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

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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.

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Fig. 1

Abbreviations

LBT:

Liverworts basal topology

HBT:

Hornworts basal topology

BBH:

Bi-directional best hit

COPs:

Common orthologous protein sequences

ML:

Maximum likelihood

BS:

Bootstrap support

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Acknowledgments

Authors are thankful to Prof. Aditya Shastri, Vice Chancellor, Banasthali University for providing necessary conditions for work. The use of internet facility of DBT Centre for Bioinformatics is also duly acknowledged. This study was supported by a grant from University Grants Commission, India in the form of Minor Research Project to AS.

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Authors and Affiliations

  1. Department of Bioscience and Biotechnology, Banasthali University, Banasthali, 304022, Rajasthan, India

    Asheesh Shanker & Vinay Sharma

  2. Department of Molecular Biology & Microbiology, Biomolecular Science, College of Medicine, University of Central Florida, Bldg # 20, Room 336, Orlando, FL, 32816–2364, USA

    Henry Daniell

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  1. Asheesh Shanker
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  2. Vinay Sharma
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  3. Henry Daniell
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Correspondence to Vinay Sharma.

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Shanker, A., Sharma, V. & Daniell, H. Phylogenomic evidence of bryophytes’ monophyly using complete and incomplete data sets from chloroplast proteomes. J. Plant Biochem. Biotechnol. 20, 288–292 (2011). https://doi.org/10.1007/s13562-011-0054-5

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