ArticlePDF Available

The complete mitochondrial genome of Paracolopha morrisoni (Baker, 1919) (Hemiptera: Aphididae)

Authors:

Abstract

We have determined the mitochondrial genome of Paracolopha morrisoni (Baker, 1919), a gall-forming aphid collected from Korea. The circular mitogenome of Paracolopha morrisoni is 16,330 bp long including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 932 bp. The base composition was AT-biased (84.9%). Gene order of P. morrisoni is identical to all other aphid mitochondrial genomes. Phylogenetic trees show that P. morrisoni is sister to Eriosoma lanigerum both belonging to tribe. The mitochondrial genome of P. morrisoni will be useful in understanding the genetic backgrounds of the species.
Full Terms & Conditions of access and use can be found at
https://www.tandfonline.com/action/journalInformation?journalCode=tmdn20
Mitochondrial DNA Part B
Resources
ISSN: (Print) 2380-2359 (Online) Journal homepage: https://www.tandfonline.com/loi/tmdn20
The complete mitochondrial genome of
Paracolopha morrisoni (Baker, 1919) (Hemiptera:
Aphididae)
Jieun Lee, Jonghyun Park, Hyobin Lee, Jongsun Park & Wonhoon Lee
To cite this article: Jieun Lee, Jonghyun Park, Hyobin Lee, Jongsun Park & Wonhoon Lee
(2019) The complete mitochondrial genome of Paracolopha�morrisoni (Baker, 1919) (Hemiptera:
Aphididae), Mitochondrial DNA Part B, 4:2, 3037-3039, DOI: 10.1080/23802359.2019.1666046
To link to this article: https://doi.org/10.1080/23802359.2019.1666046
© 2019 The Author(s). Published by Informa
UK Limited, trading as Taylor & Francis
Group.
Published online: 18 Sep 2019.
Submit your article to this journal
View related articles
View Crossmark data
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Paracolopha morrisoni (Baker, 1919)
(Hemiptera: Aphididae)
Jieun Lee
a
, Jonghyun Park
b,c
, Hyobin Lee
a
, Jongsun Park
b,c
and Wonhoon Lee
a,d
a
Department of Plant Medicine, Gyeongsang National University, Jinju, The Republic of Korea;
b
InfoBoss Co., Ltd, Seoul, The Republic of
Korea;
c
InfoBoss Research Center, Seoul, The Republic of Korea;
d
Institute of Agriculture & Life Science, Gyeongsang National University,
Jinju, The Republic of Korea
ABSTRACT
We have determined the mitochondrial genome of Paracolopha morrisoni (Baker, 1919), a gall-forming
aphid collected from Korea. The circular mitogenome of Paracolopha morrisoni is 16,330 bp long includ-
ing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding
region of 932bp. The base composition was AT-biased (84.9%). Gene order of P. morrisoni is identical
to all other aphid mitochondrial genomes. Phylogenetic trees show that P. morrisoni is sister to
Eriosoma lanigerum both belonging to tribe. The mitochondrial genome of P. morrisoni will be useful in
understanding the genetic backgrounds of the species.
ARTICLE HISTORY
Received 2 August 2019
Accepted 16 August 2019
KEYWORDS
Paracolopha morrisoni;
mitochondrial genome;
Eriosomatinae;
Aphididae; Korea
Paracolopha morrisoni is an aphid widely occurring in eastern
Asian countries (China, Japan, and Korea), Unites States
(Maryland, and South Carolina), and Europe (Belgium. Britain,
Italy, and The Netherlands; Si 1985;Malumphy2012). In Asia, P.
morrisoni are known to be heteroecious, altering their hosts
from a primary host Zelkova serrata to the secondary host,
bamboo (Sasa spp.; Si 1985). Outside of Asia on the other
hand, they are only found on roots of bamboo species, both
introduced (Phyllostachys and Pleioblastus spp., native to China)
and native species (Arundinaria gigantea,nativetotheUS).
Since P. morrisoni, in America and Europe, are mostly found in
cultivated bamboos and do not alternate hosts, it has been
believed these aphids originated in east Asia but were intro-
duced overseas hitchhiking international trades of host plants.
This is not completely confirmed, however, since the North
American populations show novel characteristics such as alates
occurringinspring(Si1985). To understand genetic back-
ground of this species, we determined the complete mitochon-
drial genome of P. morrisoni collected from South Korea.
Total DNA of P. morrisoni was extracted from wingless
females collected on Zelkova serrata from Haymang-gun,
Gyeongsangnam-do, Korea in 2019 (355402000 N, 1267608400 E;
the specimen is stored in Gyeongsang National University,
Korea accession number: Coll#JE147) using DNeasy Brood &
Tissue Kit (QIAGEN, Hilden, Germany). Raw sequences obtained
from Illumina HiSeqX at Macrogen Inc., Korea, were filtered by
Trimmomatic 0.33 (Bolger et al. 2014)andde novo assembled
and confirmed by Velvet 1.2.10 (Zerbino and Birney 2008),
SOAPGapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17 (Li et al.
2009), and SAMtools 1.9 (Li 2013). Geneious R11 11.1.5
(Biomatters Ltd., Auckland, New Zealand) was used for annota-
tion based on that of Eriosoma lanigerum (NC_033352). ARWEN
(Laslett and Canb
ack 2008) was used to annotate tRNAs.
Paracolopha morrisoni mitochondrial genome length
(Genbank accession is MN167467) is 16,330 bp and GC ratio
is 15.1%, showing AT-biased. It contains 13 protein-coding
genes, 2 rRNAs, and 22 tRNAs. The tRNAs size ranges from 53
to 73 bp, similar to other aphids (5290 bp). Gene order of
P. morrisoni is identical to that of all other aphid mitoge-
nomes which are apparently the ancestral gene order of all
insects (Wang et al. 2013).
All available complete mitochondrial genomes of 34
aphids including P. morrisoni and Bembisia tabaci
(NC_006279) as an outgroup were aligned by MAFFT 7.388
(Katoh and Standley 2013). Bootstrapped maximum-likelihood
(bootstrap repeat is 1000) and neighbor-joining (bootstrap
repeat is 10,000) trees were constructed using MEGA X
(Kumar et al. 2018). Phylogenetic trees show that all valid
aphid tribes are monophyletic with P. morrisoni in Erisomatini
(Figure 1). However, our tree topologies also presented
Erisomatini grouped with Greenideidae resulting in paraphy-
letic manner of subfamily Eristomatinae, which is not the first
time to be reported (Nov
akov
a et al. 2013). Our mitochon-
drial genome will be a key resource in understanding the
genetic backgrounds and phylogenetic position of
P. morrisoni.
CONTACT Jongsun Park starflr@infoboss.co.kr InfoBoss Co., Ltd., 301 Room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul 06088, The Republic of
Korea; Wonhoon Lee wonhoon@gnu.ac.kr Department of Plant Medicine, Gyeongsang National University, Jinjudaero 501, Jinju 52828, The Republic
of Korea
Co-first authors.
ß2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
MITOCHONDRIAL DNA PART B
2019, VOL. 4, NO. 2, 30373039
https://doi.org/10.1080/23802359.2019.1666046
Disclosure statement
The authors declare that they have no competing interests.
Funding
This research was supported by Research of Animal and Plant
Quarantine Agency of South Korea Fund [1545018425].
ORCID
Jongsun Park http://orcid.org/0000-0003-0786-4701
References
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for
Illumina sequence data. Bioinformatics. 30:21142120.
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment soft-
ware version 7: improvements in performance and usability. Mol Biol
Evol. 30:772780.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular
Evolutionary Genetics Analysis across computing platforms. Mol Biol
Evol. 35:15471549.
Laslett D, Canb
ack B. 2008. ARWEN: a program to detect tRNA genes in
metazoan mitochondrial nucleotide sequences. Bioinformatics. 24:172175.
Li H. 2013. Aligning sequence reads, clone sequences and assembly con-
tigs with BWA-MEM. Genomics. Preprint at https://arxiv.org/abs/1303.
3997
Figure 1. Maximum-likelihood (bootstrap repeat is 1000) and neighbor-joining (bootstrap repeat is 10,000) phylogenetic trees of 34 aphids and one whitefly mito-
chondrial genomes: Paracolopha morrisoni (MN167467, this study), Acyrthosiphon pisum (NC_011594), Sitobion avenae (NC_024683), Myzus persicae (NC_029727,
KU877171), Diuraphis noxia (NC_022727), Cavariella salicicola (NC_022682), Schizaphis graminum (NC_006158), Aphis gossypii(NC_024581), Aphis fabae mordvilkoi
(NC_039988), Aphis craccivora (NC_031387, KX447142), Hormaphis betula (NC_029495), Cervaphis quercus (NC_024926), Greenidea psidii (NC_041198), Eriosoma lani-
gerum (NC_033352), Baizongia pistaciae (NC_035314), Nurudea yanoniella (NC_035313, MK435595), Nurudea shiraii (NC_035301), Melaphis rhois (NC_036065),
Nurudea ibofushi (NC_035311), Schlechtendalia chinensis (NC_032386), Schlechtendalia peitan (NC_035302), Nurudea choui (NC_035310), Nurudea meitanensis
(NC_035316), Schlechtendalia elongallis (NC_035315), Schlechtendalia flavogallis (NC_035312), Kaburagia rhusicola ovatirhusicola (MF043985), Kaburagia rhusicola
ensigallis (MF043984), Kaburagia rhusicola ovagallis (MF043986), Kaburagia rhusicola rhusicola (MF043987), Mindarus keteleerifoliae (NC_033410), Appendiseta robiniae
(NC_042165), and Bemisia tabaci (NC_006279) as an outgroup. Phylogenetic tree was drawn based on the maximum-likelihood tree. The numbers above branches
indicate bootstrap support values of maximum-likelihood and neighbor joining phylogenetic tree, respectively.
3038 J. LEE ET AL.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G,
Abecasis G, Durbin R. 2009. The sequence alignment/map format and
SAMtools. Bioinformatics. 25:20782079.
Malumphy C. 2012. Paracolopha morrisoni (Hemiptera: Aphididae,
Pemphiginae), an Asian aphid established in Britain. British J Entomol
Nat Hist. 25:7983.
Nov
akov
a E, Hyp
sa V, Klein J, Foottit RG, von Dohlen CD, Moran NA.
2013. Reconstructing the phylogeny of aphids (Hemiptera: Aphididae)
using DNA of the obligate symbiont Buchnera aphidicola. Mol
Phylogenet Evol. 68:4254.
Si A. 1985. Taxonomic study on gall aphids, Colopha,Paracolopha and
Kaltenbachiella (Aphidoidea: Pemphigidae) in East Asia, with special
reference to their origins and distributional patterns. Insecta
Matsumurana New Series: J Faculty Agric Hokkaido University, Series
Entomol. 31:179.
Wang Y, Huang X-L, Qiao G-X. 2013. Comparative analysis of mitochon-
drial genomes of five aphid species (Hemiptera: Aphididae) and phylo-
genetic implications. PLoS One. 8:e77511.
Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo
short read assembly using de Bruijn graphs. Genome Res. 18:
821829.
Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P. 2011. Optimizing de
novo transcriptome assembly from short-read RNA-Seq data: a com-
parative study. BMC Bioinformatics. 12:S2.
MITOCHONDRIAL DNA PART B 3039
... Recent rapid development and utilization of next-generation sequencing (NGS) technologies have driven us to generate a large amount of NGS raw read sequences for various purposes, 1-3 such as the sequencing of the whole genome, 4-6 organelle genomes, [7][8][9] and phylogenetic and phylogenomic studies. 10,11 NGS raw read sequences can provide additional research opportunities because usually they cover almost all genomic DNA. ...
Article
Full-text available
Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylo-genetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mito-chondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.
Article
Full-text available
We have sequenced mitochondrial genome of Uroleucon erigeronense (Thomas, 1878) isolated from Erigeron canadensis in Korea. The circular mitogenome of U. erigeronense is 15,691 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single control region of 968 bp. AT ratio is 84.2%. Additional phylogenetic studies of aphid mitogenomes are required due to the inconsistency found in the three phylogenetic trees.
Article
Full-text available
Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.
Article
Full-text available
Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.
Article
Full-text available
In this study, the complete mitochondrial genome of the pest aphid Greenidea ficicola was determined. The mitogenome was 17,361 bp in length, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 long control region located between srRNA and tRNAIle, and a repeat region located between tRNAGlu and tRNAPhe. Thirteen protein-coding genes have typical ATN start codon and TAA termination codon. All tRNAs were predicted to contain typical clover-leaf secondary structures except tRNASer(gct). The length of lrRNA and srRNA are 1270 bp and 773 bp, respectively. Phylogenetic analysis shows that Greenideinae speices form a highly supported clade.
Article
Full-text available
Rhopalosiphum nymphaeae (Linnaeus, 1761) is a heteroecious polyphagous aphid, which can survive underwater. We have determined mitochondrial genome of R. nymphaeae collected in Korea. The circular mitogenome of R. nymphaeae is 15,594 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 874 bp. The base composition was AT-biased (84.3%). Phylogenetic trees present that genus Rhopalosiphum is polyphyletic, requiring more investigation of mitochondrial genomes.
Article
Full-text available
The molecular evolutionary genetics analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
Article
Full-text available
Although many NGS read pre-processing tools already existed, we could not find any tool or combination of tools which met our requirements in terms of flexibility, correct handling of paired-end data, and high performance. We have developed Trimmomatic as a more flexible and efficient pre-processing tool, which could correctly handle paired-end data. The value of NGS read pre-processing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output which is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available from http://www.usadellab.org/cms/index.php?page=trimmomatic CONTACT: usadel@bio1.rwth-aachen.de SUPPLEMENTARY INFORMATION: Manual and source code are available from http://www.usadellab.org/cms/index.php?page=trimmomatic.
Article
Full-text available
Insect mitochondrial genomes (mitogenomes) are of great interest in exploring molecular evolution, phylogenetics and population genetics. Only two mitogenomes have been previously released in the insect group Aphididae, which consists of about 5,000 known species including some agricultural, forestry and horticultural pests. Here we report the complete 16,317 bp mitogenome of Cavariella salicicola and two nearly complete mitogenomes of Aphis glycines and Pterocomma pilosum. We also present a first comparative analysis of mitochondrial genomes of aphids. Results showed that aphid mitogenomes share conserved genomic organization, nucleotide and amino acid composition, and codon usage features. All 37 genes usually present in animal mitogenomes were sequenced and annotated. The analysis of gene evolutionary rate revealed the lowest and highest rates for COI and ATP8, respectively. A unique repeat region exclusively in aphid mitogenomes, which included variable numbers of tandem repeats in a lineage-specific manner, was highlighted for the first time. This region may have a function as another origin of replication. Phylogenetic reconstructions based on protein-coding genes and the stem-loop structures of control regions confirmed a sister relationship between Cavariella and pterocommatines. Current evidence suggest that pterocommatines could be formally transferred into Macrosiphini. Our paper also offers methodological instructions for obtaining other Aphididae mitochondrial genomes.
Article
Full-text available
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Article
Full-text available
With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected assembly outcomes, and there was no consensus on how to approach an optimal solution by selecting software tool and suitable strategy based on the properties of RNA-Seq data. To reveal the performance of different programs for transcriptome assembly, this work analyzed some important factors, including k-mer values, genome complexity, coverage depth, directional reads, etc. Seven program conditions, four single k-mer assemblers (SK: SOAPdenovo, ABySS, Oases and Trinity) and three multiple k-mer methods (MK: SOAPdenovo-MK, trans-ABySS and Oases-MK) were tested. While small and large k-mer values performed better for reconstructing lowly and highly expressed transcripts, respectively, MK strategy worked well for almost all ranges of expression quintiles. Among SK tools, Trinity performed well across various conditions but took the longest running time. Oases consumed the most memory whereas SOAPdenovo required the shortest runtime but worked poorly to reconstruct full-length CDS. ABySS showed some good balance between resource usage and quality of assemblies. Our work compared the performance of publicly available transcriptome assemblers, and analyzed important factors affecting de novo assembly. Some practical guidelines for transcript reconstruction from short-read RNA-Seq data were proposed. De novo assembly of C. sinensis transcriptome was greatly improved using some optimized methods.
Article
Full-text available
The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
Article
Full-text available
Mitochondrial genomes encode their own transfer RNAs (tRNAs). These are often degenerate in sequence and structure compared to tRNAs in their bacterial ancestors. This is one of the reasons why current tRNA gene predictor programs perform poorly identifying mitochondrial tRNA genes. As a consequence there is a need for a new program with the specific aim of predicting these tRNAs. In this study, we present the software ARWEN that identifies tRNA genes in metazoan mitochondrial nucleotide sequences. ARWEN detects close to 100% of previously annotated genes. An online version, software for download and test results are available at www.acgt.se/online.html
Article
BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment. The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners to date. Availability and implementation: BWA-MEM is implemented as a component of BWA, which is available at http://github.com/lh3/bwa. Contact: hengli@broadinstitute.org