http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919474
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Aphis gossypii Glover (Hemiptera: Aphididae) Shuai Zhang, Junyu Luo, Chunyi Wang, Limin Lv, Chunhua Li, Weili Jiang, Jinjie Cui, and Lubna Bashir Rajput
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 04/18/15 For personal use only.
State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, People’s Republic of China Abstract
Keywords
The complete mitochondrial genome of the cotton-melon aphid, Aphis gossypii Glover, was sequenced using a combination of high-throughput sequencing, traditional PCR amplification, and Sanger sequencing. The genome is 15,869 bp in length, and contains 37 typical coding genes, one non-coding AT-rich region, and a repeat region found exclusively in aphids. The base composition of the genome is A (45.4%), T (38.3%), C (10.4%), and G (5.9%). All protein coding genes start with a typical ATN initiation codon; all genes use the standard termination codon (TAA) except ND4 that ends with a single TA.
Aphis gossypii, Aphididae, Hemiptera, mitochondrial genome
The cotton-melon aphid, Aphis gossypii Glover is a worldwide insect pest that damages important crops including melon, cotton, potato, chili pepper, sweet pepper, and eggplant (Carletto et al., 2009). A. gossypii is very diverse in terms of geographical range, life cycle, and host plant spectrum (Carletto et al., 2009). Inaizumi listed 912 possible host plant species belonging to 116 different botanical families (Ininaizumi, 1980). Five A. gossypii host races have been
History Received 17 April 2014 Accepted 26 April 2014 Published online 27 May 2014
identified using microsatellites to analyze the genetic diversity of aphids collected over several years on a large geographical scale from annual crops from different plant families (Carletto et al., 2009). To further our understanding of aphid molecular evolution, phylogenetics, and population genetics, we determined the complete mitogenome sequence of A. gossypii collected on cotton.
Table 1. Organization of the A. gossypii mitochondrial genome. Gene name COI tRNALeu COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly ND3 tRNAAla tRNAArg tRNAAsn tRNALeu tRNAGlu Repeat region tRNAPhe ND5 tRNAHis ND4 ND4L
Direction J J J J J J J J J J J J J J J J N N N N N
Position 1–1566 1562–1629 1633–2304 2307–2379 2380–2442 2452–2601 2582–3235 3235–4020 4020–4082 4083–4436 4437–4500 4500–4564 4564–4627 4633–4708 4691–4752 4747–5530 5519–5582 5583–7253 7309–7372 7372–8681 8690–8980
Size (bp)
Anti/start codon
Stop codon
1563 68 672 73 63 150 654 786 63 354 64 65 64 76 62 784 64 1671 64 1310 291
ATT TAA ATA CTT GTC ATA ATT ATG TCC ATT TGC TCG GTT TAA TTC
TAA
GAA ATT GTG ATA ATA
TAA TAA TAA TAA TAA
TAA TA– TAA
Intergenic nucleotides* 5 3 2 0 9 20 1 1 0 0 1 1 5 18 6 12 0 55 1 8 (continued )
Correspondence: Jinjie Cui, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, People’s Republic of China. Tel: +86 3722562217. E-mail: [email protected]
2
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Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Gene name
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 04/18/15 For personal use only.
Thr
tRNA tRNAPro ND6 Cytb tRNASer ND1 tRNALeu lrRNA tRNAVal srRNA AT-rich region tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNACys tRNATyr
Direction
Position
Size (bp)
Anti/start codon
J N J J J N N N N N
8982–9043 9047–9114 9116–9607 9611–10,726 10,733–10,798 10,809–11,744 11,745–11,809 11,810–13,069 13,055–13,131 13,142–13,909 13,916–14,542 14,537–14,600 14,598–14,663 14,668–14,733 14,734–15,711 15,710–15,771 15,764–15,830 15,832–15,869 & 1–29
62 68 492 1116 66 936 65 1260 77 768 627 64 66 66 978 62 67 66
TGT TGG ATT ATG TGA ATT TAG
J N J J J N N
Stop codon
Intergenic nucleotides*
TAA TAA TAA
TAC GAT TTG CAT ATT TCA GCA GTA
TAA
1 3 1 3 6 10 0 0 15 10 6 6 3 4 0 2 8 1
*A positive number indicates the base-pair interval between genes; a negative number indicates overlapping base-pairs between genes.
Sequences of putative mitogenome fragments were identified in cotton-melon aphid transcriptome data (Li et al., 2013). Primers were designed according to the identified sequences and PCR template DNA was extracted from single A. gossypii (collected on cotton, 36 040 57.5500 N, 114 300 33.7400 E). Fragments of the mitogenomes were amplified by long-distance PCR using LA Taq (Takara Bio, Dalian, China) and sequenced in both directions. The programs tRNAscan-SE 1.21 and ARWEN v1.2.3 (Laslett & Canback, 2008; Lowe & Eddy, 1997) were used for transfer RNA (tRNA) prediction. The complete mitogenome of A. gossypii is a circular molecule, 15,869 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes (rrnL and rrnS), 22 tRNA genes, one major non-coding AT-rich region, and a repeat region found uniquely in aphids (Table 1). Overall, the A. gossypii mitogenome has a high A + T content of 83.7% (A ¼ 45.4%; T ¼ 38.3%; C ¼ 10.4%; G ¼ 5.9%), which is within the range of values observed in three other aphids (83.9–84.7%) (Wang et al., 2013). The gene order within A. gossypii mitogenome is highly conserved with that of Cavariella salicicola, except for a position change of one tRNA (tRNASer to tRNALeu). All protein-coding genes are initiated by a typical ATN codon, and all genes use the standard termination codon (TAA), except ND4 that ends with a single TA (Table 1). Such incomplete stop codons have been found frequently in most insect mitogenomes sequenced to date (Wang et al., 2014). The aphid-specific mitogenome tandem repeat exists in the A. gossypii mitogenome. The repeat region includes three 196-bp tandem repeats (near tRNAGlu) and one 189-bp copy of the anterior portion of the repeat unit. It has a different composition, length, and number among the three aphids in which it is known to be present (Wang et al., 2013).
Nucleotide sequence accession number The complete mitogenome sequence of A. gossypii has been assigned GenBank accession number KJ669654.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. This study was supported by the National Natural Science Foundation of China (31201518) and grants from the Ministry of Agriculture, China (2014ZX08011-002).
References Carletto J, Lombaert E, Chavigny P, Brevault T, Lapchin L, Vanlerberghe-Masutti F. (2009). Ecological specialization of the aphid Aphis gossypii Glover on cultivated host plants. Mol Ecol 18: 2198–212. Ininaizumi M. (1980). Studies on the life-cycle and polymorphism of Aphis gossypii Glover (Homoptera, Aphididae). Spec Bull Coll Agriculture, Utsunomia University 37:1–132. Laslett D, Canback B. (2008). ARWEN: A program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24: 172–5. Li ZQ, Zhang S, Luo JY, Wang CY, Lv LM, Dong SL, Cui JJ. (2013). Ecological adaption analysis of the cotton Aphid (Aphis gossypii) in different phenotypes by transcriptome comparison. PLoS One 8: e83180. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Wang Y, Huang XL, Qiao GX. (2013). Comparative analysis of mitochondrial genomes of five Aphid species (Hemiptera: Aphididae) and phylogenetic implications. PLoS One 8:e77511. Wang Y, Peng C, Yao Q, Shi Q, Hao J. (2014). The complete mitochondrial genome of Gonepteryx rhamni (Lepidoptera: Pieridae: Coliadinae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.855755.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Aphis gossypii Glover (Hemiptera: Aphididae) Shuai Zhang, Junyu Luo, Chunyi Wang, Limin Lv, Chunhua Li, Weili Jiang, Jinjie Cui, and Lubna Bashir Rajput
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 04/18/15 For personal use only.
State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, People’s Republic of China Abstract
Keywords
The complete mitochondrial genome of the cotton-melon aphid, Aphis gossypii Glover, was sequenced using a combination of high-throughput sequencing, traditional PCR amplification, and Sanger sequencing. The genome is 15,869 bp in length, and contains 37 typical coding genes, one non-coding AT-rich region, and a repeat region found exclusively in aphids. The base composition of the genome is A (45.4%), T (38.3%), C (10.4%), and G (5.9%). All protein coding genes start with a typical ATN initiation codon; all genes use the standard termination codon (TAA) except ND4 that ends with a single TA.
Aphis gossypii, Aphididae, Hemiptera, mitochondrial genome
The cotton-melon aphid, Aphis gossypii Glover is a worldwide insect pest that damages important crops including melon, cotton, potato, chili pepper, sweet pepper, and eggplant (Carletto et al., 2009). A. gossypii is very diverse in terms of geographical range, life cycle, and host plant spectrum (Carletto et al., 2009). Inaizumi listed 912 possible host plant species belonging to 116 different botanical families (Ininaizumi, 1980). Five A. gossypii host races have been
History Received 17 April 2014 Accepted 26 April 2014 Published online 27 May 2014
identified using microsatellites to analyze the genetic diversity of aphids collected over several years on a large geographical scale from annual crops from different plant families (Carletto et al., 2009). To further our understanding of aphid molecular evolution, phylogenetics, and population genetics, we determined the complete mitogenome sequence of A. gossypii collected on cotton.
Table 1. Organization of the A. gossypii mitochondrial genome. Gene name COI tRNALeu COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly ND3 tRNAAla tRNAArg tRNAAsn tRNALeu tRNAGlu Repeat region tRNAPhe ND5 tRNAHis ND4 ND4L
Direction J J J J J J J J J J J J J J J J N N N N N
Position 1–1566 1562–1629 1633–2304 2307–2379 2380–2442 2452–2601 2582–3235 3235–4020 4020–4082 4083–4436 4437–4500 4500–4564 4564–4627 4633–4708 4691–4752 4747–5530 5519–5582 5583–7253 7309–7372 7372–8681 8690–8980
Size (bp)
Anti/start codon
Stop codon
1563 68 672 73 63 150 654 786 63 354 64 65 64 76 62 784 64 1671 64 1310 291
ATT TAA ATA CTT GTC ATA ATT ATG TCC ATT TGC TCG GTT TAA TTC
TAA
GAA ATT GTG ATA ATA
TAA TAA TAA TAA TAA
TAA TA– TAA
Intergenic nucleotides* 5 3 2 0 9 20 1 1 0 0 1 1 5 18 6 12 0 55 1 8 (continued )
Correspondence: Jinjie Cui, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, People’s Republic of China. Tel: +86 3722562217. E-mail: [email protected]
2
S. Zhang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Gene name
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 04/18/15 For personal use only.
Thr
tRNA tRNAPro ND6 Cytb tRNASer ND1 tRNALeu lrRNA tRNAVal srRNA AT-rich region tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNACys tRNATyr
Direction
Position
Size (bp)
Anti/start codon
J N J J J N N N N N
8982–9043 9047–9114 9116–9607 9611–10,726 10,733–10,798 10,809–11,744 11,745–11,809 11,810–13,069 13,055–13,131 13,142–13,909 13,916–14,542 14,537–14,600 14,598–14,663 14,668–14,733 14,734–15,711 15,710–15,771 15,764–15,830 15,832–15,869 & 1–29
62 68 492 1116 66 936 65 1260 77 768 627 64 66 66 978 62 67 66
TGT TGG ATT ATG TGA ATT TAG
J N J J J N N
Stop codon
Intergenic nucleotides*
TAA TAA TAA
TAC GAT TTG CAT ATT TCA GCA GTA
TAA
1 3 1 3 6 10 0 0 15 10 6 6 3 4 0 2 8 1
*A positive number indicates the base-pair interval between genes; a negative number indicates overlapping base-pairs between genes.
Sequences of putative mitogenome fragments were identified in cotton-melon aphid transcriptome data (Li et al., 2013). Primers were designed according to the identified sequences and PCR template DNA was extracted from single A. gossypii (collected on cotton, 36 040 57.5500 N, 114 300 33.7400 E). Fragments of the mitogenomes were amplified by long-distance PCR using LA Taq (Takara Bio, Dalian, China) and sequenced in both directions. The programs tRNAscan-SE 1.21 and ARWEN v1.2.3 (Laslett & Canback, 2008; Lowe & Eddy, 1997) were used for transfer RNA (tRNA) prediction. The complete mitogenome of A. gossypii is a circular molecule, 15,869 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes (rrnL and rrnS), 22 tRNA genes, one major non-coding AT-rich region, and a repeat region found uniquely in aphids (Table 1). Overall, the A. gossypii mitogenome has a high A + T content of 83.7% (A ¼ 45.4%; T ¼ 38.3%; C ¼ 10.4%; G ¼ 5.9%), which is within the range of values observed in three other aphids (83.9–84.7%) (Wang et al., 2013). The gene order within A. gossypii mitogenome is highly conserved with that of Cavariella salicicola, except for a position change of one tRNA (tRNASer to tRNALeu). All protein-coding genes are initiated by a typical ATN codon, and all genes use the standard termination codon (TAA), except ND4 that ends with a single TA (Table 1). Such incomplete stop codons have been found frequently in most insect mitogenomes sequenced to date (Wang et al., 2014). The aphid-specific mitogenome tandem repeat exists in the A. gossypii mitogenome. The repeat region includes three 196-bp tandem repeats (near tRNAGlu) and one 189-bp copy of the anterior portion of the repeat unit. It has a different composition, length, and number among the three aphids in which it is known to be present (Wang et al., 2013).
Nucleotide sequence accession number The complete mitogenome sequence of A. gossypii has been assigned GenBank accession number KJ669654.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. This study was supported by the National Natural Science Foundation of China (31201518) and grants from the Ministry of Agriculture, China (2014ZX08011-002).
References Carletto J, Lombaert E, Chavigny P, Brevault T, Lapchin L, Vanlerberghe-Masutti F. (2009). Ecological specialization of the aphid Aphis gossypii Glover on cultivated host plants. Mol Ecol 18: 2198–212. Ininaizumi M. (1980). Studies on the life-cycle and polymorphism of Aphis gossypii Glover (Homoptera, Aphididae). Spec Bull Coll Agriculture, Utsunomia University 37:1–132. Laslett D, Canback B. (2008). ARWEN: A program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24: 172–5. Li ZQ, Zhang S, Luo JY, Wang CY, Lv LM, Dong SL, Cui JJ. (2013). Ecological adaption analysis of the cotton Aphid (Aphis gossypii) in different phenotypes by transcriptome comparison. PLoS One 8: e83180. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Wang Y, Huang XL, Qiao GX. (2013). Comparative analysis of mitochondrial genomes of five Aphid species (Hemiptera: Aphididae) and phylogenetic implications. PLoS One 8:e77511. Wang Y, Peng C, Yao Q, Shi Q, Hao J. (2014). The complete mitochondrial genome of Gonepteryx rhamni (Lepidoptera: Pieridae: Coliadinae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.855755.
