Displaying publications 1 - 20 of 51 in total

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  1. Grandjean F, Tan MH, Gan HY, Gan HM, Austin CM
    PMID: 25738217 DOI: 10.3109/19401736.2015.1018207
    The Austropotamobius pallipes complete mitogenome has been recovered using Next-Gen sequencing. Our sample of A. pallipes has a mitogenome of 15,679 base pairs (68.44% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 877 bp non-coding AT-rich region. This is the first mitogenome sequenced for a crayfish from the family Astacidae and the 4(th) for northern hemisphere genera.
  2. Gan HM, Gan HY, Tan MH, Penny SS, Willan RC, Austin CM
    PMID: 25648928 DOI: 10.3109/19401736.2015.1007355
    The complete mitochondrial genome of the commercially and ecologically important and internationally vulnerable giant clam Tridacna squamosa was recovered by genome skimming using the MiSeq platform. The T. squamosa mitogenome has 20,930 base pairs (62.35% A+T content) and is made up of 12 protein-coding genes, 2 ribosomal subunit genes, 24 transfer RNAs, and a 2594 bp non-coding AT-rich region. The mitogenome has a relatively large insertion in the atp6 gene. This is the first mitogenome to be sequenced from the genus Tridacna, and the family Tridacnidae and represents a new gene order.
  3. Gan HM, Tan MH, Gan HY, Lee YP, Austin CM
    PMID: 25648918 DOI: 10.3109/19401736.2015.1007325
    The clawed lobster Nephrops norvegicus is an important commercial species in European waters. We have sequenced the complete mitochondrial genome of the species from a partial genome scan using Next-Gen sequencing. The N. norvegicus has a mitogenome of 16,132 base pairs (71.22% A+ T content) comprising 13 protein-coding genes, 2 ribosomal subunit genes, 21 transfer RNAs, and a putative 1259 bp non-coding AT-rich region. This mitogenome is the second fully characterized for the family Nephropidae and the first for the genus Nephrops. The mitogenome gene order is identical to the Maine lobster, Homarus americanus with the exception of the possible loss of the trnI gene.
  4. Gan HM, Gan HY, Lee YP, Grandjean F, Austin CM
    PMID: 25648916 DOI: 10.3109/19401736.2015.1007326
    The invasive freshwater crayfish Orconectes limosus mitogenome was recovered by genome skimming. The mitogenome is 16,223 base pairs in length consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The O. limosus mitogenome has an AT bias of 71.37% and base composition of 39.8% for T, 10.3% for C, 31.5% for A, and 18.4% for G. The mitogene order is identical to two other genera of northern hemisphere crayfish that have been sequenced for this organelle.
  5. Gan HY, Gan HM, Tan MH, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4099-4100.
    PMID: 25629489
    The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.
  6. Gan HY, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3985-3986.
    PMID: 25543913
    The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.
  7. Gan HM, Tan MH, Lee YP, Hammer MP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4187-4188.
    PMID: 25600740
    The mitogenome of an Australian sample of the mudskipper, Periophthalmus minutus, was recovered from partial sequencing using the MiSeq sequencer. This mudskipper has a mitogenome of 16,506 base pairs (55% A + T content) made up of two ribosomal subunit genes, 13 protein-coding genes, 22 transfer RNAs, and a 838 bp non-coding AT-rich region. This is the first sequenced mitogenome for the genus Periophthalmus and the fifth for the subfamily Oxudercinae.
  8. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25423510 DOI: 10.3109/19401736.2014.982585
    The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.
  9. Lee YP, Gan HM, Tan MH, Lys I, Page R, Dias Wanigasekera B, et al.
    PMID: 25707411 DOI: 10.3109/19401736.2015.1018209
    The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.
  10. Gan HM, Tan MH, Lee YP, Austin CM
    PMID: 25329292 DOI: 10.3109/19401736.2014.974174
    The mitogenome of the Australian freshwater blackfish, Gadopsis marmoratus was recovered coverage by genome skimming using the MiSeq sequencer (GenBank Accession Number: NC_024436). The blackfish mitogenome has 16,407 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the 5th mitogenome sequence to be reported for the family Percichthyidae.
  11. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25423512 DOI: 10.3109/19401736.2014.982587
    The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.
  12. Gan HM, Tan MH, Lee YP, Austin CM
    PMID: 25329290 DOI: 10.3109/19401736.2014.974173
    The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compared with other Triops species. Triops australiensis has a mitochondrial genome of 15,125 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The T. australiensis mitogenome is composed of 36.4% A, 16.1% C, 12.3% G and 35.1% T. The mitogenome gene order conforms to the primitive arrangement for Branchiopod crustaceans, which is also conserved within the Pancrustacean.
  13. Gan HY, Gan HM, Lee YP, Austin CM
    PMID: 25693707 DOI: 10.3109/19401736.2015.1007312
    The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.
  14. Gan HY, Gan HM, Lee YP, Austin CM
    PMID: 25693708 DOI: 10.3109/19401736.2015.1007311
    The mitochondrial genome of the rock pool prawn (Palaemon serenus), is sequenced, making it the third for genera of the family Palaemonidae and the first for the genus Palaemon. The mitogenome is 15,967 base pairs in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The P. serenus mitogenome has an AT bias of 58.97% and a base composition of 29.79% for T, 24.14% for C, 29.18% for A, and 16.89% for G. The mitogenome gene order of P. serenus is identical to Exopalaemon carinicauda.
  15. Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3981-3982.
    PMID: 25541307
    The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.
  16. Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3983-3984.
    PMID: 25541305
    The mitochondrial genome sequence of the porcellanid crab, Petrolisthes haswelli is provided, making it the second for the family Porcellanidae and the third for the superfamily Galatheoidea. Petrolisthes haswelli has a mitogenome of 15,348 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the P. haswelli mitogenome is 35.66% for T, 18.65% for C, 34.35% for A and 11.34% for G, with an AT bias of 70.01%. The mitogenome gene order is identical to the mitogenome of Neopetrolisthes maculatus, the only other species of the family with a sequenced mitogenome.
  17. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25103440 DOI: 10.3109/19401736.2014.945554
    The mitochondrial genome sequence of the Morton Bay bug, Thenus orientalis, is documented, which makes it the second mitogenome for species of the family Scyllaridae and the ninth for members of the superfamily Palinuroidae. Thenus orientalis has a mitogenome of 16,826 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of the T. orientalis mitogenome is 31.31% for T, 23.77% for C, 31.05% for A, and 13.87% for G, with an AT bias of 62.36%. In addition to a duplicated trnS1 and several other tRNA gene rearrangements, the mitogenome gene order has novel protein coding gene order with the nad6 and cob genes translocated as a block to a location downstream of the nad3 gene.
  18. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25103431 DOI: 10.3109/19401736.2014.947587
    The mitochondrial genome sequence of the stone crab, Myomenippe fornasinii, second of the superfamily Eriphioidea is documented. Myomenippe fornasinii has a mitogenome of 15,658 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the M. fornasinii mitogenome is 36.10% for T, 18.52% for C, 35.48% for A, and 9.90% for G, with an AT bias of 71.58%. The mitogenome gene order conforms to what is the standard arrangement for brachyuran crabs.
  19. Gan HM, Tan MH, Austin CM
    PMID: 24938115 DOI: 10.3109/19401736.2014.926490
    The mitochondrial genome sequence of the Australian crayfish, Euastacus yarraensis, is documented and compared with other Australian crayfish genera. Euastacus yarraensis has a mitogenome of 15,548 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of E. yarraensis mitogenome is 32.39% for T, 22.45% for C, 34.43% for A, and 10.73% for G, with an AT bias of 66.82%. The mitogenome gene order conforms to what is considered the primitive arrangement for parastacid crayfish.
  20. Krzeminska U, Wilson R, Rahman S, Song BK, Gan HM, Tan MH, et al.
    PMID: 24938087 DOI: 10.3109/19401736.2014.926512
    The complete mitochondrial genome of the invasive house crow (Corvus splendens) was sequenced (GenBank accession number: KJ766304) using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitochondrial genome is 16,962 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal subunit genes and a non-coding control region. The mitogenome structural organization is identical to that of the other Corvus species and related genera. The overall base composition of C. splendens is 30.65% for A, 29.71% for C, 14.84% for G and 24.80% for T, with an AT content of 55.45%. We propose to use full mitochondrial genome to address taxonomic issues and to study the population genetics of crows.
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