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Citation for Study 14369

Citation title: "Chloroplast genome analysis of Australian eucalypts ? Eucalyptus Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)".

Study name: "Chloroplast genome analysis of Australian eucalypts ? Eucalyptus Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)".

This study is part of submission 14369 (Status: Published).

Citation

Bayly M.J., Rigault P., Spokevicius A., Ladiges P.Y., Ades P., Anderson C., Bossinger G., Merchant A., Udovicic F., Woodrow I., & Tibbits J. 2013. Chloroplast genome analysis of Australian eucalypts ? Eucalyptus Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae). Molecular phylogenetics and Evolution, .

Authors

• Bayly M.J. (submitter) +613 8344 5055
• Rigault P.
• Spokevicius A.
• Ladiges P.Y.
• Ades P.
• Anderson C.
• Bossinger G.
• Merchant A.
• Udovicic F.
• Woodrow I.
• Tibbits J.

Abstract

We present a phylogenetic analysis and comparison of structural features of chloroplast genomes for 39 species of the eucalypt group (genera Eucalyptus, Corymbia, Angophora, and outgroups Allosyncarpia and Stockwellia). We use 41 complete chloroplast genome sequences, adding 39 finished-quality chloroplast genomes to two previously published genomes. Maximum parsimony and Bayesian analyses, based on >7000 variable nucleotide positions, produced one fully resolved phylogenetic tree (35 supported nodes, 27 with 100% bootstrap support). Eucalyptus and its sister lineage Angophora + Corymbia show a deep divergence. Within Eucalyptus, three lineages are resolved: the ?eudesmid?, ?symphyomyrt? and ?monocalypt? groups. Corymbia is paraphyletic with respect to Angophora. Gene content and order does not vary among eucalypt chloroplasts; length mutations, especially frame shifts, are uncommon in protein-coding genes. Some non-synonymous mutations are highly incongruent with the overall phylogenetic signal, notably in rbcL, and may be adaptive. Application of custom informatics pipelines (GYDLE Inc.) enabled direct chloroplast genome assembly, resolving each genome to finished-quality with no need for PCR gap-filling or contig order resolution. Analysis of whole chloroplast genomes resolved major eucalypt clades and revealed variable regions of the genome that will be useful in lower-level genetic studies (including phylogeography and geneflow).

Keywords

Chloroplast genome, Eucalypts , Evolution , Illumina sequencing , Phylogeny

External links

• DOI: 10.1016/j.ympev.2013.07.006
• PMID: 23876290
• Other URL: http://www.sciencedirect.com/science/article/pii/S1055790313002832

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S14369
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref22110,
  	 author = {Michael James Bayly and Philippe  Rigault and Antanas  Spokevicius and Pauline Y Ladiges and Peter  Ades and Charlotte  Anderson and Gerd  Bossinger and Andrew  Merchant and Frank  Udovicic and Ian  Woodrow and Josquin  Tibbits},
  	 title = {Chloroplast genome analysis of Australian eucalypts ? Eucalyptus Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)},
  	 year = {2013},
  	 keywords = {Chloroplast genome, Eucalypts , Evolution , Illumina sequencing , Phylogeny},
  	 doi = {10.1016/j.ympev.2013.07.006},
  	 url = {http://www.sciencedirect.com/science/article/pii/S1055790313002832},
  	 pmid = {23876290},
  	 journal = {Molecular phylogenetics and Evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {We present a phylogenetic analysis and comparison of structural features of chloroplast genomes for 39 species of the eucalypt group (genera Eucalyptus, Corymbia, Angophora, and outgroups Allosyncarpia and Stockwellia).  We use 41 complete chloroplast genome sequences, adding 39 finished-quality chloroplast genomes to two previously published genomes.  Maximum parsimony and Bayesian analyses, based on >7000 variable nucleotide positions, produced one fully resolved phylogenetic tree (35 supported nodes, 27 with 100% bootstrap support).  Eucalyptus and its sister lineage Angophora + Corymbia show a deep divergence.  Within Eucalyptus, three lineages are resolved: the ?eudesmid?, ?symphyomyrt? and ?monocalypt? groups.  Corymbia is paraphyletic with respect to Angophora.  Gene content and order does not vary among eucalypt chloroplasts; length mutations, especially frame shifts, are uncommon in protein-coding genes.  Some non-synonymous mutations are highly incongruent with the overall phylogenetic signal, notably in rbcL, and may be adaptive.  Application of custom informatics pipelines (GYDLE Inc.) enabled direct chloroplast genome assembly, resolving each genome to finished-quality with no need for PCR gap-filling or contig order resolution. Analysis of whole chloroplast genomes resolved major eucalypt clades and revealed variable regions of the genome that will be useful in lower-level genetic studies (including phylogeography and geneflow).}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 22110
  AU  - Bayly,Michael James
  AU  - Rigault,Philippe 
  AU  - Spokevicius,Antanas 
  AU  - Ladiges,Pauline Y
  AU  - Ades,Peter 
  AU  - Anderson,Charlotte 
  AU  - Bossinger,Gerd 
  AU  - Merchant,Andrew 
  AU  - Udovicic,Frank 
  AU  - Woodrow,Ian 
  AU  - Tibbits,Josquin 
  T1  - Chloroplast genome analysis of Australian eucalypts ? Eucalyptus Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)
  PY  - 2013
  KW  - Chloroplast genome
  KW  - Eucalypts 
  KW  - Evolution 
  KW  - Illumina sequencing 
  KW  - Phylogeny
  UR  - http://www.sciencedirect.com/science/article/pii/S1055790313002832
  N2  - We present a phylogenetic analysis and comparison of structural features of chloroplast genomes for 39 species of the eucalypt group (genera Eucalyptus, Corymbia, Angophora, and outgroups Allosyncarpia and Stockwellia).  We use 41 complete chloroplast genome sequences, adding 39 finished-quality chloroplast genomes to two previously published genomes.  Maximum parsimony and Bayesian analyses, based on >7000 variable nucleotide positions, produced one fully resolved phylogenetic tree (35 supported nodes, 27 with 100% bootstrap support).  Eucalyptus and its sister lineage Angophora + Corymbia show a deep divergence.  Within Eucalyptus, three lineages are resolved: the ?eudesmid?, ?symphyomyrt? and ?monocalypt? groups.  Corymbia is paraphyletic with respect to Angophora.  Gene content and order does not vary among eucalypt chloroplasts; length mutations, especially frame shifts, are uncommon in protein-coding genes.  Some non-synonymous mutations are highly incongruent with the overall phylogenetic signal, notably in rbcL, and may be adaptive.  Application of custom informatics pipelines (GYDLE Inc.) enabled direct chloroplast genome assembly, resolving each genome to finished-quality with no need for PCR gap-filling or contig order resolution. Analysis of whole chloroplast genomes resolved major eucalypt clades and revealed variable regions of the genome that will be useful in lower-level genetic studies (including phylogeography and geneflow).
  L3  - 10.1016/j.ympev.2013.07.006
  JF  - Molecular phylogenetics and Evolution
  VL  - 
  IS  - 
  ER  -