Turnera subulata ASM2838606v3 Assembly & Annotation

Overview

Analysis Name Turnera subulata ASM2838606v3 Assembly & Annotation
Sequencing technology Illumina HiSeq
Assembly method DISCOVAR de novo v. June-2016
Release Date 2023-02-01
Reference Publication(s)

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.

Abstract

A 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

Assembly

The Turnera subulata ASM2838606v3 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) GCA_028386065.3_ASM2838606v3_genomic.fna.gz

Gene Predictions

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 Analysis

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

S genes

Summary

QueryScaffoldSize(bp)CoordinatesBLASTn HitBLASTn %ID
TsSPH1MK890302.1724069306236-305766MK890302.1, TsSPH1100
TsYUC6MK890302.1724069364980-353902MK890302.1, TsYUC6100
TsBAHDMK890302.1724069528602-529918MK890302.1, TsBAHD100

Nucleotide

Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences