biostudies-literatureSong YQGuizhou Provincial Science and Technology Foundationthe Science and Technology Program of Guizhou Provincethe Guizhou Education Department Youth Science and Technology Talent Growth Projectthe National Natural Science Foundation of China1103https://www.ebi.ac.uk/biostudies/studies/S-EPMC12469583biostudies-literatureUnknown16(9)<h4>Background/objectives</h4><i>Fissidens crispulus</i> Brid. is a dioicous moss with conspicuous axillary hyaline nodules and serrulate leaf margins. It features <i>Neoamblyothallia</i>-type peristome teeth and serves as an ecologically significant model for studying adaptation in the hyperdiverse genus <i>Fissidens</i> (>440 species).<h4>Methods</h4>In this study, the complete chloroplast genome of <i>F. crispulus</i> was sequenced and de novo assembled, enabling detailed comparative genomic, phylogenetic, and codon usage bias studies.<h4>Results</h4>As the third fully sequenced member of Fissidentaceae, this study deciphers its 124,264-124,440 bp quadripartite genome encoding 129 genes (83 CDS, 32 tRNAs, 8 rRNAs). Repeat analysis identified 125-127 SSRs, dominated by mono-/di-nucleotide A/T repeats (>70%), and dispersed repeats predominantly forward (F) and palindromic (P) (>85%), confirming profound AT-biased composition (GC content: 28.7%). We established 7 hypervariable loci (<i>matK</i>, <i>ycf2</i>, etc.) as novel Dicranidae-wide phylogenetic markers. Codon usage exhibited significant A/U-ending preference, with 12 optimal codons (e.g., GCA, UGU, UUU) determined. Maximum likelihood analyses resolved <i>F. crispulus</i> and <i>F. protonematicola</i> as sister groups with high support value (MBP = 100%).<h4>Conclusions</h4>This work provides the foundational cpDNA resource for <i>Fissidens</i>, filling a major gap in bryophyte chloroplast genomics and establishing a framework for resolving the genus's infrageneric conflicts. Furthermore, it offers critical insights into bryophyte plastome evolution and enables future codon-optimized biotechnological applications.GenesMolecular Structure, Comparative Analysis, and Phylogenetic Insights into the Complete Chloroplast Genomes of &lt;i&gt;Fissidens crispulus&lt;/i&gt;.PMC12469583No. 32360056No. Qiankehejichu-ZK [2024] General 432No. Qiankehejichu MS [2025] 276QianJiaoJi [2024] 50Xiang YLKang KLPeng TChen JWei YMSong YQfalseMolecular Structure, Comparative Analysis, and Phylogenetic Insights into the Complete Chloroplast Genomes of &lt;i&gt;Fissidens crispulus&lt;/i&gt;.<h4>Background/objectives</h4><i>Fissidens crispulus</i> Brid. is a dioicous moss with conspicuous axillary hyaline nodules and serrulate leaf margins. It features <i>Neoamblyothallia</i>-type peristome teeth and serves as an ecologically significant model for studying adaptation in the hyperdiverse genus <i>Fissidens</i> (>440 species).<h4>Methods</h4>In this study, the complete chloroplast genome of <i>F. crispulus</i> was sequenced and de novo assembled, enabling detailed comparative genomic, phylogenetic, and codon usage bias studies.<h4>Results</h4>As the third fully sequenced member of Fissidentaceae, this study deciphers its 124,264-124,440 bp quadripartite genome encoding 129 genes (83 CDS, 32 tRNAs, 8 rRNAs). Repeat analysis identified 125-127 SSRs, dominated by mono-/di-nucleotide A/T repeats (>70%), and dispersed repeats predominantly forward (F) and palindromic (P) (>85%), confirming profound AT-biased composition (GC content: 28.7%). We established 7 hypervariable loci (<i>matK</i>, <i>ycf2</i>, etc.) as novel Dicranidae-wide phylogenetic markers. Codon usage exhibited significant A/U-ending preference, with 12 optimal codons (e.g., GCA, UGU, UUU) determined. Maximum likelihood analyses resolved <i>F. crispulus</i> and <i>F. protonematicola</i> as sister groups with high support value (MBP = 100%).<h4>Conclusions</h4>This work provides the foundational cpDNA resource for <i>Fissidens</i>, filling a major gap in bryophyte chloroplast genomics and establishing a framework for resolving the genus's infrageneric conflicts. Furthermore, it offers critical insights into bryophyte plastome evolution and enables future codon-optimized biotechnological applications.2025-01-01T00:00:00Z2025 Sep2026-05-02T03:12:42.863Z2026-05-02T03:07:52.32ZS-EPMC124695834101004810.3390/genes16091103