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Shen X, Zong W, Li Y, Liu X, Zhuge F, Zhou Q, Zhou S, Jiang D. Evolution of Cherries ( Prunus Subgenus Cerasus) Based on Chloroplast Genomes. Int J Mol Sci 2023; 24:15612. [PMID: 37958595 PMCID: PMC10650623 DOI: 10.3390/ijms242115612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus individuals, along with 36 additional genomes from the NCBI database, resulting in a total of 90 genomes for comparative analysis. The chloroplast genomes of subg. Cerasus exhibited varying sizes and consisted of 129 genes, including protein-coding, transfer RNA, and ribosomIal RNA genes. Genomic variation was investigated through InDels and SNPs, showcasing distribution patterns and impact levels. A comparative analysis of chloroplast genome boundaries highlighted variations in inverted repeat (IR) regions among Cerasus and other Prunus species. Phylogeny based on whole-chloroplast genome sequences supported the division of Prunus into three subgenera, I subg. Padus, II subg. Prunus and III subg. Cerasus. The subg. Cerasus was subdivided into seven lineages (IIIa to IIIg), which matched roughly to taxonomic sections. The subg. Padus first diverged 51.42 Mya, followed by the separation of subg. Cerasus from subg. Prunus 39.27 Mya. The subg. Cerasus started diversification at 15.01 Mya, coinciding with geological and climatic changes, including the uplift of the Qinghai-Tibet Plateau and global cooling. The Himalayans were the refuge of cherries, from which a few species reached Europe through westward migration and another species reached North America through northeastward migration. The mainstage of cherry evolution was on the Qing-Tibet Plateau and later East China and Japan as well. These findings strengthen our understanding of the evolution of cherry and provide valuable insights into the conservation and sustainable utilization of cherry's genetic resources.
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Affiliation(s)
- Xin Shen
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Wenjin Zong
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Yingang Li
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Xinhong Liu
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Fei Zhuge
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Qi Zhou
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Shiliang Zhou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dongyue Jiang
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
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Su N, Hodel RG, Wang X, Wang JR, Xie SY, Gui CX, Zhang L, Chang ZY, Zhao L, Potter D, Wen J. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses. PLANT DIVERSITY 2023; 45:397-408. [PMID: 37601549 PMCID: PMC10435964 DOI: 10.1016/j.pld.2023.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 08/22/2023]
Abstract
Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome data recovered a well-resolved phylogeny. The species were divided into three main clades corresponding to their inflorescence types, - the racemose group, the solitary-flower group and the corymbose group - with the latter two sister to one another. Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago. The diversification of the three major clades began between the Paleocene and Miocene, suggesting that paleoclimatic events were an important driving force for Prunus diversification. Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences, and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis, respectively. We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies. Prunus has undergone extensive hybridization events, although it is difficult to identify conclusively specific instances of hybridization when using SNP data, especially deep in the phylogeny. Our study provides well-resolved nuclear and plastid phylogenies of Prunus, reveals substantial cytonuclear discord at shallow scales, and sheds new light on inflorescence evolution in this economically important lineage.
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Affiliation(s)
- Na Su
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Richard G.J. Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Xi Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Jun-Ru Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Si-Yu Xie
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Chao-Xia Gui
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Ling Zhang
- College of Life Sciences, Tarim University, Alaer 843300, China
| | - Zhao-Yang Chang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, CA 95616, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
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Lyubarsky GY, Perkovsky EE, Vasilenko DV. Unexpected Diversity of Xenoscelinae in Priabonian European Amber: The Third Xenosceline Species from Rovno Amber. Life (Basel) 2023; 13:636. [PMID: 36983791 PMCID: PMC10057667 DOI: 10.3390/life13030636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 03/30/2023] Open
Abstract
Xenophagus simutniki sp. n. is described from a late Eocene Rovno amber specimen. The new species is similar to the fossil Xenophagus popovi Lyubarsky et Perkovsky, 2017 from the late Eocene Baltic amber (W Russia), differing in the medially notched anterior margin of the pronotum. The Rovno xenosceline fauna is the richest among both extant and extinct faunas. This fauna includes the extinct genera Xenophagus Lyubarsky & Perkovsky, 2017 and Xenohimatium Lyubarsky & Perkovsky, 2012, which are closest to the extant Mediterranean Xenoscelis Wollaston 1864 and the representative of the extant boreal genus Zavaljus Reitter, 1880. A key to extinct species of the subfamily Xenoscelinae is presented. The possible reasons of xenoscelines abundance in European amber forests are discussed.
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Affiliation(s)
- Georgy Yu. Lyubarsky
- Zoological Museum, Moscow Lomonosov State University, Bol’shya Nikitskaya 2, Moscow 125009, Russia
| | - Evgeny E. Perkovsky
- I. I. Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Bogdan Khmielnitsky Str. 15, 01030 Kiev, Ukraine
- Natural History Museum of Denmark, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Dmitry V. Vasilenko
- A.A. Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow 117647, Russia
- Paleontological Laboratory, Cherepovets State University, Cherepovets 162600, Russia
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The largest amber-preserved flower revisited. Sci Rep 2023; 13:17. [PMID: 36635320 PMCID: PMC9837116 DOI: 10.1038/s41598-022-24549-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/16/2022] [Indexed: 01/13/2023] Open
Abstract
Amber exquisitely preserves the delicate organs of fossil flowers for millions of years. However, flower inclusions can be rare and usually do not exceed 10 mm in size. Here we report an exceptionally large flower from late Eocene Baltic amber, measuring 28 mm across, which is about three times as large as most floral inclusions. This fossil was described over 150 years ago as Stewartia kowalewskii (Theaceae) and has never been revised. The analysis of pollen extracted from the anthers of the flower inclusion, however, revealed strong affinities to Asian species of Symplocos (Symplocaceae), prompting the new combination Symplocos kowalewskii comb. nov. et emend. This fossil represents the first record of Symplocaceae from Baltic amber and supports affinities of its flora to evergreen broadleaved and mixed mesophytic forests of present-day East and Southeast Asia. The rarity of such large-sized flower inclusions is likely due to the size of the resin outpouring and its properties, which might affect the embedding of plant organs.
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Jabbour F, Espinosa F, Dejonghe Q, Le Péchon T. Development and Evolution of Unisexual Flowers: A Review. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020155. [PMID: 35050043 PMCID: PMC8780417 DOI: 10.3390/plants11020155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 06/12/2023]
Abstract
The development of unisexual flowers has been described in a large number of taxa, sampling the diversity of floral phenotypes and sexual systems observed in extant angiosperms, in studies focusing on floral ontogeny, on the evo-devo of unisexuality, or on the genetic and chromosomal bases of unisexuality. We review here such developmental studies, aiming at characterizing the diversity of ontogenic pathways leading to functionally unisexual flowers. In addition, we present for the first time and in a two-dimensional morphospace a quantitative description of the developmental rate of the sexual organs in functionally unisexual flowers, in a non-exhaustive sampling of angiosperms with contrasted floral morphologies. Eventually, recommendations are provided to help plant evo-devo researchers and botanists addressing macroevolutionary and ecological issues to more precisely select the taxa, the biological material, or the developmental stages to be investigated.
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Affiliation(s)
- Florian Jabbour
- Institut de Systématique Évolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, 75005 Paris, France;
| | - Felipe Espinosa
- Independent Researcher, Carrera 13 # 113-24, Bogotá 110111, Colombia;
| | - Quentin Dejonghe
- Institut de Systématique Évolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, 75005 Paris, France;
| | - Timothée Le Péchon
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium;
- Fédération Wallonie-Bruxelles, Service Général de l’Enseignement Supérieur et de la Recherche Scientifique, Rue A. Lavalée, 1, 1080 Brussels, Belgium
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Telnov D, Perkovsky EE, Vasilenko DV, Yamamoto S. The first fossil Coleoptera record from the Volyn Region, Ukraine, with description of a new Glesoconomorphus (Coleoptera, Mycteridae) in syninclusion with Winterschmidtiidae (Acari) and a key to species. Zookeys 2021; 1068:189-201. [PMID: 34819765 PMCID: PMC8592962 DOI: 10.3897/zookeys.1068.75391] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/18/2021] [Indexed: 11/12/2022] Open
Abstract
Glesoconomorphusekaterinae sp. nov. (Coleoptera, Mycteridae), representing the first ever fossil species of Coleoptera from the Volyn Region of Ukraine and the first mycterid from late Eocene Rovno amber, is described and illustrated. A key to species of the fossil mycterid genus Glesoconomorphus Alekseev, Pollock & Bukejs, 2019 is presented. The systematic position of Glesoconomorphus within Eurypinae J. Thomson, 1860 is briefly discussed. The oldest finding of phoretic Winterschmidtiidae Oudemans, 1923 mites, found on the type specimen of the new beetle species, is reported.
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Affiliation(s)
- Dmitry Telnov
- Department of Life Sciences, Natural History Museum, SW7 5BD, London, UKNatural History MuseumLondonUnited Kingdom
- Institute of Biology, University of Latvia, O. Vācieša iela 4, LV-1004, Rīga, LatviaUniversity of LatviaRīgaLatvia
- Coleopterological Research Center, Institute of Life Sciences and Technology, Daugavpils University, Vienības iela 13, LV-5401, Daugavpils, LatviaDaugavpils UniversityDaugavpilsLatvia
| | - Evgeny E. Perkovsky
- I.I. Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, B. Khmelnitskogo 15, 01601, Kiev, UkraineNational Academy of Sciences of UkraineKievUkraine
| | - Dmitry V. Vasilenko
- A.A. Borissiak Paleontological Institute, Russian Academy of Sciences, Profsoyuznaya Str. 123, 117868, Moscow, RussiaA.A. Borissiak Paleontological Institute, Russian Academy of SciencesMoscowRussia
- Cherepovets State University, Lunacharsky prospect 5, 162600, Cherepovets, RussiaCherepovets State UniversityCherepovetsRussia
| | - Shûhei Yamamoto
- Hokkaido University Museum, Hokkaido University, Kita 8, Nishi 5, Kita-ku, 060-0808, Sapporo, JapanHokkaido UniversitySapporoJapan
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