Mitochondrial DNA Part A

DNA Mapping, Sequencing, and Analysis

ISSN: 2470-1394 (Print) 2470-1408 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn21

Complete mitochondrial genome of the soybean

stem fly Melanagromyza sojae (Diptera:
Agromyzidae)

Jonas André Arnemann, Tom K. Walsh, Karl H. J. Gordon, Hugh Brier, Jerson
Vanderlei Carús Guedes & Wee Tek Tay

To cite this article: Jonas André Arnemann, Tom K. Walsh, Karl H. J. Gordon, Hugh Brier,
Jerson Vanderlei Carús Guedes & Wee Tek Tay (2016): Complete mitochondrial genome of the
soybean stem fly Melanagromyza sojae (Diptera: Agromyzidae), Mitochondrial DNA Part A,
DOI: 10.3109/19401736.2015.1101550

To link to this article: http://dx.doi.org/10.3109/19401736.2015.1101550

Published online: 22 Mar 2016.

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ISSN: 1940-1736 (print), 1940-1744 (electronic)

Mitochondrial DNA, Early Online: 1–3

! 2016 Taylor & Francis. DOI: 10.3109/19401736.2015.1101550

MITOGENOME ANNOUNCEMENT

Complete mitochondrial genome of the soybean stem fly

Melanagromyza sojae (Diptera: Agromyzidae)
Jonas André Arnemann1,2, Tom K. Walsh1, Karl H. J. Gordon1, Hugh Brier3, Jerson Vanderlei Carús Guedes2, and
Wee Tek Tay1
1
Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia, 2Department of Crop Protection, Federal University of Santa Maria (Universidade
Federal de Santa Maria), Santa Maria, Rio Grande do Sul State, Brazil, and 3Queensland Department of Agriculture, Fisheries and Forestry, Kingaroy,
Qld, Australia
Downloaded by [RMIT University Library] at 13:08 29 March 2016

Abstract Keywords
We report the complete mitochondrial DNA genome of the soybean stem fly (SSF) Biosecurity, Brazil, insect pest incursions
Melanagromyza sojae from Brazil Santa Catarina state based on Illumina MiSeq sequence
data. The estimated mitogenome is 15 475 base pairs (bp) (KT597923), with 13 protein-coding History
genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 tRNAs, and an estimated 579 bp AT-rich
control region. Similar to other insects, the SSF mitogenome is A–T bias with 40.9% A, 36.7% T, Received 30 August 2015
13.6% C, and 8.8% G. Molecular characterization of SSF mitogenome will facilitate the Accepted 9 September 2015
development of effective molecular markers, and robust and rapid identification of suspected Published online 15 March 2016
biosecurity incursions and field infestations of this insect pest.

The soybean stem fly (SSF) Melanagromyza sojae (Zehntner) is
one of the most important pests in soybean fields in Eastern Asia
(e.g. China; Wang & Gai, 2001), Southern Asia (e.g. India and
Nepal; Thapa, 2012), South East Asia (e.g. Indonesia; Van Den
Berg et al., 1995), and Eastern Europe (e.g. Russia; Strakhova
et al., 2013). In Australia, SSF is of increasing importance, with
major outbreaks reported in subtropical coastal soybeans for the
first time in 2013 (Brier & Moore, 2013). To the authors’
knowledge, previous major Australian outbreaks had been in the
tropics. SSF larvae damage the soybean stem, negatively
impacting plant growth and soybean yield (Talekar, 1989). Until
now, there has been no information on the mitochondrial DNA
genome and/or partial Cytochrome Oxidase I (mtCOI)
gene sequence for this species. The SSF has the potential to be
a significant threat in North and South America
and has been recognized as a biosecurity threat in Brazil
(Hirose & Moscardi, 2012). This work reports the detection of
Correspondence: Wee Tek Tay, Black Mountain Laboratories, CSIRO,
Clunies Ross Street, Canberra, ACT 2601, Australia. Tel: +61 2 6246
4286. E-mail: weetek.tay@csiro.au
SSF on the South American continent. Suspect fly specimens
found damaging soybean stems at Santa Catarina State were
collected on 16 April 2015, but molecular DNA identification was
prevented due to a lack of reference data for the M. sojae mtCOI
DNA sequence. Other recent incursions into S. America have
highlighted the need for mitogenome characterization as demon-
strated in the confirmation of the Helicoverpa armigera incursion
in Brazil (Tay et al., 2013).
Upon confirmation of unique M. sojae larval morphological
characters by one of the co-authors (H. B.), total gDNA from a
SSF adult was extracted following the protocol of Walsh (2014)
for the construction of an Illumina MiSeq DNA library.
Sequence data from an Illumina MiSeq run was assembled
using GeneiousÕ R8 and mitogenome annotation via MITOS
(Bernt et al., 2013) and Tandem Repeats Finder (Benson, 1999)
as described (Tay et al., 2014). Phylogeny inference based on
partial mtCOI genes included our reported M. sojae (KT597923)
and related Agromyzidae flies sequences, and Fergusonina
taylori as the outgroup (GenBank and iBoL DNA database was
accessed on 19 August 2015). We used PhyML 3.0 (Guindon
et al., 2010) for the phylogenetic analysis of Melanagromyza
species; selecting the ‘‘automatic model selection’’ option for
optimizing substitution model and 1000 bootstrap replications
for estimating node confidence. The inferred partial mtCOI
phylogeny (Figure 1) suggested a basal position for M. sojae as
compared with other Melanagromyza species, while low boot-
strap confidence (i.e. 550%) for various clades suggest that
further research is needed for this agriculturally important
dipteran group.
 2 J. A. Arnemann et al. Mitochondrial DNA, Early Online: 1–3
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Figure 1. Maximum Likelihood (ML) phylogeny analysis using PhyML (Guindon et al., 2010) of Agromyzidae species (substitution model:
GTR + G6 + I; 11 086.49 (AIC); Gamma shape parameter: 0.597, proportion of invariable sites: 0.529), based on 607 bp partial mtCOI gene. The
outgroup is Fergusonina taylori (NC_016865) (Scheffer et al., 2007). Bootstrap values of 450% are shown. The iBoL ID or GenBank accession
numbers for all samples used are provided. All sequences used are aligned to nucleotide positions 61–666 of the M. sojae mitogenome (KT597923).

Acknowledgements
The authors thank Mr. William James and Ms. Melissa Piper (CSIRO) for
their technical assistance in the laboratory. J. A. A. acknowledged the
CSIRO Health and Biosecurity Flagship for hosting his visit to enable
completion of molecular genetic laboratory component of this study.
Declaration of interest
The authors report no conflicts of interest. The authors alone are
responsible for the content and writing of this article.
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