{"doi":"10.21203/rs.2.18648/v1","title":"Comparative Chloroplast Genomics of The Genus Taxodium ","abstract":"<jats:title>Abstract</jats:title>\n        <jats:p><jats:bold>Background: </jats:bold>Chloroplast(cp) genome information would facilitate the development and utilization of <jats:italic>Taxodium</jats:italic> resources. However, cp genome characteristics of <jats:italic>Taxodium</jats:italic> were poorly understood.<jats:bold>Results: </jats:bold>We determined the complete cp genome sequences of <jats:italic>T.</jats:italic> <jats:italic>distichum</jats:italic>, <jats:italic>T. mucronatum</jats:italic>, and <jats:italic>T. ascendens</jats:italic>. The cp genomes are 131,947 bp to 132,613bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the three cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat(TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. <jats:italic>Ycf1</jats:italic> was the only one gene that has an indel in CDS, and the indel is composed of a long TR. When extended to cupressophytes, <jats:italic>ycf1</jats:italic> genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, <jats:italic>ycf1</jats:italic> also located in rearrangement endpoints  of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. <jats:bold>Conclusions: </jats:bold>This study would advance our understanding of the complexity, dynamics, and evolution of cp genome in Cupressophytes.</jats:p>","journal":"Research Square","year":null,"id":40410,"datarank":0.22210475163363305,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.05731290833341659,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.05731290833341659,"corpus_percentile":37.49516515819602,"corpus_rank":8081,"citation_count":2,"citer_count":2,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":196395,"name":"Hao Duan","orcid":null,"position":1,"is_corresponding":false},{"id":196396,"name":"Jinbo Guo","orcid":null,"position":2,"is_corresponding":false},{"id":196397,"name":"Lei Xuan","orcid":null,"position":3,"is_corresponding":false},{"id":196398,"name":"Ziyang Wang","orcid":null,"position":4,"is_corresponding":false},{"id":196399,"name":"Mingzhi Li","orcid":null,"position":5,"is_corresponding":false},{"id":196400,"name":"Yunlong Yin","orcid":null,"position":6,"is_corresponding":false},{"id":27795,"name":"Ying Yang","orcid":"0000-0002-9799-3293","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"36284789","pmcid":null,"openalex_id":"https://openalex.org/W4240983354","authors":[],"funders":[{"funder_name":"National Centre for the Replacement, Refinement and Reduction of Animals in Research","grant_id":"NC/P001076/1","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BBS/E/T/000PR9817","title":null},{"funder_name":"Wellcome Trust","grant_id":"209558/Z/17/Z","title":null},{"funder_name":"HCRW_","grant_id":"RFPPB-18-1497(T)","title":null},{"funder_name":"Medical Research Council","grant_id":"MR/S036954/1","title":null},{"funder_name":"Medical Research Council","grant_id":"MR/K010468/1","title":null}],"total_grants":6,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2020,"count":1},{"year":2024,"count":1}],"oa_status":"green","license":"cc-by","oa_locations":[{"url":"https://www.researchsquare.com/article/rs-9268/v1.pdf","host_type":"repository"},{"url":"https://www.researchsquare.com/article/rs-9268/v1.pdf","host_type":"repository"},{"url":"https://www.researchsquare.com/article/rs-9268/v1","host_type":"publisher"},{"url":"https://www.researchsquare.com/article/rs-9268/v1.html","host_type":"publisher"},{"url":"https://doi.org/10.21203/rs.2.18648/v1","host_type":"repository"}],"fields_of_study":["Protist diversity and phylogeny","Microbial Community Ecology and Physiology","Genomics and Phylogenetic Studies"],"mesh_terms":[],"keywords":["Indel","Genome","Biology","Inverted repeat","Taxodium","Genetics","Comparative genomics","INDEL Mutation","Gene","Genomics","Evolutionary biology","Single-nucleotide polymorphism","Botany","Genotype","carotid-cavernous fistula","endoscopy","endovascular treatment","transsphenoidal surgery","video"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Responsible consumption and production"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-12T05:43:18.457794Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"green","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}