Biology subjects

Triesch, S.

Publications and source records attributed to Triesch, S..

4 recordsLinked to original sources

bioRxiv2023

A transcription factor module mediating C2 photosynthesis

C4 photosynthesis has arisen from the ancestral C3 state in over sixty lineages of angio-sperms. It is widely accepted that an early step in C4 evolution is restriction of glycine decarboxylase activity to bundle sheath cells to generate the so-called C2 pathway. In C2 Moricandia species, changes to the cis-regulatory region controlling expression of the P-subunit of GLYCINE DECARBOXYLASE (GLDP) in mesophyll cells enables this trait, but the mechanism underpinning GLDP expression in the bundle sheath is not known. We identify a MYC-MYB transcription factor module previously associated with the control of glucosinolate bio-synthesis as the basis of GLDP expression in bundle sheath cells. In C3 Arabidopsis thaliana this module drives GLDP expression in bundle sheath cells along with as yet unidentified factors driving expression in mesophyll cells. In the C2 species Moricandia arvensis, GLDP expression is lost from mesophyll cells and the MYC-MYB dependent expression in the bundle sheath is revealed. Evolution of C2 photosynthesis is thus associated with a MYC-MYB based transcriptional network already present in the C3 state. This work identifies a molecular genetic mechanism underlying the bundle sheath accumulation of glycine decarboxylase required for C2 photosynthesis and thus a foundational step in the evolution of C4 photosynthesis.

plant biology↗

bioRxiv2023

Helixer--de novo Prediction of Primary Eukaryotic Gene Models Combining Deep Learning and a Hidden Markov Model.

AO_SCPLOWBSTRACTC_SCPLOWGene structural annotation is a critical step in obtaining biological knowledge from genome sequences yet remains a major challenge in genomics projects. Current de novo Hidden Markov Models are limited in their capacity to model biological complexity; while current pipelines are resource-intensive and their results vary in quality with the available extrinsic data. Here, we build on our previous work in applying Deep Learning to gene calling to make a fully applicable, fast and user friendly tool for predicting primary gene models from DNA sequence alone. The quality is state-of-the-art, with predictions scoring closer by most measures to the references than to predictions from other de novo tools. Helixers predictions can be used as is or could be integrated in pipelines to boost quality further. Moreover, there is substantial potential for further improvements and advancements in gene calling with Deep Learning. Helixer is open source and available at https://github.com/weberlab-hhu/Helixer A web interface is available at https://www.plabipd.de/helixer_main.html

bioinformatics↗

bioRxiv2023

A genomic panel for studying C3-C4 intermediate photosynthesis in the Brassiceae tribe

Research on C4 and C3-C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of this trait will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3-C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify the level of orthology using synteny maps between all pairs of taxa, (iii) describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3-C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the sampling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high-quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome-based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3-C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea. Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3-C4 intermediate photosynthesis.

genomics↗

bioRxiv2022

Transposable elements contribute to the establishment of the glycine shuttle in Brassicaceae species

C3-C4 intermediate photosynthesis has evolved at least five times convergently in the Brassicaceae, despite this family lacking bona fide C4 species. The establishment of this carbon concentrating mechanism is known to require a complex suite of ultrastructural modifications as well as changes in spatial expression patterns, which are both thought to be underpinned by a reconfiguration of existing gene-regulatory networks. However, to date, the mechanisms which underpin the reconfiguration of these gene networks are largely unknown. In this study, we used a pan-genomic association approach to identify genomic features that could confer differential gene expression toward the C3-C4 intermediate state by analysing eight C3 species and seven C3-C4 species from five independent origins in the Brassicaceae. We found a strong correlation between transposable element (TE) insertions in cis-regulatory regions and the C3-C4 intermediacy. Specifically, our study revealed 113 gene models in which presence of a TE within a gene correlates with C3-C4 intermediate photosynthesis. In this set, genes involved in the photorespiratory glycine shuttle are enriched, including the glycine decarboxylase P-protein whose expression domain undergoes a spatial shift during the transition to C3-C4 photosynthesis. When further interrogating this gene, we discovered independent TE insertions in its upstream region which we conclude to be responsible for causing the spatial shift in GLDP1 gene expression. Our findings hint at a pivotal role of TEs in the evolution of C3-C4 intermediacy, especially in mediating differential spatial gene expression.

plant biology↗