Phylogenomic evidence of bryophytes' monophyly using complete and incomplete data sets from chloroplast proteomes

    Authors

    A. Shanker; V. Sharma;H. Daniell

    Comments

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    Abbreviated Journal Title

    J. Plant Biochem. Biotechnol.

    Keywords

    Chloroplast; Bryophytes; Phylogeny; Missing data; EARLIEST LAND PLANTS; RIBOSOMAL-RNA GENE; MOLECULAR PHYLOGENY; EARLY; EVOLUTION; GREEN-ALGAE; LIVERWORTS; SEQUENCES; ORIGIN; TRACHEOPHYTES; HORNWORTS; Biochemistry & Molecular Biology; Plant Sciences

    Abstract

    It is well recognized that bryophytes form the basal clade of land plants. However, the paraphyletic or monophyletic origin of bryophytes remains controversial. To get new insight into bryophytes' relationship we analyzed four data sets, 1 complete (common orthologous protein sequences; COPs) and 3 incomplete (COPs + 1, COPs + 1 + 3 and COPs + 1 + 3 + 2 data sets with 0.16%, 3.2% and 3.77% missing data, respectively) from chloroplast proteomes, representing 1 charophycean alga (outgroup), 5 bryophytes, 4 pteridophytes and 6 gymnosperms. Maximum likelihood analyses under cpREV model of all four data sets showed monophyly of bryophytes with 100% bootstrap support. Further, sister relationship of mosses and liverworts has been inferred with strong bootstrap support in all data sets. Although all incomplete data sets have gradually increasing missing data, the trees obtained from them have higher levels of bootstrap support for most of the nodes in comparison to the tree from complete data set. This study also demonstrated the importance of using longer sequences even with missing data for phylogeny reconstruction.

    Journal Title

    Journal of Plant Biochemistry and Biotechnology

    Volume

    20

    Issue/Number

    2

    Publication Date

    1-1-2011

    Document Type

    Article

    Language

    English

    First Page

    288

    Last Page

    292

    WOS Identifier

    WOS:000292048900022

    ISSN

    0971-7811

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