Open Access Highly Accessed Research article

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species

Yeting Zhang12, Monica Fernandez-Aparicio34, Eric K Wafula5, Malay Das3, Yuannian Jiao5, Norman J Wickett56, Loren A Honaas5, Paula E Ralph5, Martin F Wojciechowski7, Michael P Timko8, John I Yoder9, James H Westwood3 and Claude W dePamphilis125*

Author Affiliations

1 Intercollege Graduate Program in Genetics, Institute of Molecular Evolutionary Genetics, Penn State University, University Park, PA 16802, USA

2 Huck Institutes of the Life Science, Penn State University, University Park, PA 16802, USA

3 Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA

4 Department of Plant Breeding, Institute for Sustainable Agriculture, IAS-CSIC, Córdoba, 14080, Spain

5 Department of Biology and Institute of Molecular Evolutionary Genetics, Penn State University, University Park, 16802, PAU.S.A

6 Chicago Botanic Garden, Glencoe, IL, 60022, U.S.A

7 School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA

8 Department of Biology, University of Virginia, Charlottesville, VA 22904, U.S.A

9 Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A

For all author emails, please log on.

BMC Evolutionary Biology 2013, 13:48  doi:10.1186/1471-2148-13-48

Published: 20 February 2013

Additional files

Additional file 1: Figure S1:

Phylogeny of major lineage of plants, adapted from Soltis et al [42]. Legumes belong to the rosid order Fabales (blue box), while the parasites Phelipanche and Cuscuta represent derived lineages within the asterid orders Lamiales, (red box) and Solanales (green box), respectively.

Format: PNG Size: 277KB Download file

Open Data

Additional file 2: Figure S2:

NCBI BLAST result (database: nr, BLASTp) of (A) P. aegyptiaca albumin1-1 (unigene 12653) and (B) P. aegyptiaca albumin1-2 (unigene 75797).

Format: PDF Size: 277KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3: Figure S3:

Amino acid alignment of insect toxin albumin 1 protein (Medicago_truncatula_albumin1_Q7XZC5) and inferred protein sequences for the two homologs in P. aegyptiaca, and (B) structure of the M. truncatula toxic albumin 1 gene. (A) Inferred protein sequence alignments are 57.3-58.3% identical and 72.7%-74.3% similar (= identity + conservative substitutions) in shared regions between the legume and parasite proteins. (B) The legume protein product has a 27 amino acid signal peptide and 113 amino acid mature peptide; both regions are similarly conserved between the legume and Phelipanche inferred proteins. The gene structure representation for this legume gene was obtained from EMBL-EBI databases [74] (accession #AJ574789).

Format: PDF Size: 1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4: Figure S4:

Alignments of the 3’ end of genomic and inferred CDS sequences of albumin 1 homologs from five Phelipanche species. Two genes are identified from P. aegyptiaca unigene 12653 (first five sequences, red bar) and unigene 75797 (yellow bar). Red box indicates putative stop codon.

Format: PNG Size: 319KB Download file

Open Data

Additional file 5: Figure S5:

Partial genomic DNA and cDNA alignments of M. truncatula albumin 1 (Medtr8g025950), P. aegyptiaca albumin1-1 (12653) and P. aegyptiaca albumin 1-2 (75797). Intron start and end positions are illustrated by arrows.

Format: PNG Size: 282KB Download file

Open Data

Additional file 6: Table S1:

Expression values for albumin 1 genes in P. aegyptiaca at different developmental stages. Expression levels were measured by number of mapped

    R
eads to this gene
    P
er
    K
ilobase of sequence length per
    M
illion (M) library reads (RPKM) in Illumina sequence (G) libraries (PPGP). Developmental stages described in Table S2.

Format: DOCX Size: 63KB Download file

Open Data

Additional file 7: Table S2:

Developmental stages used for transcriptome sequencing in P. aegyptiaca[54] with characteristics of each stage and the expectation of host plant tissue contamination in library preparations.

Format: DOCX Size: 80KB Download file

Open Data

Additional file 8: Figure S6:

Maximum likelihood (ML) phylogeny of KNOTTIN homologs in broomrape species, Cuscuta pentagona and papilionoid legumes. ML and Bayesian Inference (BI) methods produced the same tree topology. Three Cuscuta pentagona sequences were obtained from the 1KP project and from additional independently prepared libraries. Other information as given (Figure 2).

Format: PDF Size: 239KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9: Table S3:

HGT candidates BLAST database. Information that cannot be retrieved is marked as Not Applicable (NA). M: million; GB: Gigabase.

Format: DOCX Size: 108KB Download file

Open Data

Additional file 10: Table S4:

Evolutionary constraints in albumin 1 genes in Phelipanche and related legumes.

Format: DOCX Size: 90KB Download file

Open Data

Additional file 11: Table S5:

PCR primers used for albumin 1 amplification.

Format: DOCX Size: 52KB Download file

Open Data