Analysis Name | Turnera subulata ASM2838606v3 Assembly & Annotation |
Sequencing technology | Illumina HiSeq |
Assembly method | DISCOVAR de novo v. June-2016 |
Release Date | 2023-02-01 |
Henning PM, Roalson EH, Mir W, McCubbin AG, Shore JS. Annotation of the Turnera subulata (Passifloraceae) Draft Genome Reveals the S-Locus Evolved after the Divergence of Turneroideae from Passifloroideae in a Stepwise Manner. Plants (Basel). 2023 Jan 7;12(2):286. doi: 10.3390/plants12020286.
AbstractA majority of Turnera species (Passifloraceae) exhibit distyly, a reproductive system involving both self-incompatibility and reciprocal herkogamy. This system differs from self-incompatibility in Passiflora species. The genetic basis of distyly in Turnera is a supergene, restricted to the S-morph, and containing three S-genes. How supergenes and distyly evolved in Turnera, and the other Angiosperm families exhibiting distyly remain largely unknown. Unraveling the evolutionary origins in Turnera requires the generation of genomic resources and extensive phylogenetic analyses. Here, we present the annotated draft genome of the S-morph of distylous Turnera subulata. Our annotation allowed for phylogenetic analyses of the three S-genes’ families across 56 plant species ranging from non-seed plants to eudicots. In addition to the phylogenetic analysis, we identified the three S-genes’ closest paralogs in two species of Passiflora. Our analyses suggest that the S-locus evolved after the divergence of Passiflora and Turnera. Finally, to provide insights into the neofunctionalization of the S-genes, we compared expression patterns of the S-genes with close paralogs in Arabidopsis and Populus trichocarpa. The annotation of the T. subulata genome will provide a useful resource for future comparative work. Additionally, this work has provided insights into the convergent nature of distyly and the origin of supergenes.
Assembly statistics
Genome size | 544.6 Mb |
Number of scaffolds | 7,883 |
Scaffold N50 | 111 kb |
Scaffold L50 | 1,396 |
Number of contigs | 21,513 |
Contig N50 | 55.1 kb |
Contig L50 | 2,789 |
Assembly level | Scaffold |
The Turnera subulata ASM2838606v3 Assembly file is available in FASTA format.
Downloads
Chromosomes (FASTA file) | GCA_028386065.3_ASM2838606v3_genomic.fna.gz |
The Turnera subulata ASM2838606v3 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
Genes (GFF3 file) | GCA_028386065.3_ASM2838606v3_genomic.gff.gz |
CDS sequences (FASTA file) | GCA_028386065.3_ASM2838606v3_cds_from_genomic.fna.gz |
Protein sequences (FASTA file) | GCA_028386065.3_ASM2838606v3_protein.faa.gz |
Functional annotation for the Turnera subulata ASM2838606v3 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
Domain from InterProScan | Turnera_subulata_ASM2838606v3.Pfam.tsv.gz |
Summary
Query | Scaffold | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID |
TsSPH1 | MK890302.1 | 724069 | 306236-305766 | MK890302.1, TsSPH1 | 100 |
TsYUC6 | MK890302.1 | 724069 | 364980-353902 | MK890302.1, TsYUC6 | 100 |
TsBAHD | MK890302.1 | 724069 | 528602-529918 | MK890302.1, TsBAHD | 100 |
Nucleotide
Protein