the exception of trnS(AGN), of which the dihydrouridine arm formed a 8 bp loop rather than a stem. Six mismatched base pairs (1 A–A and 5 U–U) were present in the tRNA secondary structures in the T C stems of trnQ (1), trnW (2), trnE (1), and acceptor stem of trnL(UUR) (1) and trnD (1). Nineteen G–U wobble pairs were found in all four stems, including acceptor stem (4), T C stem (3), anticodon stem (3), DHU stem (9).
Declaration of interest The authors declare no conflicts of interests. The authors are responsible for the contents of the manuscript. This work was funded by the National Natural Science Foundation of China (31272035) and Beijing Natural Science Foundation (5144032).
Mitochondrial DNA, Early Online: 1–2
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Fereres A, Gutierrez C, Del Estal P, Castanera P. (1988). Impact of the english grain aphid, Sitobion avenae (F.) (Homoptera: Aphididae), on the yield of wheat plants subjected to water deficits. Environ Entomol 17:596–602. Llewellyn KS, Loxdale HD, Harrington R, Brookes CP, Clark SJ, Sunnucks P. (2003). Migration and genetic structure of the grain aphid (Sitobion avenae) in Britain related to climate and clonal fluctuation as revealed using microsatellites. Mol Ecol 12:21–34. Thao ML, Baumann L, Baumann P. (2004). Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evol Biol 4:25. Trdan A, Milevoj L. (1999). The cereal aphid as a wheat pest. SodobonoKmetijstro 32:119–28. Wang Y, Huang XL, Qiao GX. (2014). The complete mitochondrial genome of Cervaphis quercus (Insecta: Hemiptera: Aphididae: Greenideinae). Insect Sci 21:278–90. Xu ZH, Chen J, Cheng DF, Liu Y, Fre´de´ric, F. (2011). Genetic variation among the geographic population of the grain aphid, Sitobion avenae (Hemiptera: Aphididae) in China inferred from mitochondrial COI gene sequence. Agric Sci China 10:1041–8. Zhang B, Ma C, Edwards O, Fuller S, Kang L. (2014). The mitochondrial genome of the Russian wheat aphid Diuraphis noxia: Large repetitive sequences between trnE and trnF in aphids. Gene 533:253–60.
