Systematics Section / ASPT
Zhengqiu, Cai , Peñaflor, Cynthia , Leebens-Mack, Jim , Kuehl, Jennifer V. , Carlson, John , dePamphilis, Claude W. , Boore, Jeffrey , Jansen, Robert K. .
Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids and evolution of GC content.
WE have sequenced the complete chloroplast genomes of Drimys, Liriodendron, and Piper. The genomes have identical gene order and gene content as other unrearranged angiosperms. We extracted 72 shared genes from these three genomes and 31 other publicly available genomes and developed a semi-automated procedure to align them. The alignment begins with the translation of nucleotide sequences into amino acids followed by automated alignment of amino acids with MUSCLE. The resulting amino acid alignment is adjusted manually and then used to constrain the nucleotide alignment to create a data matrix in Nexus format. We divided this data matrix into three functional categories: photosynthetic genes, genetic system genes, and NADH genes. The GC distribution pattern was then examined for each group of genes. GC content is unevenly distributed among both genes and the three codon positions. Photosynthetic genes have the highest GC content, followed by genetic system genes, and NADH genes have the lowest GC content. The GC content is highest in the first codon position and lowest in the third position for all the three functional groups. These results are consistent with previous studies. We used the aligned data matrix of 61 shared genes to reconstruct phylogenetic trees to resolve phylogenetic relationships of Drimys, Liriodendron, Piper, and Calycanthus with both maximum parsimony (MP) and maximum likelihood (ML) methods. Both MP and ML trees are congruent with regard to the relationships of magnoliids. There is strong support for the monophyly of magnoliids (92-100% bootstrap values) and this clade is sister to a large clade that includes monocots and eudicots. A single genome from each of the four orders of magnoliids was included and there is strong support for the sister relationship between Canellales/Piperales and Laurales/Magnoliales.
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1 - University of Texas Austin, Section of Integrative Biology, 1 University Station, A6700, Austin, Texas, 78712-7640, USA
2 - Brigham Young University, Department of Integrative Biology, 401 Widtsoe Building, Provo, Utah, 84602, USA
3 - University of Georgia, Department of Plant Biology, Athens, Georgia, 30602, USA
4 - DOE Joint Genome Institute and Lawrence Berkeley National Lab, Evolutionary Genomics Program, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA
5 - Pennsylvania State University, School of Forest Resources, University Park, Pennsylvania, 16802, USA
6 - Pennsylvania State University, Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, University Park, Pennsylvania, 16802, USA
Presentation Type: Poster:Posters for Sections
Location: Auditorium/Bell Memorial Union
Date: Tuesday, August 1st, 2006
Time: 12:30 PM