Evaluating Genome Assemblies for Optimized Completeness and Accuracy of Reference Gene Sequences in Wheat, Rye, and...

Area of Science:

• Genomics
• Plant Science
• Bioinformatics

Background:

• Dozens of Triticeae crop genome assemblies have advanced research in wheat, rye, and triticale.
• Selecting universally efficient reference genomes remains challenging due to phylogenetic diversity.

Purpose of the Study:

• To assess the completeness and accuracy of wheat, rye, and triticale genome assemblies.
• To identify the most robust reference genomes for gene-related studies in Triticeae crops.

Main Methods:

• Comparative benchmarking universal single-copy orthologue (BUSCO) analysis.
• Transcript mapping using RNA-seq data (alignment rate, covered length, total depth).
• Analysis of internal stop codon frequency as an indicator of assembly accuracy.

Main Results:

• BUSCO completeness correlated positively with RNA-seq read mappability.
• Internal stop codon frequency negatively indicated assembly accuracy and mappability in wheat.
• SY Mattis, Lo7, and SY Mattis plus Lo7 were identified as the most robust references for wheat, rye, and triticale, respectively.

Conclusions:

• The identified reference assemblies (SY Mattis, Lo7) are optimal for gene research in wheat, rye, and triticale.
• Incorporating the D genome sequence is recommended for triticale reference assemblies.
• Internal stop codon frequency can aid future assembly quality evaluation.