Displaying publications 1 - 20 of 62 in total

Abstract:
Sort:
  1. Fulltext Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species
    Harrisson K, Pavlova A, Gan HM, Lee YP, Austin CM, Sunnucks P
    Heredity (Edinb), 2016 Jun;116(6):506-15.
    PMID: 26883183 DOI: 10.1038/hdy.2016.8
    Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.
  2. Fulltext Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish
    Pavlova A, Gan HM, Lee YP, Austin CM, Gilligan DM, Lintermans M, et al.
    Heredity (Edinb), 2017 05;118(5):466-476.
    PMID: 28051058 DOI: 10.1038/hdy.2016.120
    Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6113) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.
  3. Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity
    Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis-Scott M, Rourke ML, et al.
    Mol Ecol, 2017 Nov;26(22):6253-6269.
    PMID: 28977721 DOI: 10.1111/mec.14368
    Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired-end restriction site-associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies.
  4. Fulltext Population mitogenomics provides insights into evolutionary history, source of invasions and diversifying selection in the House Crow (Corvus splendens)
    Krzemińska U, Morales HE, Greening C, Nyári ÁS, Wilson R, Song BK, et al.
    Heredity (Edinb), 2018 04;120(4):296-309.
    PMID: 29180719 DOI: 10.1038/s41437-017-0020-7
    The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.
  5. Fulltext Genome sequencing and annotation of Cellulomonas sp. HZM
    Chua P, Har ZM, Austin CM, Yule CM, Dykes GA, Lee SM
    Genom Data, 2015 Sep;5:40-1.
    PMID: 26484221 DOI: 10.1016/j.gdata.2015.05.009
    We report the draft genome sequence of Cellulomonas sp. HZM, isolated from a tropical peat swamp forest. The draft genome size is 3,559,280 bp with a G + C content of 73% and contains 3 rRNA sequences (single copies of 5S, 16S and 23S rRNA).
  6. Fulltext Genome sequencing and annotation of Aeromonas sp. HZM
    Chua P, Har ZM, Austin CM, Yule CM, Dykes GA, Lee SM
    Genom Data, 2015 Sep;5:38-9.
    PMID: 26484220 DOI: 10.1016/j.gdata.2015.05.008
    We report the draft genome sequence of Aeromonas sp. strain HZM, isolated from tropical peat swamp forest soil. The draft genome size is 4,451,364 bp with a G + C content of 61.7% and contains 10 rRNA sequences (eight copies of 5S rRNA genes, single copy of 16S and 23S rRNA each). The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. JEMQ00000000.
  7. The complete mitogenome of the bluespotted ribbontail ray Taeniura lymma (Forsskål, 1775) (Elasmobranchii: Myliobatiformes: Dasyatidae)
    Austin CM, Tan MH, Croft LJ, Meekan MG, Gan HY, Gan HM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3205-7.
    PMID: 25693694 DOI: 10.3109/19401736.2015.1007348
    The complete mitogenome of the ray Taeniura lymma was recovered from genome skimming using the HiSeq sequencing system. The T. lymma mitogenome has 17,652 base pairs (59.13% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 1906 bp non-coding AT-rich region. This mitogenome sequence is the second for a ray from Australian waters, the first for the genus Taeniura and the ninth for the family Dasyatidae.
  8. The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae)
    Austin CM, Tan MH, Gan HY, Gan HM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4176-4177.
    PMID: 25630729
    Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.
  9. The complete mitogenome of the cow tail ray Pastinachus atrus (Macleay, 1883) (Elasmobranchii; Myliobatiformes; Dasyatidae)
    Austin CM, Tan MH, Lee YP, Croft LJ, Meekan MG, Gan HM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):1372-3.
    PMID: 25103432 DOI: 10.3109/19401736.2014.947586
    The complete mitogenome of the ray Pastinachus atrus was recovered from a partial genome scan using the HiSeq sequencing system. The P. atrus mitogenome has 18,162 base pairs (61% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 2516 bp non-coding AT-rich region. This mitogenome sequence is the first for a ray from Australian waters, the first for the Genus Pastinachus, and the 6th for the family Dasyatidae.
  10. The complete mitogenome of the whale shark parasitic copepod Pandarus rhincodonicus norman, Newbound & Knott (Crustacea; Siphonostomatoida; Pandaridae)--a new gene order for the copepoda
    Austin CM, Tan MH, Lee YP, Croft LJ, Meekan MG, Pierce SJ, et al.
    Mitochondrial DNA, 2016;27(1):694-5.
    PMID: 24779605 DOI: 10.3109/19401736.2014.913147
    The complete mitochondrial genome of the parasitic copepod Pandarus rhincodonicus was obtained from a partial genome scan using the HiSeq sequencing system. The Pandarus rhincodonicus mitogenome has 14,480 base pairs (62% A+T content) made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 384 bp non-coding AT-rich region. This Pandarus mitogenome sequence is the first for the family Pandaridae, the second for the order Siphonostomatoida and the sixth for the Copepoda.
  11. The complete mitogenome of the Murray Cod, Maccullochella peelii (Mitchell, 1838) (Teleostei: Percichthyidae)
    Austin CM, Tan MH, Lee YP, Croft LJ, Gan HM
    Mitochondrial DNA, 2016;27(1):729-30.
    PMID: 24779601 DOI: 10.3109/19401736.2014.913162
    The complete mitochondrial genome of the iconic Australian freshwater fish, the Murray Cod, Maccullochella peelii, was recovered from partial genome sequencing data using the HiSeq platform (Illumina, San Diego, CA). The mitogenome consists of 16,442 bp (58% A + T content) containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 768 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Maccullochella, and the fourth for the family Percichthyidae.
  12. The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae)
    Austin CM, Tan MH, Croft LJ, Gan HM
    Mitochondrial DNA, 2016;27(1):126-7.
    PMID: 24438281 DOI: 10.3109/19401736.2013.878907
    The complete mitochondrial genome of Cherax cainii was recovered from partial genome sequencing data using the HiSeq platform. The mitogenome consists of 15,801 base pairs (69% A + T content) containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 783 bp non-coding AT-rich region. This is the second completely sequenced mitogenome from the genus Cherax after the first reported Cherax destructor mitogenome nearly a decade ago.
  13. The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae)
    Austin CM, Tan MH, Croft LJ, Gan HM
    Mitochondrial DNA, 2016;27(1):220-1.
    PMID: 24484586 DOI: 10.3109/19401736.2014.880897
    The complete mitochondrial genome of Cherax glaber was sequenced using the HiSeq platform. The mitogenome consists of 15,806 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The Cherax glaber has a base composition of 32.39% for T, 22.42% for C, 33.73% for A and 11.46% for G, with an AT bias of 66.12%.
  14. Fulltext Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes
    Austin CM, Tan MH, Croft LJ, Hammer MP, Gan HM
    Genome Biol Evol, 2015 Oct;7(10):2885-95.
    PMID: 26446539 DOI: 10.1093/gbe/evv186
    The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is presented consisting of 42,110 scaffolds with a total size of 708 Mb (2.85% gaps) representing 93.95% of core eukaryotic genes. Using a k-mer-based method, a genome size of 900 Mb was also estimated. We present an update on the phylogenomics of fishes based on a total of 27 species (23 fish species and 4 tetrapods) using 177 orthologous proteins (71,360 amino acid sites), which supports established relationships except that arowana is placed as the sister lineage to all teleost clades (Bayesian posterior probability 1.00, bootstrap replicate 93%), that evolved after the teleost genome duplication event rather than the eels (Elopomorpha). Evolutionary rates are highly heterogeneous across the tree with fishes represented by both slowly and rapidly evolving lineages. A total of 94 putative pigment genes were identified, providing the impetus for development of molecular markers associated with the spectacular colored phenotypes found within this species.
  15. Fulltext Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly
    Tan MH, Austin CM, Hammer MP, Lee YP, Croft LJ, Gan HM
    Gigascience, 2018 03 01;7(3):1-6.
    PMID: 29342277 DOI: 10.1093/gigascience/gix137
    Background: Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes that warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics.

    Results: We generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads, representing approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 and 967 Mbp. The final assembled genome is contained in 6404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared with the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with an 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27 240 high-quality protein-coding genes were predicted from the clown anemonefish, 26 211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches.

    Conclusions: We present the first genome of any anemonefish and demonstrate the value of low coverage (∼11×) long Nanopore read sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic, and phylogenetic studies specifically for clownfish and more generally for other related fish species of the family Pomacentridae.

  16. Fulltext De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read
    Austin CM, Tan MH, Harrisson KA, Lee YP, Croft LJ, Sunnucks P, et al.
    Gigascience, 2017 08 01;6(8):1-6.
    PMID: 28873963 DOI: 10.1093/gigascience/gix063
    One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family.
  17. Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes
    Yan CZY, Austin CM, Ayub Q, Rahman S, Gan HM
    FEMS Microbiol Lett, 2019 09 01;366(17).
    PMID: 31589302 DOI: 10.1093/femsle/fnz211
    The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.
  18. Fulltext Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management
    Md Zoqratt MZH, Eng WWH, Thai BT, Austin CM, Gan HM
    PeerJ, 2018;6:e5826.
    PMID: 30397546 DOI: 10.7717/peerj.5826
    Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.
  19. Fulltext The NGS Magic Pudding: A Nanopore-Led Long-Read Genome Assembly for the Commercial Australian Freshwater Crayfish, Cherax destructor
    Austin CM, Croft LJ, Grandjean F, Gan HM
    Front Genet, 2021;12:695763.
    PMID: 35126445 DOI: 10.3389/fgene.2021.695763
    Cherax destructor, the yabby, is an iconic Australian freshwater crayfish species, which, similar to other major invertebrate groups, is grossly under-represented in genomic databases. The yabby is also the principal commercial freshwater crustacean species in Australia subject to explotation via inland fisheries and aquaculture. To address the genomics knowledge gap for this species and explore cost effective and efficient methods for genome assembly, we generated 106.8 gb of Nanopore reads and performed a long-read only assembly of the Cherax destructor genome. On a mini-server configured with an ultra-fast swap space, the de novo assembly took 131 h (∼5.5 days). Genome polishing with 126.3 gb of PCR-Free Illumina reads generated an assembled genome size of 3.3 gb (74.6% BUSCO completeness) with a contig N50 of 80,900 bp, making it the most contiguous for freshwater crayfish genome assemblies. We found an unusually large number of cellulase genes within the yabby genome which is relevant to understanding the nutritional biology, commercial feed development, and ecological role of this species and crayfish more generally. These resources will be useful for genomic research on freshwater crayfish and our methods for rapid and super-efficient genome assembly will have wide application.
  20. MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes
    Tan MH, Gan HM, Schultz MB, Austin CM
    Mol Phylogenet Evol, 2015 Apr;85:180-8.
    PMID: 25721538 DOI: 10.1016/j.ympev.2015.02.009
    The increased rate at which complete mitogenomes are being sequenced and their increasing use for phylogenetic studies have resulted in a bioinformatic bottleneck in preparing and utilising such data for phylogenetic analysis. Hence, we present MitoPhAST, an automated tool that (1) identifies annotated protein-coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files, (2) generates a maximum likelihood phylogenetic tree using optimised protein models and (3) reports various mitochondrial genes and sequence information in a table format. To demonstrate the capacity of MitoPhAST in handling a large dataset, we used 81 publicly available decapod mitogenomes, together with eight new complete mitogenomes of Australian freshwater crayfishes, including the first for the genus Gramastacus, to undertake an updated test of the monophyly of the major groups of the order Decapoda and their phylogenetic relationships. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. In comparison to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon sampling suggesting there is value in utilising more fully mitogenomic data. Additionally, the simple table output from MitoPhAST provides an efficient summary and statistical overview of the mitogenomes under study at the gene level, allowing the identification of missing or duplicated genes and gene rearrangements. The finding of new mtDNA gene rearrangements in several genera of Australian freshwater crayfishes indicates that this group has undergone an unusually high rate of evolutionary change for this organelle compared to other major families of decapod crustaceans. As a result, freshwater crayfishes are likely to be a useful model for studies designed to understand the evolution of mtDNA rearrangements. We anticipate that our bioinformatics pipeline will substantially help mitogenome-based studies increase the speed, accuracy and efficiency of phylogenetic studies utilising mitogenome information. MitoPhAST is available for download at https://github.com/mht85/MitoPhAST.
Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links