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Marchesini A, Silverj A, Torre S, Rota-Stabelli O, Girardi M, Passeri I, Fracasso I, Sebastiani F, Vernesi C. First genome-wide data from Italian European beech (Fagus sylvatica L.): Strong and ancient differentiation between Alps and Apennines. PLoS One 2023; 18:e0288986. [PMID: 37471380 PMCID: PMC10358878 DOI: 10.1371/journal.pone.0288986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 07/10/2023] [Indexed: 07/22/2023] Open
Abstract
The European beech (Fagus sylvatica L.) is one of the most widespread forest trees in Europe whose distribution and intraspecific diversity has been largely shaped by repeated glacial cycles. Previous studies, mainly based on palaeobotanical evidence and a limited set of chloroplast and nuclear genetic markers, highlighted a complex phylogeographic scenario, with southern and western Europe characterized by a rather heterogeneous genetic structure, as a result of recolonization from different glacial refugia. Despite its ecological and economic importance, the genome of this broad-leaved tree has only recently been assembled, and its intra-species genomic diversity is still largely unexplored. Here, we performed whole-genome resequencing of nine Italian beech individuals sampled from two stands located in the Alpine and Apennine mountain ranges. We investigated patterns of genetic diversity at chloroplast, mitochondrial and nuclear genomes and we used chloroplast genomes to reconstruct a temporally-resolved phylogeny. Results allowed us to test European beech differentiation on a whole-genome level and to accurately date their divergence time. Our results showed comparable, relatively high levels of genomic diversity in the two populations and highlighted a clear differentiation at chloroplast, mitochondrial and nuclear genomes. The molecular clock analysis indicated an ancient split between the Alpine and Apennine populations, occurred between the Günz and the Riss glaciations (approximately 660 kyrs ago), suggesting a long history of separation for the two gene pools. This information has important conservation implications in the context of adaptation to ongoing climate changes.
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Affiliation(s)
- Alexis Marchesini
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
- Research Institute on Terrestrial Ecosystems (IRET), The National Research Council of Italy (CNR), Porano (Terni), Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Andrea Silverj
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | - Sara Torre
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Omar Rota-Stabelli
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige, Italy
- Department CIBIO, University of Trento, Trento, Italy
- Plant Protection Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
| | - Matteo Girardi
- Conservation Genomics Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
| | - Iacopo Passeri
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
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Worth JRP, Shitara T, Kitamura K, Kikuchi S, Kanetani S, Matsui T, Uchiyama K, Tomaru N. Low‐elevation warm‐edge
Fagus crenata
populations in the core of the species range are glacial relicts with high conservation value. Ecol Res 2022. [DOI: 10.1111/1440-1703.12378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- James R. P. Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
| | - Takuto Shitara
- Institute of Agriculture Tokyo University of Agriculture and Technology Fuchu‐shi, Tokyo Japan
| | - Keiko Kitamura
- Hokkaido Research Centre, Forestry and Forest Products Research Institute Forest Research and Management Organization Sapporo, Hokkaido Japan
| | - Satoshi Kikuchi
- Hokkaido Research Centre, Forestry and Forest Products Research Institute Forest Research and Management Organization Sapporo, Hokkaido Japan
| | - Seiichi Kanetani
- Kyushu Research Center Forestry and Forest Products Research Institute Chuo‐ku, Kumamoto Japan
| | - Tetsuya Matsui
- Center for Biodiversity and Climate Change, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
- Faculty of Life and Environmental Sciences University of Tsukuba Tsukuba, Ibaraki Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences Nagoya University Chikusa‐ku, Nagoya Japan
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Jiang C, Fan W, Chen L, Gan X. Complete chloroplast genome sequence of Fagus hayatae Palib. (Fagaceae). Mitochondrial DNA B Resour 2022; 7:944-945. [PMID: 35692643 PMCID: PMC9176376 DOI: 10.1080/23802359.2022.2080015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Complete chloroplast genome (cpDNA) sequence of Fagus hayatae Palib. is yet to be reported, and the phylogenetic position of this species is still under debate. In this study, the complete cpDNA sequence of F. hayatae was determined from Illumina NovaSeq pair-end sequencing data. Results revealed that it has a sequence length of 158,360 bp and contains 131 annotated genes, which consist of 83 protein-coding genes, 40 tRNA genes, and eight rRNA genes. The phylogenetic analysis of the complete cpDNA sequence indicates that Fagus represents a monophyletic clade within Fagaceae. The species relatedness between F. hayatae and F. engleriana is relatively close.
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Affiliation(s)
- Chaoyang Jiang
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Wenqian Fan
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Lijun Chen
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Xiaohong Gan
- College of Life Sciences, China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
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