TreeBASE Search-Analyses for study 14369

@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).} }