Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles

Area of Science:

• Genomics
• Plant Science
• Evolutionary Biology

Background:

• Chaenomeles is a significant ornamental, herbal, and cash crop in East Asia.
• Traditional studies primarily focused on phenotypic evolutionary relationships.

Purpose of the Study:

• To conduct a comprehensive genomic analysis of Chaenomeles germplasms.
• To elucidate evolutionary relationships and identify genes under selection.
• To develop novel Simple Sequence Repeat (SSR) markers for breeding.

Main Methods:

• RNA sequencing (RNA-seq) was performed on 10 Chaenomeles germplasms and one outgroup.
• De novo assembly generated unigenes, followed by orthologue identification and phylogenetic analysis.
• Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted on single-copy genes.

Main Results:

• Over 40,000 unigenes were generated per germplasm, with 6,154 common single-copy orthologous genes identified.
• Phylogenetic analysis visualized evolutionary relationships among the 11 germplasms.
• Selective pressure analysis identified 45 genes under positive selection, primarily involved in plant disease defense.
• 292 genes containing SSRs were identified, leading to the development of 10 candidate SSR markers.

Conclusions:

• This research provides a genomic foundation for understanding Chaenomeles evolution and function.
• The identified genes under positive selection offer insights into adaptation and defense mechanisms.
• Developed SSR markers are valuable resources for future genetic improvement and breeding programs in Chaenomeles.