Biology subjects

Appels, R.

Publications and source records attributed to Appels, R..

4 recordsLinked to original sources

bioRxiv2026

Community Resource: A Genome-Based Extension of Large-Scale Wheat Proteogenomics

Bread wheat (Triticum aestivum L.) possesses a large and highly repetitive allohexaploid genome and annotation requires extensive protein-level validation. We developed a genome-based wheat proteogenomics workflow integrating large-scale MS/MS reanalysis, GFF3-based peptide coordinate reconstruction, thorough validation, and genome browser-compatible peptide deployment against the IWGSC RefSeq v2.1 reference genome. Public wheat proteomics datasets comprising 577 raw mass spectrometry files ([~]1.0 TB) from 32 tissues were reprocessed using FragPipe/MSFragger, generating 2,226,779 non-redundant peptides and 1,648,740 unique protein accessions. Peptide-to-genome projections using GFF3 annotation files produced 8,291,056 genomic peptide projected rows, of which 98.14% passed validation procedures. Overall, peptide evidence supported 103,095 high-confidence (HC) and 135,495 low-confidence (LC) wheat gene models, corresponding to 96.4% and 84.7% of all parsed HC and LC annotations, respectively. In total, 238,590 wheat gene models (89.4% of all parsed annotations) received protein-level support. Apollo/JBrowse-compatible BED tracks enabled exon-resolved visualisation of peptide evidence across wheat chromosomes. Together, this study establishes a scalable GFF3-based proteogenomics framework for complex polyploid plant genomes and provides an extensive community resource for wheat genome annotation refinement and visual exploration (https://bread-wheat-um.genome.edu.au/apollo/49826/jbrowse/index.html). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC="FIGDIR/small/733048v2_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@6e797org.highwire.dtl.DTLVardef@14ea4fdorg.highwire.dtl.DTLVardef@31f027org.highwire.dtl.DTLVardef@8d908a_HPS_FORMAT_FIGEXP M_FIG C_FIG

Plant Biology↗

bioRxiv2025

Expanding the TaNAS gene family in bread wheat and exploring potential for intragenic biofortification

Higher plants utilise nicotianamine synthase (NAS) enzymes to produce nicotianamine (NA), a non-protein amino acid that chelates metals such as iron (Fe) and zinc (Zn) for long-distance transport. We identified 34 TaNAS genes in bread wheat (Triticum aestivum L., cv. Chinese Spring), and four additional cultivar-specific TaNAS genes, representing the largest NAS gene family identified to date. The expression of all TaNAS genes was highest in roots and upregulated (apart from the TaNAS9 homoeologs) in response to hydroponic Fe deficiency. The TaNAS proteins ranged between 180 and 384 amino acids in length and showed variable N- and C-termini. To understand TaNAS function, we transformed bread wheat cv. Fielder to overexpress coding sequences from either TaNAS1, TaNAS3, TaNAS4, TaNAS6, or TaNAS7, and isolated three single locus homozygous events and null segregant (NS) controls for each TaNAS overexpression line for glasshouse and field evaluation. Under field conditions, grain Fe, Zn and NA concentrations were up to 1.6-fold, 1.8-fold and 3.7-fold higher, respectively, in TaNAS6 events relative to NS without any negative impacts on agronomic traits. These results demonstrate the usefulness of available online genomic resources for analysing the TaNAS gene family in bread wheat and highlight intragenic strategies to enhance grain nutritional quality. Significance statementNicotianamine synthase (NAS) genes play key roles in metal transport and homeostasis in plants. This study describes the identification of 34 TaNAS genes in bread wheat, representing a significant expansion on previous TaNAS studies, and demonstrates that constitutive overexpression of specific TaNAS genes could provide a novel intragenic approach for iron and zinc biofortification of bread wheat.

plant biology↗

bioRxiv2020

1RS.1BL molecular resolution provides novel contributions to wheat improvement

Wheat-rye 1RS.1BL translocation has a significant impact on wheat yield and hence food production globally. However, the genomic basis of its contributions to wheat improvement is undetermined. Here, we generated a high-quality assembly of 1RS.1BL translocation comprising 748,715,293 bp with 4,996 predicted protein-coding genes. We found the size of 1RS is larger than 1BS with the active centromere domains shifted to the 1RS side instead of the 1BL side in Aikang58 (AK58). The gene alignment showed excellent synteny with 1BS from wheat and genes from 1RS were expressed well in wheat especially for 1RS where expression was higher than that of 1BS for the grain-20DPA stage associated with greater grain weight and negative flour quality attributes. A formin-like-domain protein FH14 (TraesAK58CH1B01G010700) was important in regulating cell division. Two PPR genes were most likely the genes for the multi fertility restoration locus Rf multi. Our data not only provide the high-resolution structure and gene complement for the 1RS.1BL translocation, but also defined targets for enhancing grain yield, biotic and abiotic stress, and fertility restoration in wheat.

genomics↗

bioRxiv2018

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.\n\nResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.\n\nConclusionsSufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

genomics↗