Phoenix dactylifera
L. is an economically, nutritionally, and culturally important fruit crop in the arid and semi-arid regions of the Middle East and North Africa. Here, we present a gap-free, telomere-to-telomere reference genome of the variety Ajwa, along with 19 additional high-quality assemblies (18 female and 1 male). These assemblies reveal updated, corrected chromosome assemblies validated through cytogenetics, Hi-C and optical mapping. Chromosome numbering was revised based on average lengths across all sequenced genomes. The Sex Determination Region (SDR) was inferred on chromosome 14, spanning approximately 15.2 Mb. Nucleolar organizing regions (NORs) were localized on chromosome 10, where a large 45S rDNA locus displayed unique repeat spacer motifs containing transposon-like sequences. In some accessions, a second NOR was identified on the female sex chromosome. This collection of date palm assemblies, anchored by the Ajwa reference genome, provides a fundamental resource for advancing breeding strategies aimed at enhancing the genetic resilience and productivity of date palm.
Mirko Celii, N. Al-Bader, Nahed Mohammed et al.· Scientific Data· 0 citations
ABSTRACT Advancements in plant genome sequencing and assembly have enabled the production of increasingly accurate and contiguous genome sequences. Here, we present the chromosome‐level assembly of the durum wheat ( Triticum turgidum L. ssp. durum, cv. Svevo) reference genome produced using accurate long‐reads, optical mapping and Hi‐C. The new assembly (Svevo Rel.2.0) comprises 263 hybrid scaffolds with an N50 value of 112.3 Mb, arranged into 14 contiguous pseudomolecules spanning 10.4 Gb. The Svevo Rel.2.0 genome assembly was annotated using extensive short‐ and long‐read RNA sequencing data obtained from 60 tissue/treatment combinations. The resulting annotation comprises 68 154 high‐confidence protein‐coding genes, which have been integrated into a comprehensive transcriptome atlas accessible through an eFP browser. Annotation was manually curated for storage protein gene families and for Leucine‐Rich Repeat‐Containing Receptor genes yielding 3763 LRR‐CR loci. The genome assembly's accuracy and completeness were demonstrated by the correct reconstruction of the physical map of Tg1‐B (Tenacious glumes 1), a locus controlling the free threshing trait located on chromosome 2B that was not assembled in the previous genome release (Svevo Rel.1.0). A wealth of 6621 QTLs/MTAs from the literature were mapped onto Svevo Rel.2.0 to identify QTL hotspots and trait‐specific candidate genes. The ancestry of the durum genome to representative wild emmer populations from North‐Eastern and Southern‐Levant Fertile Crescent assessed by tracing haplotype transmission patterns revealed a clear mosaic pattern. This new durum reference genome, enhanced with advanced annotation and an expression atlas linked to QTLome data, is the most comprehensive tool available for durum wheat genomics.
E. Mazzucotelli, C. Forestan, Gina Zastrow-Hayes et al.· Plant Biotechnology Journal· 0 citations
