Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory

Palvalfi, Gergo; Hackl, Thomas; Terhoeven, Niklas; Shibata, Tomoko; Nishiyama, Tomoaki; Ankenbrand, Markus J.; Freund, Matthias; Iosip, Anda; Kreuzer, Ines; Saul, Franziska; Kamida, Chiharu; Fukui, Kenji; Shigenobu, Shuji; Tamada, Yosuke; Adamec, Lubomír; Hoshi, Yoshikazu; Ueda, Kazumitsu; Winkelmann, Traud; Fuchs, Jörg; Schubert, Ingo; Schwacke, Rainer; Al‐Rasheid, Khaled A. S.; Schultz, Jörg; Hasebe, Mitsuyasu; Hedrich, Rainer

doi:10.2139/ssrn.3543837

Cited by 6 publications

(4 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While this β peak is the largest peak in Hund, At, and Ft, it is very small and almost neglectable in Av. Remarkably, Av also distinguishes itself from other species with a very large first peak (α), which has been reported to be a very recent WGT event unique in Av 42 . In all other species, this α peak is much smaller and has very small 4dTv values, suggesting it might not represent a WGD but rather a smaller scale recent duplications such as tandem or dispersed duplications.…”

Section: The Draft Genome Of H Undatus Contains 11 Long Scaffolds Atmentioning

confidence: 89%

“…For example, Chr11 (Scaffold 2055) shares large syntenic gene blocks with Chr8 (Scaffold 33675) and Chr3 (Scaffold 33676), while Chr10 (Scaffold 3410) shares large syntenic gene blocks with three chromosomes: Chr2, Chr8, and Chr9. It also appears that the genomic synteny is fairly conserved between Cactaceae 40 , and Spinacia oleracea (So) 41 of Chenopodiaceae, Aldrovanda vesiculosa (Av) of Droseraceae 42 , Simmondsia chinensis (Sc) of Simmondsiaceae 43 , and Fagopyrum tataricum (Ft) of Polygonaceae 44 , Arabidopsis thaliana. A A phylogeny is built with single-copy orthologous genes (identified by OrthoFinder) in the 12 genomes (concatenated alignment with MAFFT and tree built with RAxML).…”

Section: The Draft Genome Of H Undatus Contains 11 Long Scaffolds Atmentioning

confidence: 99%

See 1 more Smart Citation

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

Zheng

Meinhardt²,

Goenaga³

et al. 2021

Hortic Res

View full text Add to dashboard Cite

Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence time between H. undatus and C. gigantea was estimated to be 9.18 MYA. Functional enrichment analysis of orthologous gene clusters (OGCs) in six Cactaceae plants found significantly enriched OGCs in drought resistance. Fruit flavor-related functions were overrepresented in OGCs that are significantly expanded in H. undatus. The H. undatus draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage time. Lastly, genes of the betacyanin (a red-violet pigment and antioxidant with a very high concentration in dragon fruits) biosynthetic pathway were found to be co-localized on a 12 Mb region of one chromosome. The consequence may be a higher efficiency of betacyanin biosynthesis, which will need experimental validation in the future. The H. undatus draft genome will be a great resource to study various cactus plants.

show abstract

Section: The Draft Genome Of H Undatus Contains 11 Long Scaffolds Atmentioning

confidence: 89%

Section: The Draft Genome Of H Undatus Contains 11 Long Scaffolds Atmentioning

confidence: 99%

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

Zheng

Meinhardt²,

Goenaga³

et al. 2021

Hortic Res

View full text Add to dashboard Cite

show abstract

“…Genome and proteome sequences were obtained from phytozome (https://phytozome.jgi.doe.gov/), with the exception of sweet potato ( Ipomoea batatas) genome v3, obtained from the Ipomoea Genome Hub (http://www.ipomoea-genome.org/); Arabis alpina genome( 53 ) v4, obtained from (http://www.arabis-alpina.org/); Aldrovanda vesiculosa genome( 54 ),obtained from (https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources) and Vigna radiata v1 from the Legume Information System (https://legumeinfo.org/). Class IB sequences were by searching the each proteome for the canonical LBD class IB sequence CGACKFLRRKC( 36 ).…”

Section: Supplementary Materials and Methodsmentioning

confidence: 99%

A conserved superlocus regulates above- and belowground root initiation

Omary

Gil-Yarom

Yahav

et al. 2020

Preprint

View full text Add to dashboard Cite

During plant post-embryonic growth new meristems and associated stem cells form in different development contexts in order to respond to environmental cues. While underground lateral roots initiate from designated cells in the main root, an unknown mechanism allows cells to bypass the root/shoot identity trajectory and generate shoot-borne-roots. Using single-cell profiling of tomato (Solanum lycoperiscum) stems we isolated a rare transient cell population that serve as progenitors for shoot-borne-root meristems. Analysis of this population identified a transcription factor required for the formation of shoot-borne-roots which we named SHOOT BORNE ROOTLESS (SBRL). Evolutionary analysis revealed that SBRL function is deeply conserved in angiosperms and that it arose as part of an ancient duplicated superlocus, only lost in root-less plants, containing both shoot-borne and lateral root initiation regulators. We propose that the ability to activate a common transition state with context-specific regulators allows the remarkable developmental plasticity found in plants.One Sentence SummaryHighly conserved superlocus of LBD genes, acting within an early transition identity, regulates shoot-borne and lateral root formation.

show abstract

“…Reticulation events caused by hybridization are common and important sources of novelty in angiosperm evolution (Wood et al 2009, Palfalvi et al 2020. The detection, investigation and representation of hybridization remains a challenge in phylogenomics (Kellog 2016, Mallet et al 2016, Spooner et al 2020.…”

Section: Introductionmentioning

confidence: 99%

HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets

Nauheimer

Weigner

Joyce

et al. 2020

Preprint

View full text Add to dashboard Cite

Premise of the study: Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into parental lineages when identified and phased. We developed HybPhaser to detect hybrids in target capture datasets and to phase reads according to haplotypes based on similarity and a phylogenetic framework. Methods and Results: HybPhaser is an extension to the HybPiper sequence assembly workflow. We used Angiosperms353 target capture data for Nepenthes including known hybrids to test the novel workflow. Reference mapping was used to record heterozygous sites and identify hybrid accessions that were phased by mapping sequence reads to multiple references. The parental lineages of known hybrids were confirmed and conflicting phylogenetic signal reduced, improving the outcomes of phylogenetic analysis. Conclusions: HybPhaser is a novel pipeline for summarizing and optimizing target capture datasets, detecting hybrid accessions as well as paralogous genes, and generating phased accessions that can provide insights into reticulated evolution.

show abstract

Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory

Cited by 6 publications

References 15 publications

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

A conserved superlocus regulates above- and belowground root initiation

HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets

Contact Info

Product

Resources

About