Biology subjects

Burguener, G. F.

Publications and source records attributed to Burguener, G. F..

4 recordsLinked to original sources

bioRxiv2023

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

Yerba mate (Ilex paraguariensis) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large yerba mate genome size is partly due to a whole-genome duplication (Ip-) during the early evolutionary history of Ilex, in addition to the hexaploidization event ({gamma}) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of its relatives, coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in yerba mate and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the x-ray diffraction data suggests structural constraints are minimal for the convergent evolution of individual reactions.

plant biology↗

bioRxiv2023

Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression

Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. New functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more non-synonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the new promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop. Significance StatementWe sequenced 4.3 million induced mutations in the promoters and 4.7 million in the coding regions of most wheat genes. We also show how this public resource can be used to understand gene function, modulate gene expression, and generate changes in valuable wheat agronomic traits.

genomics↗

bioRxiv2023

De novo assembly of the black flounder genome. Why do pleuronectiformes have such a small genome size?

Black flounder (Paralichthys orbignyanus) is an economically important ma-rine fish with aquaculture potential in Argentina due to its market value. In this study, we sequenced the whole genome using an Illumina sequencing technology. We started with two independent libraries (from one female and one pool of females; each with 150 bp paired-end reads, a mean insert length of 350 bp, and >35 X-fold coverage). Each library was assembled separately using SOAPdenovo2 and the resulting contigs were scaffolded with SSPACE3 before gaps were filled with GapCloser. In vertebrates, including teleosts, the number of transposable elements (TEs) is related to genome size, but it remains unclear whether the size of introns and exons also plays a role. Therefore, the main objective of the present study was to test whether the small genome size of Pleuronectiformes is related to the size of their introns and exons. The assemblies re-sulted in a genome size of [~]538 Mbp (41.35% GC content, 0.11% undetermined bases). Analysis of the assemblies at the core genes level (subset of the 458 universally ex-pressed KOG families) revealed that more than 98% of core genes are present, with more than 78% of them having more than 50% coverage. This indicates a fairly complete and accurate genome at the coding sequence level. Prediction of genes based on statistical predictors (geneid) and sequence-based predictors (Exonerate, using a closely related species, Paralichthys olivaceus, as a reference) was performed. This revealed 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types (including a complete set of spliceosomes and several types of snoRNA and miRNA). As a result, this study concluded that the reduced genome size of flounders is related to a reduction in transcript size, mainly through a reduction in exon number, but also through a reduction in large introns. Thus, both components seem to be involved in the strategy of genome reduction in Pleuronectiformes.

genomics↗

bioRxiv2022

Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat primary root growth

Wheat is an essential crop for global food security and is well adapted to a wide variety of soils1. However, the gene networks regulating different root architectures remain poorly understood. We report here the identification of a cluster of a monocot-specific 12-OXOPHYTODIENOATE REDUCTASE genes from subfamily III (OPRIII) that modulate key differences in wheat root architecture associated with grain yield under water-limited conditions. Wheat plants with a loss-of-function mutation in OPRIII showed longer seminal roots, whereas plants with increased OPRIII dosage or transgenic over-expression showed reduced seminal root growth, precocious development of lateral roots and increased jasmonic acid (JA). A JA-biosynthesis inhibitor eliminated the root differences, confirming a JA-mediated mechanism. Multiple transcriptome analysis of transgenic and wild-type lines revealed significant enriched JA-biosynthetic and reactive oxygen species (ROS) pathways that paralleled changes in ROS distribution. The OPRIII genes provide a useful entry point to engineer root architecture in wheat and other cereals.

plant biology↗