{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Song YQ"],"funding":["Guizhou Provincial Science and Technology Foundation","the Science and Technology Program of Guizhou Province","the Guizhou Education Department Youth Science and Technology Talent Growth Project","the National Natural Science Foundation of China"],"pagination":["1103"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12469583"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["16(9)"],"pubmed_abstract":["<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."],"journal":["Genes"],"pubmed_title":["Molecular Structure, Comparative Analysis, and Phylogenetic Insights into the Complete Chloroplast Genomes of &lt;i&gt;Fissidens crispulus&lt;/i&gt;."],"pmcid":["PMC12469583"],"funding_grant_id":["No. 32360056","No. Qiankehejichu-ZK [2024] General 432","No. Qiankehejichu MS [2025] 276","QianJiaoJi [2024] 50"],"pubmed_authors":["Xiang YL","Kang KL","Peng T","Chen J","Wei YM","Song YQ"],"additional_accession":[]},"is_claimable":false,"name":"Molecular Structure, Comparative Analysis, and Phylogenetic Insights into the Complete Chloroplast Genomes of &lt;i&gt;Fissidens crispulus&lt;/i&gt;.","description":"<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.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Sep","modification":"2026-05-02T03:12:42.863Z","creation":"2026-05-02T03:07:52.32Z"},"accession":"S-EPMC12469583","cross_references":{"pubmed":["41010048"],"doi":["10.3390/genes16091103"]}}