Open Access Research article

Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses

Adrien Jeanniard1, David D Dunigan23, James R Gurnon2, Irina V Agarkova23, Ming Kang2, Jason Vitek2, Garry Duncan4, O William McClung4, Megan Larsen45, Jean-Michel Claverie1, James L Van Etten23* and Guillaume Blanc1

Author Affiliations

1 Information Génomique & Structurale, IGS UMR7256, CNRS, Aix-Marseille Université, Marseille, FR-13288, France

2 Department of Plant Pathology, University of Nebraska, Lincoln, NE, 68583-0722, USA

3 Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0900, USA

4 Biology Department, Nebraska Wesleyan University, Lincoln, NE, 68504, USA

5 Current address: Department of Biology, Indiana University, Bloomington, IN, 47408, USA

For all author emails, please log on.

BMC Genomics 2013, 14:158  doi:10.1186/1471-2164-14-158

Published: 8 March 2013

Additional files

Additional file 1: Table S1.:

632 Chlorovirus protein families. (XLSX 118 kb)

Format: XLSX Size: 119KB Download file

Open Data

Additional file 2: Table S2.:

Example of orthologous protein clusters viewed for the first time in Chloroviruses. (PDF 16 kb)

Format: PDF Size: 16KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3: Figure S1.:

Neighbor joining tree of the reference concatenated alignment. The NJ tree of chloroviruses is based on a concatenated alignment of 32 core protein families (7762 gap-free sites). Phylogenetic distances were computed using the WAG + G + I substitution model. Branch support was estimated from 1000 bootstrap replicates. We only show bootstrap values < 90%. Branches that differed from the ML and MP trees are colored in red. (PDF 16 kb)

Format: PDF Size: 16KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4: Figure S2.:

Maximum parsimony tree of the reference concatenated alignment. The MP tree of chloroviruses is based on a concatenated alignment of 32 core protein families (7762 gap-free sites). Phylogenetic tree was computed using the close-neighbor-interchange method. Branch support was estimated from 1000 bootstrap replicates. We only show bootstrap values <90%. (PDF 14 kb)

Format: PDF Size: 14KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5: Table S3.:

PBCV-1 genes missing in the KS1B genome as the result of a 35Kb deletion. (PDF 20 kb)

Format: PDF Size: 21KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7: Table S4.:

Sister groups to non-ancestral Chlorovirus proteins based on 35 phylogenetic trees shown in Additional file 7: Figure S3.

Format: PDF Size: 19KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6: Figure S3.:

35 phylogenetic trees of non-ancestral Chlorovirus protein families. Trees were reconstructed using the ML method using the WAG + G + I substitution model. Interior branch support was estimated by the approximate likelihood ratio test (aLRT). For the sake of clarity, we only show branch support for important clades. Taxon names are colorized according to taxonomic information: Chlorovirus (red), chlorophytes (dark green), streptophytes (light green), eukaryote (violet), prokaryote (pink) and DNA virus (blue). Genbank gi numbers are given after species names. Protein family ID and functional annotation are given above each tree. )

Format: PDF Size: 149KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8: Figure S4.:

Phylogenetic trees showing potential HGT between chloroviruses and Chlorella. Trees were reconstructed using the ML method using the WAG + G + I substitution model. Interior branch support was estimated by the approximate likelihood ratio test (aLRT). For the sake of clarity, we only show branch support for important clades. Taxon names are colorized according to taxonomic information: Chlorovirus (red), chlorophytes (dark green), streptophytes (light green), eukaryote (violet), prokaryote (pink) and DNA virus (blue). Genbank gi numbers are given after species names. Protein family ID and functional annotation are given above each tree.

Format: PDF Size: 53KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9: Table S5.:

Attributes of the sequenced chloroviruses.

Format: PDF Size: 53KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 10: Figure S5.:

Schema of the multiplexed sequencing strategy.

Format: PDF Size: 83KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data