DOI: 10.5061/dryad.h18932011
title: Data from: Chromosome-scale genome assemblies of two allopolyploid <em>Cuscuta</em> species uncover genomic signatures of parasitic lifestyle and polyploid evolution

description: Dodders (Cuscuta spp.) are obligate parasitic plants that have
 lost a large portion of photosynthetic genes but gained host genes through
 parasitism-mediated horizontal gene transfer. Their migration across the
 world has contributed to the complexity of speciation via geographic
 isolation. Here, we report the de novo genome assemblies of two
 phylogenetically distinct dodders: Cuscuta campestris (2n = 4x = 60) and
 Cuscuta chinensis (2n = 4x = 60), which are classified into Clade B and
 Clade H of subgenus Grammica, respectively. Relatively low completeness of
 Benchmarking Universal Single-Copy Orthologs genes (ca. 87%) indicated
 progressive gene loss after evolution of the parasitic lifestyle due to
 release from functional constraints such as photosynthesis and organ
 development. Comparative genomics analyses revealed that the genome size
 of each species differs significantly, despite having the same cytotype
 and allopolyploidy, through independent hybridization involving different
 ancient parents. Various genomic rearrangements have likely contributed to
 the genomic diversity and sexual isolation of the two lineages, which
 partly share habitats, including (1) gene gain and loss events, (2)
 homoeologous recombination between two subgenomes, and (3)
 lineage-specific proliferation of transposable elements. Our findings not
 only provide a genomic basis for surveying parental species for
 allopolyploidization but also enhance understanding of the unique
 speciation of parasitic dodders through these chromosomal events.
description: # Chromosome-scale Genome Assemblies of Two Allopolyploid *Cuscuta*
 Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid
 Evolution ###### Principle Investigator Contact Information ``` Name:
 Tenta Segawa Institution: Research Institute, Suntory Global Innovation
 Center Ltd. Email: Tenta_Segawa@suntory.co.jp ``` ###### Alternate Contact
 Information ``` Name: Eiichiro Ono Institution: Research Institute,
 Suntory Global Innovation Center Ltd. Email: Eiichiro_Ono@suntory.co.jp
 ``` ## Dataset Overview This dataset comprises the raw and key
 intermediate data supporting our study on genome construction for two
 allopolyploid *Cuscuta* genomes. * Repeat data for the *Cuscuta* genomes *
 Divergence time estimation inputs * Gene prediction results for
 *Calystegia* *soldanella* * *d*s calculations * Trinity-based
 transcriptome assembly results for *Cuscuta* *pentagona* ## Files and
 Folders ### Repeat data for the *Cuscuta* genomes The files are contained
 in repeat_data.tar.gz Details are provided below. #####
 Cuscuta_campestris_Kyotango.TE-families.fa RepeatModeler results for
 *Cuscuta* *campestris*. Consensus sequences of TE families are provided in
 FASTA format. ##### Cuscuta_campestris_Kyotango.TE.v1.gff RepeatMasker
 results for *Cuscuta* *campestris*. Genomic locations of TEs are provided
 in GFF format. ##### Cuscuta_chinensis_Kaifu.TE-families.fa RepeatModeler
 results for *Cuscuta* *chinensis*. Consensus sequences of TE families are
 provided in FASTA format. ##### Cuscuta_chinensis_Kaifu.TE.v1.gff
 RepeatMasker results for *Cuscuta* *chinensis*. Genomic locations of TEs
 are provided in GFF format. ### Divergence time estimation inputs The
 files are contained in divergence_time.tar.gz Details are provided below.
 ##### Orthogroups.txt Orthofinder results. A table listing each OrthoID
 and the gene IDs belonging to that group. ##### alignment folder This
 folder has the following structure. ``` alignment---OrthoID---prot.fa |
 |-aligned_prot.fa | |-aligned_cds.fa : ``` Inside the alignment folder,
 there are subfolders named after the OrthoIDs listed in Orthogroups.txt.
 prot.fa contains the amino acid sequences from multiple species
 corresponding to that OrthoID. aligned_prot.fa contains the multiple
 sequence alignment of prot.fa produced with MAFFT. aligned_cds.fa contains
 the codon-aware alignment obtained by converting aligned_prot.fa with
 pal2nal. ##### 4Dtv.fa The concatenated nucleotides from 4Dtv sites are
 provided in FASTA format. ##### Untitled.xml File containing the prior
 settings for divergence time estimation created with BEAUti. ### Gene
 prediction results for *Calystegia* *soldanella* The files are contained
 in Calystegia_soldanella_braker3.tar.gz Details are provided below. #####
 Csol_braker.gtf Gene prediction results generated by BRAKER3 in GTF
 format. ##### Csol_cds.fa Predicted CDS sequences generated by BRAKER3,
 provided in FASTA format. ##### Csol_prot.fa Predicted amino acid
 sequences generated by BRAKER3, provided in FASTA format. ### Gene
 prediction results for *d*s calculations The files are contained in
 ds_analysis.tar.gz Details are provided below. ##### yn00.ctl yn00 control
 (.ctl) file used for the *d*s calculations. #####
 ds_Ccampestris_Caustralis folder Raw data used for *d*s calculations
 between *C*. *campestris* and *C*. *australis*. This folder has the
 following structure. ``` ds_Ccampestris_Caustralis---blast.txt
 |-calc_dS---gene_id_vs_geneid---aligned_cds.fa | |-aligned_prot.fa : ```
 Inside the ds_Ccampestris_Caustralis folder, the BLAST results linking
 *C*. *campestris* and *C*. *australis* genes are provided in blast.txt.
 The calc_dS subfolder contains per-ortholog subdirectories named with the
 best-hit gene IDs from the BLAST search. aligned_prot.fa stores the MAFFT
 multiple alignment of the corresponding amino acid sequences.
 aligned_cds.fa stores the codon-aware alignment obtained by converting
 aligned_prot.fa with pal2nal. ##### ds_Ccampestris_Cpentagona folder Raw
 data used for *d*s calculations between *C*. *campestris* and *C*.
 *pentagona*. The folder structure and file contents are the same as in
 ds_Ccampestris_Caustralis. ##### ds_Cchinensis_HI_HII folder Raw data used
 for *d*s calculations between the HI and HII subgenomes of *C*.
 *chinensis*. The folder structure and file contents are the same as in
 ds_Ccampestris_Caustralis. ### Trinity-based transcriptome assembly
 results for *Cuscuta* *pentagona* The files are contained in
 Cuscuta_pentagona_trinity.tar.gz Details are provided below. #####
 trinity_out.Trinity.fasta Trinity-assembled transcriptome of *C*.
 *pentagona*, provided in FASTA format. #####
 trinity_out.Trinity.fasta.transdecoder.cds Predicted CDS sequences from
 TransDecoder run on trinity_out.Trinity.fasta, provided in FASTA format.
 ##### trinity_out.Trinity.fasta.transdecoder.pep Predicted amino acid
 sequences from TransDecoder run on trinity_out.Trinity.fasta, provided in
 FASTA format.