Atypical plastid genome evolution: Cereus Mill. from distinct environments harbor one of the largest plastid genomes in Cactaceae

Badia, C. C. V.; Silva, M. C.; de Baura, V. A.; Balsanelli, E.; de Souza, E. M.; Pedrosa, F. d. O.; Fregonezi, J.; Rogalski, M.

doi:10.1101/2025.08.18.670840

bioRxiv · 10.1101/2025.08.18.670840

Atypical plastid genome evolution: Cereus Mill. from distinct environments harbor one of the largest plastid genomes in Cactaceae

Badia, C. C. V.·Silva, M. C.·de Baura, V. A.·Balsanelli, E.·de Souza, E. M.·Pedrosa, F. d. O.·Fregonezi, J.·Rogalski, M.

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Abstract

BackgroundCactaceae has successfully radiated in xeric habitats across the Americas, presenting very distinct morphologies and evolutionary patterns within tribes. This study presents the complete plastomes of C. jamacaru subsp. jamacaru and C. hildmannianus subsp. hildmannianus, which inhabit distinct habitats, providing insights into their genomic structure and evolutionary history, with implications for conservation. Methods and ResultsChloroplast genomes of the two Cereus were assembled and analyzed to investigate plastome evolution in Cactoideae. Fresh cladodes were collected and their mesophyll manually extracted, chloroplasts were extracted from the mesophyll, and cpDNA sequenced using Illumina MiSeq. De novo assembly and annotation were conducted using BLAST, Expasy, and tRNAScan as validation tools. We compared the genome structure, gene content, codon usage, and RNA editing predictions between tribes. The genome was 141.884 and 141.600 bp for C. jamacaru and C. hildmannianus, respectively, and dotplot analysis confirmed highly syntenic plastomes. The genes trnV-GAC, trnV-UAC, rpl23, ndhA, ndhE, ndhG, ndhI, and ndhK were lost, and ndhB, ndhC, ndhF, and rpl33 are pseudogenes. The tRNAval losses indicate putative superwobbling or nuclear-coded tRNA import from cytosol. We identified an insertion in rps18 for both Cereus, suggesting that intron retention may be in course for these species. We identified [~]190 single sequence repeats and 50 tandem repeats for each species, and eight exclusive RNA editing sites. Synteny analysis revealed rearrangements distinguishing taxa within Cactoideae. Phylogenetic results supported Cereus monophyly, corroborating existing classifications, and clarifies unresolved relationships, enhancing understanding of phylogenetic relationships within Cactaceae. ConclusionsOur results provide evidence on the evolutionary patterns and putative signatures of adaptation to distinct environments, providing insights into genomic evolution and conservation of Cereus.

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Badia, C. C. V., Silva, M. C., de Baura, V. A., Balsanelli, E., de Souza, E. M., Pedrosa, F. d. O., Fregonezi, J., Rogalski, M.. 2025-08-22. Atypical plastid genome evolution: Cereus Mill. from distinct environments harbor one of the largest plastid genomes in Cactaceae. https://doi.org/10.1101/2025.08.18.670840

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