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Ma XG, Ren YB, Sun H. Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China. Cladistics 2024; 40:357-373. [PMID: 38197450 DOI: 10.1111/cla.12570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 01/11/2024] Open
Abstract
Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.
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Affiliation(s)
- Xiang-Guang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yue-Bo Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Hopkins L, Yim K, Rumora A, Baykus MF, Martinez L, Jimenez L. Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities. Genes (Basel) 2024; 15:865. [PMID: 39062644 PMCID: PMC11275894 DOI: 10.3390/genes15070865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.
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Affiliation(s)
| | | | | | | | | | - Luis Jimenez
- Biology and Horticulture Department, Bergen Community College, 400 Paramus Road, Paramus, NJ 07652, USA; (L.H.); (K.Y.); (A.R.); (M.F.B.); (L.M.)
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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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Kersten B, Rellstab C, Schroeder H, Brodbeck S, Fladung M, Krutovsky KV, Gugerli F. The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation. BMC Genomics 2022; 23:776. [PMID: 36443651 PMCID: PMC9703787 DOI: 10.1186/s12864-022-08993-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/05/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Plant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm species that is widely distributed in Europe and occupies a large range of environmental conditions. Reference sequences of the nuclear and chloroplast genome of A. alba are available, however, the mitogenome has not yet been assembled and studied. RESULTS Here, we used paired-end Illumina short reads generated from a single haploid megagametophyte in combination with PacBio long reads from high molecular weight DNA of needles to assemble the first mitogenome sequence of A. alba. Assembly and scaffolding resulted in 11 mitogenome scaffolds, with the largest scaffold being 0.25 Mbp long. Two of the scaffolds displayed a potential circular structure supported by PCR. The total size of the A. alba mitogenome was estimated at 1.43 Mbp, similar to the size (1.33 Mbp) of a draft assembly of the Abies firma mitogenome. In total, 53 distinct genes of known function were annotated in the A. alba mitogenome, comprising 41 protein-coding genes, nine tRNA, and three rRNA genes. The proportion of highly repetitive elements (REs) was 0.168. The mitogenome seems to have a complex and dynamic structure featured by high combinatorial variation, which was specifically confirmed by PCR for the contig with the highest mapping coverage. Comparative analysis of all sequenced mitogenomes of gymnosperms revealed a moderate, but significant positive correlation between mitogenome size and proportion of REs. CONCLUSIONS The A. alba mitogenome provides a basis for new comparative studies and will allow to answer important structural, phylogenetic and other evolutionary questions. Future long-read sequencing with higher coverage of the A. alba mitogenome will be the key to further resolve its physical structure. The observed positive correlation between mitogenome size and proportion of REs will be further validated once available mitogenomes of gymnosperms would become more numerous. To test whether a higher proportion of REs in a mitogenome leads to an increased recombination and higher structural complexity and variability is a prospective avenue for future research.
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Affiliation(s)
- Birgit Kersten
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Christian Rellstab
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Hilke Schroeder
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Sabine Brodbeck
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Konstantin V. Krutovsky
- grid.7450.60000 0001 2364 4210Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Felix Gugerli
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
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Dong PB, Wang LJ, Jia Y, Li ZH, Wang HY, Guo FX, Chen Y. Niche divergence at the intraspecific level in an endemic rare peony ( Paeonia rockii): A phylogenetic, climatic and environmental survey. FRONTIERS IN PLANT SCIENCE 2022; 13:978011. [PMID: 36388470 PMCID: PMC9663928 DOI: 10.3389/fpls.2022.978011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Ecological factors have received increasing attention as drivers of speciation but also in the maintenance of postspeciation divergence. However, the relative significance of the responses of species to climate oscillations for driving niche divergence or conservatism in the evolution of many species that pass through diverse environments and limited geographical boundaries remains poorly understood. Paeonia rockii (one of the ancient species of Paeonia) comprising two subspecies called Paeonia rockii subsp. rockii and Paeonia rockii subsp. taibaishanica is an endemic, rare, and endangered medicinal plant in China. In this study, we integrated whole chloroplast genomes, and ecological factors to obtain insights into ecological speciation and species divergence in this endemic rare peony. RAxML analysis indicated that the topological trees recovered from three different data sets were identical, where P. rockii subsp. rockii and P. rockii subsp. taibaishanica clustered together, and molecular dating analyses suggested that the two subspecies diverged 0.83 million years ago. In addition, ecological niche modeling showed that the predicted suitable distribution areas for P. rockii subsp. rockii and P. rockii subsp. taibaishanica differed considerably, although the predicted core distribution areas were similar, where the population contracted in the last interglacial and expanded in the last glacial maximum. Under the emissions scenarios for the 2050s and 2070s, the suitable distribution areas were predicted to contract significantly, where the migration routes of the two subspecies tended to migrate toward high latitudes and elevations, thereby suggesting strong responses of the distributions of the two subspecies to climate change. These findings combined with the phylogeographic relationships provide comprehensive insights into niche variation and differentiation in this endemic rare peony, and they highlight the importance of geological and climatic changes for species divergence and changes in the population geographic patterns of rare and endangered medicinal plants in East Asia.
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Affiliation(s)
- Peng-Bin Dong
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Ling-Juan Wang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Jia
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) College of Life Sciences, Northwest University, Xi’an, China
| | - Hong-Yan Wang
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Feng-Xia Guo
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Chen
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
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Complex Physical Structure of Complete Mitochondrial Genome of Quercus acutissima (Fagaceae): A Significant Energy Plant. Genes (Basel) 2022; 13:genes13081321. [PMID: 35893058 PMCID: PMC9331829 DOI: 10.3390/genes13081321] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/06/2023] Open
Abstract
Quercus acutissima Carruth. is a Chinese important energy plant with high ecological and economic values. While the species chloroplast genome has been reported, its mitochondrial genome (mitogenome) is still unexplored. Here, we assembled and annotated the Q. acutissima mitogenome, and we compared its characteristic differences with several closely related species. The Q. acutissima mitogenome’s main structure is branched with three distinguished contigs (linear molecule 1, circular molecule 2, and circular molecule 3) with 448,982 bp total length and 45.72% GC content. The mitogenome contained 51 genes, including 32 protein-coding, 16 tRNA and 3 rRNA genes. We examined codon usage, repeated sequences, genome recombination, chloroplast to mitochondrion DNA transformation, RNA editing, and synteny in the Q. acutissima mitogenome. Phylogenetic trees based on 29 species mitogenomes clarified the species classification. Our results provided comprehensive information of Q. acutissima mitogenome, and they are expected to provide valuable information for Fagaceae evolutionary biology and to promote the species germplasm utilization.
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Feng Y, Xiang X, Akhter D, Pan R, Fu Z, Jin X. Mitochondrial Phylogenomics of Fagales Provides Insights Into Plant Mitogenome Mosaic Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:762195. [PMID: 34733309 PMCID: PMC8558628 DOI: 10.3389/fpls.2021.762195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 09/17/2021] [Indexed: 05/13/2023]
Abstract
Fagales are an order of woody plants and comprise more than 1,100 species, most of which produce economically important timbers, nuts, and fruits. Their nuclear and plastid genomes are well-sequenced and provided valuable resources to study their phylogeny, breeding, resistance, etc. However, little is known about the mitochondrial genomes (mitogenomes), which hinder a full understanding of their genome evolution. In this study, we assembled complete mitogenomes of 23 species, covering five of the seven families of Fagales. These mitogenomes had similar gene sets but varied 2.4 times in size. The mitochondrial genes were highly conserved, and their capacity in phylogeny was challenging. The mitogenomic structure was extremely dynamic, and synteny among species was poor. Further analyses of the Fagales mitogenomes revealed extremely mosaic characteristics, with horizontal transfer (HGT)-like sequences from almost all seed plant taxa and even mitoviruses. The largest mitogenome, Carpinus cordata, did not have large amounts of specific sequences but instead contained a high proportion of sequences homologous to other Fagales. Independent and unequal transfers of third-party DNA, including nuclear genome and other resources, may partially account for the HGT-like fragments and unbalanced size expansions observed in Fagales mitogenomes. Supporting this, a mitochondrial plasmid-like of nuclear origin was found in Carpinus. Overall, we deciphered the last genetic materials of Fagales, and our large-scale analyses provide new insights into plant mitogenome evolution and size variation.
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Affiliation(s)
- Yanlei Feng
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- College of Agriculture and Biotechnology, Institute of Crop Science, Zhejiang University, Hangzhou, China
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Xiaoguo Xiang
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Delara Akhter
- College of Agriculture and Biotechnology, Institute of Crop Science, Zhejiang University, Hangzhou, China
- Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Ronghui Pan
- College of Agriculture and Biotechnology, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Zhixi Fu
- College of Life Science, Sichuan Normal University, Chengdu, China
- Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, China
| | - Xiaohua Jin
- Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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Ulaszewski B, Meger J, Mishra B, Thines M, Burczyk J. Complete Chloroplast Genomes of Fagus sylvatica L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs. Genes (Basel) 2021; 12:1357. [PMID: 34573338 PMCID: PMC8468245 DOI: 10.3390/genes12091357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 12/17/2022] Open
Abstract
Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of Fagus sylvatica, an important broadleaved tree species of European forests, based on complete chloroplast genomes of 18 individuals sampled widely across the species distribution. Our results confirm the hypothesis of a low cpDNA diversity in European beech. The chloroplast genome size was remarkably stable (158,428 ± 37 bp). The polymorphic markers, 12 microsatellites (SSR), four SNPs and one indel, were found only in the single copy regions, while inverted repeat regions were monomorphic both in terms of length and sequence, suggesting highly efficient suppression of mutation. The within-individual analysis of polymorphisms showed >9k of markers which were proportionally present in gene and non-gene areas. However, an investigation of the frequency of alternate alleles revealed that the source of this diversity originated likely from nuclear-encoded plastome remnants (NUPTs). Phylogeographic and Mantel correlation analysis based on the complete chloroplast genomes exhibited clustering of individuals according to geographic distance in the first distance class, suggesting that the novel markers and in particular the cpSSRs could provide a more detailed picture of beech population structure in Central Europe.
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Affiliation(s)
- Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
| | - Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (B.M.); (M.T.)
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60483 Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (B.M.); (M.T.)
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60483 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany
| | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
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