title: Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda).
abstract: BACKGROUND
  Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information.
  
  
  METHODS
  Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements.
  
  
  RESULTS
  We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps,Callianassa ceramicaandTrypaea australiensis, along with three caridean shrimps,Macrobrachium bullatum,Alpheus lobidens, andCaridinacf.nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders.
  
  
  CONCLUSIONS
  Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.
authors.affiliation: School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia; Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia.
authors.forename: Mun Hua
authors.initials: MH
authors.lastname: Tan
authors.affiliation: School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia; Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia.
authors.forename: Han Ming
authors.initials: HM
authors.lastname: Gan
authors.affiliation: School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia; Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia.
authors.forename: Yin Peng
authors.initials: YP
authors.lastname: Lee
authors.affiliation: Museums Victoria , Melbourne, VIC , Australia.
authors.forename: Gary C B
authors.initials: GC
authors.lastname: Poore
authors.affiliation: School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia; Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia; School of Life and Environmental Sciences, Deakin University, Burwood, VIC, Australia.
authors.forename: Christopher M
authors.identifier: 0000-0003-1848-6267
authors.initials: CM
authors.lastname: Austin
keywords: Codon usage; Gene order; Ghost shrimps; Mitochondrial genomics; Phylogenetics; Shrimps; True shrimps