Abstract
The mitochondrial genomes possess genes of five complexes involved in respiration. Mitochondrial gene content greatly varies across eukaryotes. Frequent gene losses have been reported in the mitogenomes of halophytes. In this study, we report, assemble, and annotate complete mitochondrial genome of a halophyte Pandanus odorifer (Forssk.) Kuntze (Pandanaceae). It is a commercially important species for its essential oil. It grows naturally in coastal regions and can withstand winds as well as salt sprays. The mitogenome of P. odorifer is circular with length of 330,962 bp. The genome contains 33 protein coding genes, 3 rRNAs, and 6 tRNAs. The analysis revealed that the important respiratory genes ccmC, cox1, nad1, nad4, and nad9 were pseudogenized in mitogenome but nuclear encoded copies of cox1, nad1, and nad9 were recovered. The phylogenetic analysis placed P. odorifer sister to P. tectorius. Further, mitogenome was compared with the other monocot mitogenomes for their gene contents. Thus, the study provides first complete mitochondrial genome for the family Pandanaceae and order Pandanales.
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Data availability
The mitogenome sequence can be accessed via accession number ON055386 on NCBI website https://www.ncbi.nlm.nih.gov. The associated transcriptome data is available in NCBI repository as SRA BioProject ID: PRJNA389238.
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Acknowledgements
Authors are grateful to Savitribai Phule Pune University for providing facilities and financial support. The work was supported by SERB, Department of Science & Technology, India vide project no. CRG/2021/005730. AMD is thankful to SPPU-PDF [SPPU-PDF/ST/BL/2021/0001] for the post-doctoral fellowship support. VTB acknowledges partial funding support received from IQAC, Savitribai Phule Pune University under ASPIRE- scheme research mentorship program (18TEC000030).
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AMD and VTB: designed the study. SSP: carried out DNA extraction. AMD and VTB: performed analyses. AMD and SSP: wrote the original draft. AAP, ABN, and VTB: reviewed and contributed to the rewriting, editing the manuscript, and were involved in funding acquisition.
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11816_2023_841_MOESM2_ESM.xlsx
Supplementary file2 RNA editing sites in the mitogenome of P. odorifer when compared to Arabidopsis thaliana, Oryza sativa Japonica group, Cocos nucifera (XLSX 30 KB)
11816_2023_841_MOESM3_ESM.tif
Supplementary file3 Fig. S1 Secondary structures of tRNAs present in the mitogenome of P. odorifer. The colour code is following the RNAfold webserver. (Green: Stems (canonical helices), Red: Multiloops (junctions), Yellow: Interior Loops, Blue: Hairpin loops, Orange: 5' and 3' unpaired region) (TIF 3039 KB)
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Darshetkar, A.M., Patil, S.S., Pable, A.A. et al. Loss of mitogenome-encoded respiratory genes complemented by nuclear transcripts in halophyte Pandanus odorifer (Forssk.) Kuntze. Plant Biotechnol Rep 18, 91–104 (2024). https://doi.org/10.1007/s11816-023-00841-w
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DOI: https://doi.org/10.1007/s11816-023-00841-w