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. 2025 Jun 3;10(7):548–553. doi: 10.1080/23802359.2025.2509798

The complete mitochondrial genome of Poncelet’s giant rat (Solomys ponceleti) from the Solomon Islands Archipelago

Andrew G King 1, Sandy Ingleby 1, Matthew J Lott 1, Kristofer M Helgen 1, Mark D B Eldridge 1, David E Alquezar-Planas 1,✉
PMCID: PMC12135083  PMID: 40475210

Abstract

Poncelet’s giant rat (Solomys ponceleti Troughton 1935), is a rare, large murine rodent that is endemic to the Solomon Islands Archipelago in the southwest Pacific Ocean. The species is only known from the adjacent islands of Bougainville and Choiseul and is the largest member of the genus. Here, we describe the complete mitochondrial genome of S. ponceleti and compare it to other Rodentia. The S. ponceleti circular mitogenome was 16,246 bp and contained 13 protein-coding genes, two rRNA genes, 22 tRNAs, and a control region (D-loop). Phylogenetic analysis of selected, published mitogenomes reveals a close relationship to other Australo-Papuan murine rodents.

Keywords: Chordata, Poncelet’s giant rat, mitogenome, Muridae, Solomon Islands

Introduction

The giant rats of the Solomon Islands Archipelago in the southwest Pacific Ocean are largely arboreal rodents from the endemic genus Solomys (Muridae: Murinae) (Musser and Carleton 2005). The genus forms part of a large and diverse tribe of rodents (the Hydromyini), that evolved from a single colonization event of the paleocontinent Sahul – encompassing the modern-day landmasses of Australia, New Guinea and its neighboring islands (Rowe et al. 2019). A total of five species of Solomys are recognized, including Poncelet’s giant rat Solomys ponceleti (Troughton 1935), which is the largest living species weighing over 1 kg, and one of the world’s largest rats (Flannery and Wickler 1990; Flannery 1995). S. ponceleti is rare, with fewer than 15 specimens in world natural history museums, mostly collected before 1940. Living animals have only been recorded from the adjacent islands of Bougainville (Papua New Guinea, PNG) and Choiseul (Solomon Islands), although fossil remains are known from nearby Buka (PNG) (Flannery and Wickler 1990). It has an unusual appearance with long, coarse, dark sparsely distributed fur and pale skin. Little is known about the biology of these nocturnal, arboreal rodents, although they are mostly reported from undisturbed lowland forest and build stick nests high in the canopy of large trees (Flannery 1995; Burgin 2017). Records of S. ponceleti are becoming increasingly rare and the species is listed as critically endangered on the IUCN Red List (Leary et al. 2008) due to habitat loss and hunting.

The evolutionary relationships of the endemic genus Solomys, and more broadly the Australo-Papuan rodents, are of considerable interest (Rowe et al. 2008; Roycroft et al. 2020). Phylogenetic analysis using mitochondrial DNA (mtDNA) complement studies based on nuclear DNA markers (Gupta et al. 2015) and will enhance our understanding of rodent evolution. To our knowledge, the mitochondrial genome (mitogenome) has not been established for any species of Solomys. Therefore, we sequenced the complete mitogenome for S. ponceleti to enable genetic comparisons to be made.

Materials and methods

The S. ponceleti DNA was sourced from a liver sample from a voucher specimen (AM M.21863), an adult female collected on Choiseul, Solomon Islands in 1990. All samples are registered within the Australian Museum Research Institute (AMRI – https://australian.museum/get-involved/amri/). The physical specimen (Figure 1(A,B)) is stored within the Mammals Department, while the tissue and isolated DNA are deposited within the Australian Centre for Wildlife Genomics’ Frozen Tissue Collection; contact: Karen-Ann Gray, karen.gray@australian.museum or tissue@australian.museum.

Figure 1.

Figure 1.

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(A) Dorsal and (B) lateral images of the female Solomys ponceleti voucher specimen (AM M.21863) used in this study. Photographs were taken by Harry Leung in May 2024 at the Australian Museum Research Institute, Australian Museum, Sydney, Australia.

Total genomic DNA was extracted from 10 mg of frozen liver (EBU24432) using the Isolate II Genomic DNA Kit (Meridian Bioscience, Melbourne, Australia) as per the manufacturer’s recommendations. DNA was sheared by sonication to 350–400 bp (Covaris M220) before library construction using the NEBNext DNA Library Prep Kit (E6040). The NEBNext Multiplex Oligos for Illumina (NEB Dual Index Primer set 1 – E7600S) were used for adapter ligation and the incorporation of unique indexes via PCR to enable multiplexing with 42 other samples of interest. Index PCR was performed using Q5® Hot Start High-Fidelity DNA Polymerase (NEB #M0493) (New England Biolabs, Ipswich, MA). The indexed S. ponceleti library was then pooled with two other indexed libraries of interest. MyBaits (Arbor Biosciences, Ann Arbor, MI) biotinylated RNA hybridization baits were used for next-generation sequencing library target enrichment of mtDNA. These baits covered the complete mitogenomes of two Rodentia (Rattus rattus and Mus musculus) and the complete or partial mitogenomes of 33 bat species (Chiroptera). Refer to Table S1 for all reference species and gene sequences used in bait design. Refer to Table S2 for primer sequences used in the amplification of unpublished gene sequences that was used in bait design. The enriched library pool was then amplified using KAPA HiFi HotStart ReadyMix (Cat No. 07958927001) (Roche, Basel, Switzerland), purified and subsequently sequenced at the Ramaciotti Centre for Genomics (UNSW Sydney, Kensington, Australia) on the Illumina NextSeq 500 Platform (Illumina, San Diego, CA), which produced 5,229,176 × 150 bp reads totaling 0.742 Gbp. QC was performed in CLC Genomics Workbench v2021.0.5 (Qiagen Ltd, Hilden, Germany) including the removal of read-through adapter sequences, low-quality sequence (limit = 0.05) ambiguous nucleotides (maximal two nucleotides allowed), terminal nucleotides (four bases 3′ and 5′) and sequences <50 nucleotides. This resulted in 3,429,144 curated reads.

CLC Genomic Workbench was used to de novo assemble the complete mitogenome using 3,429,144 reads to produce a circular mitogenome of size 16,246 bp with an average coverage of 29,972×. Curated paired-end and singleton reads were mapped back to the assembled mitogenome sequence, which resulted in, base coverage ranging from 70× to 135,854× across the length of the mitogenome (Figure S1). Annotations for the protein-coding, tRNA, and rRNA genes were retrieved from the published Melomys burtoni mitogenome (NC 049118) using the ‘Annotate and Predict’ feature of Geneious Prime v2021.0.3. The sequence with annotated features has been deposited in GenBank Accession number ON598383.

Phylogenetic analysis was conducted using the concatenated protein-coding gene sequences, (excluding mt-rRNA genes, tRNA, intergenic regions, and control regions) sourced from 20 complete mitogenomes. The phylogeny was inferred using the maximum-likelihood method and general time reversal (GTR) model (+G + I) of best fit in the program MEGA 11 (Tamura et al. 2021).

Results

The S. ponceleti complete mitogenome sequence length was 16,246 bp with typical vertebrate mitogenome organization (Westerman et al. 2016) containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a non-coding control region (D-loop). The overall base composition was 36.2% A, 26.0% T, 26.3% C, and 11.5% G, with a GC% content of 37.8% which is similar to other murid mitogenomes (Figure 2). Of the 13 protein-coding genes, nine initiated with ATG, two with ATC (ND3 and ND5) and one with ATA (ND2). Additionally, one protein gene (ND1) started with the alternative start codon GTG. This initiation codon has been observed in other rodent species (Lamelas et al. 2020), including a few species within the large and diverse tribe Hydromyini, for which a few complete mitogenomes have been sequenced (Nilsson et al. 2010). A total of eight protein-coding genes ended with the stop codon TAA within the gene sequence (COX1, COX2, ATP6, ATP8, ND3, ND4L, ND5, and ND6). The other five genes (ND1, ND2, COX3, ND4, and CYTB) had a stop codon completed by poly-adenylation of the 3′-end of the mRNA, occurring after transcription, but giving rise to functional termination of the gene. This included two genes (NDI and ND2) that had a TAG stop codon directly following the protein coding sequence but using the last nucleotide (‘T’) from within the gene region. The phylogenetic analysis demonstrated that S. ponceleti is a member of the Murinae, with its closest relatives being other Australo-Papuan rodents (Figure 3).

Figure 2.

Figure 2.

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The mitogenome feature map of Solomys ponceleti, drawn using Geneious Prime v2024.0.3 (http://geneious.com). Genes are shaded in green, coding sequences (CDS) in yellow, ribosomal RNA in red and transfer RNAs (tRNAs) in pink. The control region D-loop is shaded in orange. Sequences encoded in the forward or reverse strand are indicated by the direction of the arrowheads (right facing arrows indicate genes on the forward strand, while left facing arrows indicate genes on the reverse strand). GC content is also displayed in the center of the figure.

Figure 3.

Figure 3.

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Phylogenetic reconstruction of the family Muridae showing the placement of S. ponceleti (in bold text) based on a comparison of 19 concatenated mitochondrial DNA sequences (i.e. 13 protein-coding genes). The evolutionary relationships of these taxa were inferred using the maximum-likelihood method and General Time Reversible model (Nei and Kumar 2000) in MEGA 11 (Tamura et al. 2021). The tree with the highest log likelihood is depicted (−76,837.92). To generate this tree, Neighbour-Joining and BioNJ algorithms were applied to a matrix of pairwise distances, estimated using the maximum composite likelihood (MCL) method, to obtain the initial tree(s) for the heuristic search. The topology with the superior log likelihood value was then selected. The percentage of trees in which the same clades were observed (based on 1000 bootstrap replicates) is shown next to the branches. To model evolutionary rate differences among sites, we utilized a discrete Gamma distribution (five categories (+G, parameter = 0.4529)). Some sites were allowed to be evolutionarily invariable under the selected rate variation model ([+I], 26.7% sites). The final tree is drawn to scale, with branch lengths measured in the number of substitutions per site. There was a total of 11,364 positions in the final dataset, and the following 19 reference nucleotide sequences were used Melomys cervinipes MZ286973.1 (unpublished), Melomys burtoni NC_049118.1 (Nicolas et al. 2020), Pseudomys chapmani EU305669.1 (Nilsson et al. 2010), Zyzomys argurus MT741674.1 (Zandberg et al. 2021), Leggadina lakedownensis EU305668.1 (Nilsson et al. 2010), Maxomys ochraceiventer NC_056988.1 (Forcina et al. 2021), Maxomys whiteheadi MW209722.1 (Forcina et al. 2021), Maxomys surifer KY464181.1 (Camacho-Sanchez et al. 2017), Chiropodomys gliroides NC_049121.1 (Nicolas et al. 2020), Rattus rattus NC_012374.1 (Robins et al. 2008), Rattus norvegicus NC_001665.2 (unpublished), Mus spretus NC_025952.1 (Chang et al. 2016), Mus musculus NC_005089.1 (Bayona-Bafaluy et al. 2003), Mus fragilicauda NC_025287.1 (Tsangaras et al. 2014), Mus caroli NC_025268.1 (Tsangaras et al. 2014), Mus cervicolor NC_025269.1 (Tsangaras et al. 2014), Mus famulus NC_030342.1 (Wu and Liu 2016), Mus cookii NC_025270.1 (Tsangaras et al. 2014), and Lepus timidus (outgroup) NC_024040.1 (Melo-Ferreira et al. 2014).

Discussion and conclusions

In this study, we report on the first complete mitogenome of Poncelet’s giant rat (S. ponceleti) from a museum voucher specimen collected from the Solomon Islands archipelago. The mitogenome was enriched via a hybridization capture technique using a multi-species bait design, sequenced, and then assembled. Our original study design, which aimed to retrieve whole mitogenomes from 42 mammalian species (across 19 genera and six families), precluded the selection of additional species within the genus Solomys. Nevertheless, the orientation, gene arrangement and nucleotide composition of the mitogenome was very similar to other Australo-Papuan rodents published to date. This is also evident from the topology of our phylogenetic tree that supports a close relationship between these species. Fundamentally, this study provides a valuable genetic resource as it represents the first complete mitogenome from a species within the genus Solomys. This will aid future investigations into the evolutionary history of rodents, particularly those endemic to the southwest Pacific region.

Supplementary Material

Table S2 Primers sequences used to amplify specific gene regions used in the hybridization capture baits.pdf
TMDN_A_2509798_SM6029.pdf (61.5KB, pdf)
Figure S1 Solomys ponceleti_read coverage_20250428.pdf
TMDN_A_2509798_SM6028.pdf (54.7KB, pdf)
Table S1 Reference material for bait design_simplified_pdf.pdf
TMDN_A_2509798_SM6027.pdf (160.9KB, pdf)

Acknowledgements

We thank the Vudutaru area community for their assistance. We also thank Harry Leung for producing high-resolution images of the specimen, Scott Ginn for facilitating the tissue loan, Harry Parnaby for discussion, as well as Rebecca Johnson, Cameron Slatyer, Tim Flannery, Paul Flemons, and Tracey McVea for support throughout this project.

Geolocation information: Geospatial coordinates for the voucher material of S. ponceleti are near Vudutaru Village, on Choiseul, Solomon Islands (−6° 49′ S, 156° 31′ E). Australian Museum voucher number M.21863.

Funding Statement

The laboratory and sequencing work were funded by a grant from the Australian Museum Foundation for World Class Collections – Multi-dimensional access to Australia’s Natural History Icons Online – a Pilot Project.

Ethics statement

This study features work on a critically endangered species, Poncelet’s giant rat (S. ponceleti). The authors have complied with the International Union for Conservation of Nature (IUCN) policies on research involving species at risk of extinction. The authors also acknowledge compliance with the Convention on Biological Diversity and the Convention on the Trade in Endangered Species of Wild Fauna and Flora (CITES). Field work on Choiseul was part of a multi-year program of biodiversity surveys facilitated by the Ministry of Natural Resources, Honiara, Solomon Islands. An S. ponceleti specimen was collected and deposited at the AMRI in Sydney, Australia under registration number AM M.21863. We obtained DNA from this specific museum specimen and used published data available on GenBank for reference mitogenomes and to generate the phylogeny.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The BioProject, BioSample and SRA accession numbers related to the sample analyzed in this study are PRJNA1162666, SAMN43041058, and SRR30718060, respectively. The complete mitochondrial sequence data that support the findings of this study are openly available in GenBank of NCBI under accession number ON598383 (https://www.ncbi.nlm.nih.gov/nuccore/ON598383).

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Table S2 Primers sequences used to amplify specific gene regions used in the hybridization capture baits.pdf
TMDN_A_2509798_SM6029.pdf (61.5KB, pdf)
Figure S1 Solomys ponceleti_read coverage_20250428.pdf
TMDN_A_2509798_SM6028.pdf (54.7KB, pdf)
Table S1 Reference material for bait design_simplified_pdf.pdf
TMDN_A_2509798_SM6027.pdf (160.9KB, pdf)

Data Availability Statement

The BioProject, BioSample and SRA accession numbers related to the sample analyzed in this study are PRJNA1162666, SAMN43041058, and SRR30718060, respectively. The complete mitochondrial sequence data that support the findings of this study are openly available in GenBank of NCBI under accession number ON598383 (https://www.ncbi.nlm.nih.gov/nuccore/ON598383).

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