Refining dual RNA-seq mapping: sequential and combined approaches in host-parasitic plant dynamics.

ABSTRACT: Transcriptional profiling in host plant-parasitic plant interactions is challenging due to the tight interface between host and parasitic plants and the percentage of homologous sequences shared. Dual RNA-seq offers a solution by enabling in silico separation of mixed transcripts from the interface region. However, it has to deal with issues related to multiple mapping and cross-mapping of reads in host and parasite genomes, particularly as evolutionary divergence decreases. In this paper, we evaluated the feasibility of this technique by simulating interactions between parasitic and host plants and refining the mapping process. More specifically, we merged host plant with parasitic plant transcriptomes and compared two alignment approaches: sequential mapping of reads to the two se

SUBMITTER: Fruggiero C 

PROVIDER: S-EPMC11581871 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature