# *Cuscuta campestris* genome, additional data
Additional Data for the manuscript:
**Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris** (under review)
## Data supplied here
### Alignments for calculation of synonymous substitution rate
#### Alignments_dS/
The dS was calculated from these alignments and used in Fig 3B,
and Supplementary figure 1.
Alignments of *C. campestris* genes to their paralogs (for single duplications only), and to their 1:1 orthologs in *Arabidopsis Thaliana*, *Solanum lycopersicum*, and *Ipomoea nil*.
*A. Thaliana* and *S. lycopersicum* Sequences were acquired from Phytozome v12 (https://phytozome.jgi.doe.gov). *I. nil* was acquired from ftp://ftp.ncbi.nlm.nih.gov/genomes/Ipomoea_nil/, and C. cuscuta sequences were generated as described in the main manuscript.
Alignments were performed in protein space with PRANK<sup>1</sup>, and translated back to nucleotide alignments with pal2nal<sup>2</sup>.
### Amino acid sequence alignments for horizontal gene transfer candidate search using MEGAN v.6.0.0
#### Alignments_HGT/
For each Cuscuta campestris candidate listed in Supplementary Table 4, the alignment for the best hit as identified by MEGAN v.6.0.0<sup>3</sup> is provided. The parameters were: minSupportPercent=0.01 minSupport=1 minScore=50.0 maxExpected=0.01 minPercentIdentity=0.0 topPercent=40 lcaPercent=100 minComplexity=0.0 paired reads=false, useIdentityFilter=false.
## Additional data related to the manuscript
Raw reads, the assembled genome sequence and annotations are available
from the European Nucleotide Archive (ENA) under accession number **PRJEB19879**.
## References
1. Loytynoja, A. & Goldman, N. An algorithm for progressive
multiple alignment of sequences with insertions. *Proc. Natl. Acad.
Sci. USA* **102**, 10557-10562 (2005).
2. Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion
of protein 749 sequence alignments into the corresponding codon
alignments. *Nucleic Acids Res.* **34**, W609-612 (2006).
3. Huson, D. H. et al. MEGAN community edition - interactive
exploration and analysis of large-scale microbiome sequencing data.
*PLoS Comput. Biol.* **12**, e1004957 (2016).
