biostudies-literatureLee SYEcological Forestry Development Project of Guangdong Forestry BureauBasic and Applied Basic Research Foundation of Guangdong ProvincePRESTO Strategic Basic Research Programs of the Japan Science and Technology Agency841https://www.ebi.ac.uk/biostudies/studies/S-EPMC12220141biostudies-literatureUnknown25(1)<h4>Background</h4>Achlorophyllous mycoheterotrophic plant species demonstrate drastic evolutionary shifts in their photosynthetic machinery as encoded in their chloroplast and nuclear genomes. We used next-generation sequencing to scrutinize these genome-level alterations linked to their distinctive life history. The plastome, a partial nuclear rDNA operon gene sequence, and the transcriptome of Cyrtosia lindleyana were assembled and characterized.<h4>Results</h4>The plastome, despite its reduction to 89,414 base pairs, maintained its quadripartite structure. We detected 63 potentially intact genes, of which nine protein-coding genes exhibited predicted RNA-editing sites. Relative to Vanilla pompona, three genes, rpl23, rps14, and rps19, had undergone positive selection (Ka/Ks > 1), and gBMC plant biologyPlastome and transcriptome analysis reveals a degenerated photosynthesis-related pathway in the mycoheterotrophic vanilloid orchid Cyrtosia lindleyana.PMC122201412018B0303200012019-42091278JPMJPR21D6Suetsugu KLee SYChen ZLiao WZou PfalsePlastome and transcriptome analysis reveals a degenerated photosynthesis-related pathway in the mycoheterotrophic vanilloid orchid Cyrtosia lindleyana.<h4>Background</h4>Achlorophyllous mycoheterotrophic plant species demonstrate drastic evolutionary shifts in their photosynthetic machinery as encoded in their chloroplast and nuclear genomes. We used next-generation sequencing to scrutinize these genome-level alterations linked to their distinctive life history. The plastome, a partial nuclear rDNA operon gene sequence, and the transcriptome of Cyrtosia lindleyana were assembled and characterized.<h4>Results</h4>The plastome, despite its reduction to 89,414 base pairs, maintained its quadripartite structure. We detected 63 potentially intact genes, of which nine protein-coding genes exhibited predicted RNA-editing sites. Relative to Vanilla pompona, three genes, rpl23, rps14, and rps19, had undergone positive selection (Ka/Ks > 1), and g2025-01-01T00:00:00Z2025 Jul2026-06-03T06:38:50.63Z2026-04-25T03:21:54.418ZS-EPMC122201414060444510.1186/s12870-025-06850-x