{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T00:22:05Z","timestamp":1791073325325,"version":"4.1.0"},"reference-count":88,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2024,1,15]],"date-time":"2024-01-15T00:00:00Z","timestamp":1705276800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Research Funds for the Natural Science Foundation of Zhejiang Province","award":["LY21C030002"],"award-info":[{"award-number":["LY21C030002"]}]},{"name":"Research Funds for the Natural Science Foundation of Zhejiang Province","award":["2021KFLY06"],"award-info":[{"award-number":["2021KFLY06"]}]},{"name":"Research Funds for the Natural Science Foundation of Zhejiang Province","award":["32001086"],"award-info":[{"award-number":["32001086"]}]},{"name":"Scientific Research Project of Baishanzu National Park","award":["LY21C030002"],"award-info":[{"award-number":["LY21C030002"]}]},{"name":"Scientific Research Project of Baishanzu National Park","award":["2021KFLY06"],"award-info":[{"award-number":["2021KFLY06"]}]},{"name":"Scientific Research Project of Baishanzu National Park","award":["32001086"],"award-info":[{"award-number":["32001086"]}]},{"name":"Innovation Program of Chinese Academy of Agricultural Sciences and the National Natural Science Foundation of China","award":["LY21C030002"],"award-info":[{"award-number":["LY21C030002"]}]},{"name":"Innovation Program of Chinese Academy of Agricultural Sciences and the National Natural Science Foundation of China","award":["2021KFLY06"],"award-info":[{"award-number":["2021KFLY06"]}]},{"name":"Innovation Program of Chinese Academy of Agricultural Sciences and the National Natural Science Foundation of China","award":["32001086"],"award-info":[{"award-number":["32001086"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the Orobanchaceae family, and provide clues for molecular breeding.<\/jats:p>","DOI":"10.3390\/genes15010098","type":"journal-article","created":{"date-parts":[[2024,1,15]],"date-time":"2024-01-15T11:15:01Z","timestamp":1705317301000},"page":"98","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family"],"prefix":"10.3390","volume":"15","author":[{"given":"Ying","family":"Han","sequence":"first","affiliation":[{"name":"College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan-Lei","family":"Feng","sequence":"additional","affiliation":[{"name":"College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0038-1045","authenticated-orcid":false,"given":"Jie","family":"Wang","sequence":"additional","affiliation":[{"name":"Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan-Shan","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Marine Sciences, Ningbo University, Ningbo 315211, China"},{"name":"State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin-Jie","family":"Jin","sequence":"additional","affiliation":[{"name":"College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China"},{"name":"Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4238-7317","authenticated-orcid":false,"given":"Zhi-Qiang","family":"Wu","sequence":"additional","affiliation":[{"name":"Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2676-9059","authenticated-orcid":false,"given":"Yong-Hua","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China"},{"name":"Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,1,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1111\/jse.12655","article-title":"Genomic architectural variation of plant mitochondria\u2014A review of multichromosomal structuring","volume":"60","author":"Wu","year":"2020","journal-title":"J. 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