Wayne Reeve
Murdoch University, School of Veterinary and Life Sciences, Faculty Member
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Abstract The Common Rock Rat Zyzomys argurus is an abundant small- to medium-sized Murid rodent that is endemic to Australia. It is a nocturnal mammal with a mostly herbivorous diet. This species is native to the wet/dry tropics of... more
Abstract The Common Rock Rat Zyzomys argurus is an abundant small- to medium-sized Murid rodent that is endemic to Australia. It is a nocturnal mammal with a mostly herbivorous diet. This species is native to the wet/dry tropics of Northern Australia and can be identified from other rock rats on the basis of its small size and its tail length (which is at least equivalent to its head-body length). Here, we describe the complete mitochondrial genome of Z. argurus and compare it to other Rodentia. The Z. argurus circular mitogenome was 16,261 bp and contained 13 protein-coding genes, two rRNA genes, 22 tRNAs and a control region (D-loop) of 859 bp. Phylogenetic analysis of selected, published sequenced mitogenomes reveal it is most closely related to the Lakeland Downs mouse Leggadina lakedownensis in the order Rodentia.
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Pseudomonas syringae MUP17 was isolated from Western Australian frost-damaged barley. The MUP17 complete genome contained a 5,850,185-bp single circular chromosome with a GC content of 59.12%. IMG/M genome annotation identified 5,012... more
Pseudomonas syringae MUP17 was isolated from Western Australian frost-damaged barley. The MUP17 complete genome contained a 5,850,185-bp single circular chromosome with a GC content of 59.12%. IMG/M genome annotation identified 5,012 protein-coding genes, 1 of which encoded an ice-nucleation protein containing 19 occurrences of a highly repetitive PF00818 domain.
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Additional file 8: Table S3. Cupriavidus strains compared in this study (as bacterial isolates and/or sequenced genomes).
Additional file 6: Table S1. General attributes and Minimum Information for the Genome Sequence (MIGS) of Cupriavidus strain STM 6070.
Additional file 7: Table S2. Number of protein coding genes of STM 6070 associated with the general COG functional categories.
Additional file 12: Figure S7. A comparison of proximal and distal sites in Cupriavidus neocaledonicus STM 6070 RND-HME proteins compared to related proteins in other bacterial strains.
Additional file 10: Table S5. Comparison of TransAAP identified transporter genes in the genomes of Cupriavidus neocaledonicus STM 6070 and other Cupriavidus species.
Associated MIGS record. (DOC 73 kb)
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Rhizobium leguminosarum symbiovar trifolii strains TA1 and CC275e are nitrogen-fixing microsymbionts of Trifolium spp. and have been used as commercial inoculant strains for clovers in pastoral agriculture in Australia and New Zealand.... more
Rhizobium leguminosarum symbiovar trifolii strains TA1 and CC275e are nitrogen-fixing microsymbionts of Trifolium spp. and have been used as commercial inoculant strains for clovers in pastoral agriculture in Australia and New Zealand. Here we present the complete genome sequences of both strains, resolving their multipartite genome structures and allowing for future studies using genomic approaches. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
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The coming avalanche of genomic data is bringing opportunities for new insights into the genome architecture and evolution of root nodule bacteria. Comparative genomic analyses of root nodule bacteria reveal that mobile genetic elements... more
The coming avalanche of genomic data is bringing opportunities for new insights into the genome architecture and evolution of root nodule bacteria. Comparative genomic analyses of root nodule bacteria reveal that mobile genetic elements ranging from transposons, integrons, genomic islands and plasmids are widespread in these genomes. Genomic islands are plasmid-like DNA regions that are integrated into prokaryotic chromosomes and confer a variety of functions (resistance, degradation, metabolism, pathogenicity, secretion and symbiosis) to the host genome. Acquisition can extend the capacity of the host bacterium to adapt to new environments. Genomic islands that confer nitrogen fixation capacity to non symbiotic bacteria are termed 'symbiosis islands' because they carry nodulation and nitrogen fixation genes required for the legume symbiosis as well as genes required for the excision, insertion and transfer of the island.
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Root nodule bacteria isolated from Zambian Lotononis angolensis (1) and southern USA Lupinus texensis (2) form a group that is distinct from other named and described legume root nodule bacteria. A phylogenetic tree based on the sequence... more
Root nodule bacteria isolated from Zambian Lotononis angolensis (1) and southern USA Lupinus texensis (2) form a group that is distinct from other named and described legume root nodule bacteria. A phylogenetic tree based on the sequence of nearly full-length portions of the 16S rRNA gene indicates these isolates are affiliated to the α-proteobacterial genus Microvirga. Microvirga spp isolated from soil, air and thermal waters or hot springs have previously been formally described but none has been reported as capable of symbiotic nitrogen fixation. These isolates therefore represent a new lineage of nitrogen-fixing legume symbionts. We present here a polyphasic description of these novel species. A phylogenetic tree based on rpoB sequences supports the topography of the 16S rRNA tree in affiliating these isolates with Microvirga. Sequences of nifD and nifH are closely related in the L. angolensis and L. texensis strains, and there is no indication of horizontal gene transfer. In contrast, the nodA sequence of a L. angolensis strain grouped with Burkholderia tuberum and Methylobacterium nodulans nodA sequences, while that of a L. texensis strain was placed within a different group of rhizobia. The 16S rRNA phylogenetic tree indicates that L. texensis strains do not form a single lineage that is phylogenetically divergent from the African L. angolensis strains; rather, multiple lineages of these root nodule bacteria seem to be distributed across both geographic regions. DNA:DNA hybridization, fatty acid composition and % G+C data are consistent with these isolates forming several novel species. This study presents additional characterisation of these isolates, such as morphology, physiology, substrate utilisation, antibiotic resistance and legume host range that differentiates them from other Microvirga spp. These novel root nodule bacteria tolerate comparatively high temperatures and may have potential as inoculants in hot climates.
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Pseudomonas syringae MUP20 was isolated from Western Australian frost-damaged wheat. The MUP20 complete genome contained a 6,045,198-bp single circular chromosome with a GC content of 59.03%. IMG/M genome annotation identified 5,245... more
Pseudomonas syringae MUP20 was isolated from Western Australian frost-damaged wheat. The MUP20 complete genome contained a 6,045,198-bp single circular chromosome with a GC content of 59.03%. IMG/M genome annotation identified 5,245 protein-coding genes, 1 of which encoded an ice nucleation protein containing 20 occurrences of a highly repetitive PF00818 domain.
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The poor availability of nitrogen is one of the principal factors limiting global biomass. Legumes are vital components of agricultural systems because of their ability to associate symbiotically with root nodule bacteria (RNB) and... more
The poor availability of nitrogen is one of the principal factors limiting global biomass. Legumes are vital components of agricultural systems because of their ability to associate symbiotically with root nodule bacteria (RNB) and subsequently fix atmospheric nitrogen to a form that can be utilised by the plant partner. Furthermore, this symbiotic relationship provides available soil nitrogen for subsequent non-leguminous crops. This RNB-legume interaction is affected by a number of environmental factors. Progressive acidification of agricultural soils is one of the big challenges in agriculture as soil acidity negatively impacts legume productivity. One genus of RNB, Sinorhizobium, is particularly acid-sensitive causing a major reduction in Medicago productivity in acidic soils. Due to the importance of Medic pasture production, alternative strains have been captured, and are still being captured, from the genetic pool that display superior acid tolerance characteristics. This pre...
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The rhizobia-legume symbiosis is a highly important source of nitrogen (N) in both natural and agricultural systems. Nodulated legumes are found in nearly all terrestrial and even some aquatic ecosystems. Rhizobial microsymbionts are... more
The rhizobia-legume symbiosis is a highly important source of nitrogen (N) in both natural and agricultural systems. Nodulated legumes are found in nearly all terrestrial and even some aquatic ecosystems. Rhizobial microsymbionts are phylogenetically and genetically diverse. Their symbiotic ability is conferred by a group of approximately 400 genes, which enable nodulation and N2-fixation with the legume host and can be acquired by horizontal gene transfer. While certain rhizobial species are known to be specifically associated with particular legume hosts, recent studies also provide evidence of emerging trends in rhizobial biogeography, in which edaphic and climatic factors strongly influence rhizobial distribution patterns. Research at the Centre for Rhizobium Studies (CRS) has shown that an understanding of these distribution patterns is critical in assessing the suitability of novel legumes and their associated rhizobia for introduction into agricultural systems. Rhizobial biog...
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Background Cupriavidus strain STM 6070 was isolated from nickel-rich mine roadside soil near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly... more
Background Cupriavidus strain STM 6070 was isolated from nickel-rich mine roadside soil near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. Results The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6,118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica -nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins be...
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Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract colouration and breeding.... more
Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract colouration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana ‘Mrs. Butt’, a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151,756,278 bp and contains 86,572 genes which undergone a recent WGD. We confirmed that multiple rounds of whole genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryoph...
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Although Medicago sativa forms highly effective symbioses with the comparatively acid-sensitive genus Ensifer, its introduction into acid soils appears to have selected for symbiotic interactions with acid-tolerant R. favelukesii strains.... more
Although Medicago sativa forms highly effective symbioses with the comparatively acid-sensitive genus Ensifer, its introduction into acid soils appears to have selected for symbiotic interactions with acid-tolerant R. favelukesii strains. Rhizobium favelukesii has the unusual ability of being able to nodulate and fix nitrogen, albeit sub-optimally, not only with M. sativa but also with the promiscuous host Phaseolus vulgaris. Here we describe the genome of R. favelukesii OR191 and genomic features important for the symbiotic interaction with both of these hosts. The OR191 draft genome contained acid adaptation loci, including the highly acid-inducible lpiA/acvB operon and olsC, required for production of lysine- and ornithine-containing membrane lipids, respectively. The olsC gene was also present in other acid-tolerant Rhizobium strains but absent from the more acid-sensitive Ensifer microsymbionts. The OR191 symbiotic genes were in general more closely related to those found in Me...
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Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root... more
Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome sequence for a microsymbiont of the group of annual medic species adapted to acid soils. We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes. The genome contains a chromosome of size 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp. The smallest plasmid is a feature unique to...