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The complete chloroplast genome sequence of the Australian Mirbelioid pea Platylobium obtusangulum Hook. (Leguminosae: subf. Papilionoideae, tribe Bossiaeeae)

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Mitochondrial DNA Part B
Authors:
Harvey K. Orel
Harvey K. Orel
Harvey K. Orel
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Patrick Fahey at The University of Queensland
Patrick Fahey
Rachael M. Fowler
Rachael M. Fowler
Rachael M. Fowler
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Michael Bayly at University of Melbourne
Michael Bayly
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Abstract and Figures

We sequenced and assembled the whole chloroplast genome of the Australian-endemic shrub Platylobium obtusangulum. The total size of the genome is 150,090 base pairs (bp), including two inverted repeat regions of 25,511 bp each, one large single copy region of 80,567 bp and a small single copy region of 18,501 bp. The genome has a GC content of 36.7% and includes 127 annotated genes (83 protein coding, 36 tRNA genes and eight rRNA genes). Phylogenetic analysis of chloroplast genomes placed the Platylobium obtusangulum genome in the expected position of the Mirbelioid clade in the legume family (Leguminosae: Papilionoideae).
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MITOGENOME ANNOUNCEMENT
The complete chloroplast genome sequence of the Australian Mirbelioid pea
Platylobium obtusangulum Hook. (Leguminosae: subf. Papilionoideae,
tribe Bossiaeeae)
Harvey K. Orel , Patrick S. Fahey, Rachael M. Fowler and Michael J. Bayly
School of Biosciences, The University of Melbourne, Parkville, Australia
ABSTRACT
We sequenced and assembled the whole chloroplast genome of the Australian-endemic shrub
Platylobium obtusangulum. The total size of the genome is 150,090 base pairs (bp), including two
inverted repeat regions of 25,511 bp each, one large single copy region of 80,567 bp and a small single
copy region of 18,501bp. The genome has a GC content of 36.7% and includes 127 annotated genes
(83 protein coding, 36 tRNA genes and eight rRNA genes). Phylogenetic analysis of chloroplast
genomes placed the Platylobium obtusangulum genome in the expected position of the Mirbelioid
clade in the legume family (Leguminosae: Papilionoideae).
ARTICLE HISTORY
Received 19 August 2019
Accepted 23 September 2019
KEYWORDS
Fabales; Fabaceae;
Mirbelieae; Bossiaeeae;
plastome; rps16
Platylobium Sm. is an Australian genus of nine species
(Thompson 2011) in the legume family, Leguminosae, which
includes important crop species such as soybean (Glycine
max) and chickpea (Cicer arietinum).
Here we report the complete chloroplast genome
sequence of Platylobium obtusangulum (GenBank accession:
MN275233), a species of sclerophyll shrub that is widespread
in south-eastern Australia. This represents the first complete
chloroplast genome for any species in the Mirbelioid clade of
subfamily Papilionoideae (Wojciechowski et al. 2004; Cardoso
et al. 2013). The sequence was generated for use as a refer-
ence in further studies assessing phylogeography and sys-
tematics of the genus.
Plant material was sampled from a population of P. obtu-
sangulum c. 16 km east of Vivonne Bay, Kangaroo Island,
South Australia (Lat: –35.98188, Long: 137.00061; Permit num-
ber: Q26846-1; Herbarium voucher specimen:
MELUD155101a). Total genomic DNA was isolated from silica-
dried leaf tissue using a modified CTAB protocol (Shepherd
and McLay 2011), prepared for sequencing according to the
protocol of Schuster et al. (2018), and sequenced on an
Illumina NextSeq 550 (mid-output, 2 150 Paired End kit) at
The Walter and Eliza Hall Institute of Medical Research
(WEHI), Melbourne, Australia. The genome was assembled by
mapping contigs built in CLC genomics workbench 10.0.1
using default settings to the reference genome of Indigofera
tinctoria (GenBank accession: NC_026680.1) in Geneious 9.1.8
(Kearse et al. 2012). Paired reads were re-mapped to the con-
sensus sequence for quality control. Annotations were trans-
ferred from the reference genome and manually adjusted
where different to the reference.
The chloroplast genome of P. obtusangulum is 150,090 bp
long, with two inverted repeat (IR) regions (25,511 bp), one
large single copy region (LSC; 80,567 bp) and one small single
copy region (18,501 bp). In total 127 genes were annotated,
comprising 83 protein coding genes, 36 tRNA genes and
eight rRNA genes. The genome has a GC content of 36.7%.
Notably, the essential rps16 gene has been functionally lost
from the chloroplast. This is a feature that occurs in other
legume lineages, and most likely means that its function has
been replaced by the nuclear rps16 gene (Keller et al. 2017).
One copy of the ycf1 gene is truncated, with 393 bp occur-
ring inside the inverted repeat at the IRb-LSC junction.
The phylogenetic tree presented herein (Figure 1) includes
representatives from subfamily Papilionoideae, subfamily
Caesalpiniodeae and the early branching subfamily
Cercidoideae of the Leguminosae (sensu LPWG 2017).
Platylobium obtusangulum, representing the Mirbelioid clade,
was resolved as sister to Millettia pinnata, representing
the Millettioids. This placement is consistent with the
CONTACT Harvey K. Orel horel@student.unimelb.edu.au School of Biosciences, The University of Melbourne, Parkville, Australia
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, 3618–3620
https://doi.org/10.1080/23802359.2019.1677187
phylogenetic relationships of the major lineages in the
Papilionoideae posited by previous studies (Wojciechowski
et al. 2004; Cardoso et al. 2013).
Acknowledgments
We acknowledge Stephen Wilcox (WEHI) for Illumina sequencing, Will
Neal for herbarium accessioning and Cat Clowes for advice on manu-
script preparation.
Disclosure statement
No potential conflict of interest was reported by the authors.
ORCID
Harvey K. Orel http://orcid.org/0000-0001-7971-8709
References
Cardoso D, Pennington RT, De Queiroz LP, Boatwright JS, Van Wyk BE,
Wojciechowski MF, Lavin M. 2013. Reconstructing the deep-branching
relationships of the papilionoid legumes. S Afr J Bot. 89:58–75.
Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for
rapid multiple sequence alignment based on fast Fourier transform.
Nucleic Acids Res. 30:3059–3066.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S,
Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic:
an integrated and extendable desktop software platform for the
organization and analysis of sequence data. Bioinformatics. 28:
1647–1649.
Keller J, Rousseau-Gueutin M, Martin GE, Morice J, Boutte J, Coissac E,
Ourari M, Aïnouche M, Salmon A, Cabello-Hurtado F, et al. 2017. The
evolutionary fate of the chloroplast and nuclear rps16 genes as
revealed through the sequencing and comparative analyses of four
novel legume chloroplast genomes from Lupinus. DNA Res. 24:
343–358.
Legume Phylogeny Working Group. 2017. A new subfamily classification
of the Leguminosae based on a taxonomically comprehensive
Platylobium obtusangulum (MN275233)*
Millettia pinnata (NC_016708)
Dalbergia hainanensis (NC_036961)
Maackia floribunda (NC_034774)
Acacia dealbata (NC_034985)
Acacia ligulata (NC_026134)
Cercis glabra (NC_036762)
Quillaja saponaria (MH880827)
100
100
100
100
100
Leguminosae Caesalpinioideae
Outgroup
Papilionoideae
Mirbelioids
Millettioids
Dalbergioids
Genistoids
Figure 1. Bootstrap 50% majority rule consensus tree based on complete chloroplast genome sequences from eight taxa, including seven species from the family
Leguminosae and Quillaja saponaria (Quillajaceae) as the outgroup (CI ¼0.9039, RI ¼0.8404). Genes were aligned in MAFFT using default settings (Katoh et al.
2002). Sequences were analyzed with maximum parsimony (MP), using a heuristic tree search with Max. Trees set to 10,000 and 1000 bootstrap replicates in PAUP
4.0a 165 (Swofford 2003). Bootstrap values are provided above branches. GenBank accession numbers are provided in brackets. Platylobium obtusangulum is indi-
cated with an asterisk.
MITOCHONDRIAL DNA PART B 3619
phylogeny: The Legume Phylogeny Working Group (LPWG). Taxon. 66:
44–77.
Schuster TM, Setaro SD, Tibbits JF, Batty EL, Fowler RM, McLay TG,
Wilcox S, Ades PK, Bayly MJ. 2018. Chloroplast variation is incongruent
with classification of the Australian bloodwood eucalypts (genus
Corymbia, family Myrtaceae). PLOS One. 13:e0195034.
Shepherd LD, McLay TG. 2011. Two micro-scale protocols for the isolation of
DNA from polysaccharide-rich plant tissue. J Plant Res. 124:311–314.
Swofford DL. 2003. PAUP: phylogenetic analysis using parsimony, ver-
sion 4.0a 165. Cary (NC): SAS Institute.
Thompson IR. 2011. A revision of Platylobium (Fabaceae: Bossiaeeae).
Muelleria. 29:154–172.
Wojciechowski MF, Lavin M, Sanderson MJ. 2004. A phylogeny of
legumes (Leguminosae) based on analysis of the plastid matK gene
resolves many well-supported subclades within the family. Am J Bot.
91:1846–1862.
3620 H. K. OREL ET AL.
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