Petunia axillaris subsp. axillaris 'N (cultivar)' Peax403 Assembly & Annotation

Overview

Analysis Name Petunia axillaris subsp. axillaris 'N (cultivar)' Peax403 Assembly & Annotation
Sequencing technology PacBio Sequel
Assembly method wtdbg2 v. MAY-2020
Release Date 2023-02-20
Reference Publication(s)

Li, C., Binaghi, M., Pichon, V. et al. Tight genetic linkage of genes causing hybrid necrosis and pollinator isolation between young species. Nat. Plants 9, 420–432 (2023). https://doi.org/10.1038/s41477-023-01354-8.

Abstract

The mechanisms of reproductive isolation that cause phenotypic diversifcation and eventually speciation are a major topic of evolutionary research. Hybrid necrosis is a post-zygotic isolation mechanism in which cell death develops in the absence of pathogens. It is often due to the incompatibility between proteins from two parents. Here we describe a unique case of hybrid necrosis due to an incompatibility between loci on chromosomes 2 and 7 between two pollinator-isolated Petunia species. Typical immune responses as well as endoplasmic reticulum stress responses are induced in the necrotic line. The locus on chromosome 2 encodes ChiA1, a bifunctional GH18 chitinase/lysozyme. The enzymatic activity of ChiA1 is dispensable for the development of necrosis. We propose that the extremely high expression of ChiA1 involves a positive feedback loop between the loci on chromosomes 2 and 7. ChiA1 is tightly linked to major genes involved in the adaptation to diferent pollinators, a form of pre-zygotic isolation. This linkage of pre- and post-zygotic barriers strengthens reproductive isolation and probably contributes to rapid diversifcation and speciation.

Assembly statistics

Genome size 1.2G
Number of chromosomes 7
Number of Scaffolds 341
Scaffold L50 4
Scaffold N50 173 Mb
Number of Contigs 600
Contig L50 23
Contig N50 15.2 Mb
Assembly level Chromosome

Assembly

The Petunia axillaris subsp. axillaris 'N (cultivar)' Peax403 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Petunia_axillaris_Peax403_genome.fasta.gz

Gene Predictions

The Petunia axillaris subsp. axillaris 'N (cultivar)' Peax403 genome gene prediction files are not available.

Downloads

Genes (GFF3 file) -
CDS sequences (FASTA file) -
Protein sequences (FASTA file) -

Functional Analysis

Functional annotation for the Petunia axillaris subsp. axillaris 'N (cultivar)' Peax403 is not available.

Downloads

Domain from InterProScan -

S genes

Summary

Query Chromosome Size(bp) Coordinates BLASTp Hit BLASTp %ID Domain
SLF1-1 CM049421.1 156255816 127457386-127458555 AGL76530, S5-SLF1 99 F-box domain
SFL1-2 CM049421.1 156255816 128296822-128295653 ADD21612, S1-SLF1 99 F-box domain
SLF2 CM049421.1 156255816 118000713-118001879 BAJ24857, S19-SLF2 95 F-box domain
SLF3 CM049421.1 156255816 127544332-127545489 BAJ24858, S5-SLF3 98 F-box domain
SLF4 CM049421.1 156255816 124359456-124360667 BAJ24865, S7-SLF4 94 F-box domain
SLF5 CM049421.1 156255816 117059536-117060705 BAJ24871, S7-SLF5 95 F-box domain
SLF6 CM049421.1 156255816 117265699-117264521 BAJ24881, S19-SLF6 96 F-box domain
SLF8 CM049421.1 156255816 127420965-127422140 ABX82525, S2-SLF8 90 F-box domain
SLF10 CM049421.1 156255816 136581105-136582244 BAQ19011, SLF10-S22 100 F-box domain
SLF11 CM049421.1 156255816 122951004-122949847 BAQ18962, SLF11-S10 95 F-box domain
SLF12 CM049421.1 156255816 127479292-127480473 AIK66457, S3-SLF12 99 F-box domain
SLF13 CM049421.1 156255816 127633471-127634634 AIK66461, S2-SLF13 98 F-box domain
SLF14 CM049421.1 156255816 117175082-117176275 AIK66466, S2-SLF14 98 F-box domain
SLF15 CM049421.1 156255816 127897883-127896690 BAQ19016, SLF15-S22 99 F-box domain
SLF16 CM049421.1 156255816 126657295-126658455 AIK66479, S6a-SLF16 99 F-box domain
SLF18-1 CM049421.1 156255816 124745350-124744208 BAQ19002, S19-FBX2 84 F-box domain
SLF18-2 CM049421.1 156255816 123944057-123942879 BAQ18968.1, SLF18-S10 100 F-box domain
SLF19-1 CM049421.1 156255816 124930094-124931254 BAQ19002, S19-FBX2 80 F-box domain
SLF19-2 CM049421.1 156255816 125161084-125162244 BAQ19002, S19-FBX2 80 F-box domain
S-RNase CM049421.1 156255816 136395439-136395675,
136395794-136396225
AAA60465, S1-RNase 100 Ribonuclease T2 family

Nucleotide

Protein

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