title: Chloroplast genome analysis of Australian eucalypts--Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae).
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 do 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).
authors.affiliation: School of Botany, The University of Melbourne, Vic. 3010, Australia.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Bayly
authors.forename: Philippe
authors.initials: P
authors.lastname: Rigault
authors.forename: Antanas
authors.initials: A
authors.lastname: Spokevicius
authors.forename: Pauline Y
authors.initials: PY
authors.lastname: Ladiges
authors.forename: Peter K
authors.initials: PK
authors.lastname: Ades
authors.forename: Charlotte
authors.initials: C
authors.lastname: Anderson
authors.forename: Gerd
authors.initials: G
authors.lastname: Bossinger
authors.forename: Andrew
authors.initials: A
authors.lastname: Merchant
authors.forename: Frank
authors.initials: F
authors.lastname: Udovicic
authors.forename: Ian E
authors.initials: IE
authors.lastname: Woodrow
authors.forename: Josquin
authors.initials: J
authors.lastname: Tibbits
mesh_terms: D001499:Bayes Theorem; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D005052:Eucalyptus / Q000235:genetics; D016368:Frameshift Mutation; D014644:Genetic Variation; D054628:Genome, Chloroplast; D018745:Genome, Plant; D027822:Myrtaceae / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase
keywords: Chloroplast genome; Eucalypts; Evolution; Illumina sequencing; Phylogeny