The first genome for the Cape Primrose Streptocarpus rexii (Gesneriaceae), a model plant for studying meristem‐driven shoot diversity

Abstract

Cape Primroses ( Streptocarpus , Gesneriaceae) are an ideal study system for investigating the genetics underlying species diversity in angiosperms. Streptocarpus rexii has served as a model species for plant developmental research for over five decades due to its unusual extended meristem activity present in the leaves. In this study, we sequenced and assembled the complete nuclear, chloroplast, and mitochondrial genomes of S. rexii using Oxford Nanopore Technologies long read sequencing. Two flow cells of PromethION sequencing resulted in 32 billion reads and were sufficient to generate a draft assembly including the chloroplast, mitochondrial and nuclear genomes, spanning 776 Mbp. The final nuclear genome assembly contained 5,855 contigs, spanning 766 Mbp of the 929‐Mbp haploid genome with an N50 of 3.7 Mbp and an L50 of 57 contigs. Over 70% of the draft genome was identified as repeats. A genome repeat library of Gesneriaceae was generated and used for genome annotation, with a total of 45,045 genes annotated in the S. rexii genome. Ks plots of the paranomes suggested a recent whole genome duplication event, shared between S. rexii and Primulina huaijiensis . A new chloroplast and mitochondrial genome assembly method, based on contig coverage and identification, was developed, and successfully used to assemble both organellar genomes of S. rexii . This method was developed into a pipeline and proved widely applicable. The nuclear genome of S. rexii and other datasets generated and reported here will be invaluable resources for further research to aid in the identification of genes involved in morphological variation underpinning plant diversification.

The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments

“…Several scaffolds did not attain chromosome lengths possibly due to chimeric read mapping. The GC content of the H. rhodopensis’ genome (38.08%) is similar to that of Arabidopsis thaliana (36%), Streptocarpus rexii (38.89%; member of Gesneriaceae family; [ 44 ]) and Xerophyta viscosa (36.51%), a resurrection species from the Velloziaceae family [ 45 ], but lower than that of other resurrection species including Boea hygrometrica (42.30%; Gesneriaceae family; [ 46 ]), and two from the Linderniaceae family ( C. plantagineum (40.26%; [ 47 ]) and L. brevidens (39.26%; [ 48 ])) (Fig. S2A).…”

A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants

“…The protocol described here was developed from a previous method used for ONT sequencing [ 15 , 16 ]. However, this protocol uses a guanidine-based lysis buffer (Qiagen buffer G2, 800 mM guanidine hydrochloride; 30 mM Tris-HCl, pH 8.0; 30 mM EDTA, pH 8.0; 5% Tween 20; 0.5% Triton X-100), unsuitable for PacBio HiFi sequencing [ 3 ], and was replaced with a CTAB buffer (see “ Methods ” section) [ 17 , 18 ].…”

“…The first Streptocarpus genome, of S. rexii , a species with a 1C genome size of ca. 929 Mb and 2 n = 32 chromosomes [ 14 ], was recently published [ 15 ] using Oxford Nanopore Technologies (ONT) PromethION sequencing with a DNA extraction method specifically developed for the ONT genome sequencing of Streptocarpus [ 15 , 16 ]. However, the DNA extraction protocol for PacBio HiFi sequencing has specific requirements; for example, the guanidine lysis buffer, phenol and chloroform purification need to be avoided as they interfere with sequencing performance [ 3 ].…”

Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation

“…We applied a combination of approaches to infer WGD events across the backbone phylogeny of Gesneriaceae, including synonymous substitution rate ( Ks ) estimation, gene tree mapping, and syntenic analysis. These analyses used 138 transcriptomes, as well as four Gesneriaceae genomes, that is, P. huaijiensis ( Feng et al 2020 ), Dorcoceras hygrometricum (≡ Boea hygrometrica ; Xiao et al 2015 ; Puglisi et al 2016 ), S. rexii ( Nishii et al 2022 ), and Henckelia pumila .…”

“…Recently, using a high-quality genome of Primulina huaijiensis and eight transcriptomes of other gesneriads, Feng et al (2020) detected a lineage-specific WGD (referred to as the “ D event”) in subtribe Didymocarpinae, the largest subtribe in Gesneriaceae with about 57% of species. More recently, Nishii et al (2022) , comparing the genome of Streptocarpus rexii with P. huaijiensis, suggested that the D event might be shared with subtribe Streptocarpinae. However, due to limited taxon sampling, the exact phylogenetic placement of the D event is still uncertain.…”