{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T15:55:23Z","timestamp":1788364523342,"version":"build-2803163510"},"reference-count":66,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2024,9,2]],"date-time":"2024-09-02T00:00:00Z","timestamp":1725235200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Plant Cell &amp; Environment"],"published-print":{"date-parts":[[2024,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of <jats:italic>PPR<\/jats:italic> genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove <jats:italic>Kandelia obovata<\/jats:italic>, we systematically identified 298 <jats:italic>PPR<\/jats:italic> genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point,\u00a0and so forth. Furthermore, we combined genome\u2010wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential <jats:italic>PPR<\/jats:italic> genes associated with propagule leaves colour variations of <jats:italic>K. obovata<\/jats:italic>. As a result, we prioritized 16 <jats:italic>PPR<\/jats:italic> genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS\u2010type) and Maker00003187 (P\u2010type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (<jats:italic>rps14<\/jats:italic>, <jats:italic>rpoC1<\/jats:italic>\u00a0and <jats:italic>rpoC2<\/jats:italic>) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of <jats:italic>rps14<\/jats:italic>, <jats:italic>rpoC1<\/jats:italic>,\u00a0and <jats:italic>rpoC2<\/jats:italic> in our previous study\u00a0and the verification of interaction between Maker00002998 and <jats:italic>rps14<\/jats:italic> transcript using in vitro RNA\u00a0pull\u2010down assays revealed that Maker00002998 PPR protein might be involved in the post\u2010transcriptional process of chloroplast genes. Our result provides new insights into the roles of <jats:italic>PPR<\/jats:italic> genes in the albinism mechanism of <jats:italic>K. obovata<\/jats:italic> propagule leaves.<\/jats:p>","DOI":"10.1111\/pce.15132","type":"journal-article","created":{"date-parts":[[2024,9,2]],"date-time":"2024-09-02T14:24:27Z","timestamp":1725287067000},"page":"5498-5510","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genome\u2010Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi\u2010Omics Analysis Provide New Insights Into the Albinism Mechanism of <i>Kandelia obovata<\/i> Propagule Leaves"],"prefix":"10.1111","volume":"47","author":[{"given":"Chaoqun","family":"Xu","sequence":"first","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji\u2010Cheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling","family":"Sun","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li\u2010Han","family":"Zhuang","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ze\u2010Jun","family":"Guo","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"},{"name":"Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Coral Reef Research Center of China Guangxi University Nanning China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian\u2010Su","family":"Ding","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong\u2010Na","family":"Ma","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"},{"name":"National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology Jiangnan University Wuxi Jiangsu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling\u2010Yu","family":"Song","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han\u2010Chen","family":"Tang","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1227-0759","authenticated-orcid":false,"given":"Xue\u2010Yi","family":"Zhu","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8588-1529","authenticated-orcid":false,"given":"Hai\u2010Lei","family":"Zheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology Xiamen University Xiamen China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,9,2]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/plphys\/kiad341"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-021-04556-z"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv416"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-arplant-050213-040159"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp348"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-5088-9"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.13121"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.15448"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0025-326X(02)00221-7"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.16297"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2019.11.002"},{"key":"e_1_2_8_15_1","first-page":"2353","article-title":"Plastid Development of Albino Viviparous Propagules in the Woody Mangrove Species of Kandelia obovata","volume":"42","author":"Hao S.","year":"2022","journal-title":"Tree Physiology"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41438-020-0300-x"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2022.100461"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.13672"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2024.100858"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/ery139"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02662-2"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"e_1_2_8_23_1","first-page":"205","article-title":"A Benchmark of Gene Expression Tissue\u2010Specificity Metrics","volume":"18","author":"Kryuchkova\u2010Mostacci N.","year":"2017","journal-title":"Briefings in Bioinformatics"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1111\/jipb.13477"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-559"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.12584"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.15088"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/ery214"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1111\/jipb.13147"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/erab185"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.104.022236"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.239244.118"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msn057"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.108.064667"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.12687"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.20.00311"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac993"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky448"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.1095"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1086\/519795"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41477-019-0412-1"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-021-02062-9"},{"key":"e_1_2_8_44_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.14578"},{"key":"e_1_2_8_45_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl315"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1131"},{"key":"e_1_2_8_47_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11103-017-0654-0"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1192002"},{"key":"e_1_2_8_49_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11103-010-9616-5"},{"key":"e_1_2_8_50_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.marpolbul.2019.110667"},{"key":"e_1_2_8_51_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.01.036"},{"key":"e_1_2_8_52_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq603"},{"key":"e_1_2_8_53_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr1293"},{"key":"e_1_2_8_54_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-022-03819-y"},{"key":"e_1_2_8_55_1","article-title":"Clusterprofiler 4.0: A Universal Enrichment Tool for Interpreting Omics Data","volume":"2","author":"Wu T.","year":"2021","journal-title":"Innovation"},{"key":"e_1_2_8_56_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-21269-1"},{"key":"e_1_2_8_57_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/erae007"},{"key":"e_1_2_8_58_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00299-023-03042-5"},{"key":"e_1_2_8_59_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz075"},{"key":"e_1_2_8_60_1","doi-asserted-by":"publisher","DOI":"10.1038\/nplants.2017.37"},{"key":"e_1_2_8_61_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7713"},{"key":"e_1_2_8_62_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyaa017"},{"key":"e_1_2_8_63_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms232113640"},{"key":"e_1_2_8_64_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2023.100611"},{"key":"e_1_2_8_65_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2012.02.101"},{"key":"e_1_2_8_66_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122-020-03742-6"},{"key":"e_1_2_8_67_1","doi-asserted-by":"publisher","DOI":"10.1093\/plphys\/kiac222"}],"container-title":["Plant, Cell &amp; Environment"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/pce.15132","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T13:31:21Z","timestamp":1747229481000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/pce.15132"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,2]]},"references-count":66,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2024,12]]}},"alternative-id":["10.1111\/pce.15132"],"URL":"https:\/\/doi.org\/10.1111\/pce.15132","archive":["Portico"],"relation":{},"ISSN":["0140-7791","1365-3040"],"issn-type":[{"value":"0140-7791","type":"print"},{"value":"1365-3040","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,2]]},"assertion":[{"value":"2024-04-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-08-19","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-09-02","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}