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Bontpart T, Weiss A, Vile D, Gérard F, Lacombe B, Reichheld JP, Mari S. Growing on calcareous soils and facing climate change. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00069-4. [PMID: 38570279 DOI: 10.1016/j.tplants.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
Soil calcium carbonate (CaCO3) impacts plant mineral nutrition far beyond Fe metabolism, imposing constraints for crop growth and quality in calcareous agrosystems. Our knowledge on plant strategies to tolerate CaCO3 effects mainly refers to Fe acquisition. This review provides an update on plant cellular and molecular mechanisms recently described to counteract the negative effects of CaCO3 in soils, as well as recent efforts to identify genetic bases involved in CaCO3 tolerance from natural populations, that could be exploited to breed CaCO3-tolerant crops. Finally, we review the impact of environmental factors (soil water content, air CO2, and temperature) affecting soil CaCO3 equilibrium and plant tolerance to calcareous soils, and we propose strategies for improvement in the context of climate change.
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Affiliation(s)
- Thibaut Bontpart
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Alizée Weiss
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
| | - Denis Vile
- LEPSE, INRAE, Institut Agro, Université de Montpellier, 2 Place P. Viala, F-34060, Montpellier cédex 2, France
| | - Frédéric Gérard
- UMR Eco&Sols, INRAE, IRD, CIRAD, Institut Agro, Université de Montpellier, Montpellier, France
| | - Benoît Lacombe
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | | | - Stéphane Mari
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.
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Zhou H, Zhang X, Liu H, Ma J, Hao F, Ye H, Wang Y, Zhang S, Yue M, Zhao P. Chromosome-level genome assembly of Platycarya strobilacea. Sci Data 2024; 11:269. [PMID: 38443357 PMCID: PMC10914804 DOI: 10.1038/s41597-024-03107-4] [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: 10/17/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
Platycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases. This new high-quality assembly of P. strobilacea provide valuable resource for the phylogenetic and evolutionary analysis of the walnut family and angiosperm.
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Affiliation(s)
- Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Xuedong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Fan Hao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yaling Wang
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ming Yue
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China.
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Groh JS, Vik DC, Stevens KA, Brown PJ, Langley CH, Coop G. Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.23.573205. [PMID: 38187547 PMCID: PMC10769452 DOI: 10.1101/2023.12.23.573205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The maintenance of stable mating type polymorphisms is a classic example of balancing selection, underlying the nearly ubiquitous 50/50 sex ratio in species with separate sexes. One lesser known but intriguing example of a balanced mating polymorphism in angiosperms is heterodichogamy - polymorphism for opposing directions of dichogamy (temporal separation of male and female function in hermaphrodites) within a flowering season. This mating system is common throughout Juglandaceae, the family that includes globally important and iconic nut and timber crops - walnuts (Juglans), as well as pecan and other hickories (Carya). In both genera, heterodichogamy is controlled by a single dominant allele. We fine-map the locus in each genus, and find two ancient (>50 Mya) structural variants involving different genes that both segregate as genus-wide trans-species polymorphisms. The Juglans locus maps to a ca. 20 kb structural variant adjacent to a probable trehalose phosphate phosphatase (TPPD-1), homologs of which regulate floral development in model systems. TPPD-1 is differentially expressed between morphs in developing male flowers, with increased allele-specific expression of the dominant haplotype copy. Across species, the dominant haplotype contains a tandem array of duplicated sequence motifs, part of which is an inverted copy of the TPPD-1 3' UTR. These repeats generate various distinct small RNAs matching sequences within the 3' UTR and further downstream. In contrast to the single-gene Juglans locus, the Carya heterodichogamy locus maps to a ca. 200-450 kb cluster of tightly linked polymorphisms across 20 genes, some of which have known roles in flowering and are differentially expressed between morphs in developing flowers. The dominant haplotype in pecan, which is nearly always heterozygous and appears to rarely recombine, shows markedly reduced genetic diversity and is over twice as long as its recessive counterpart due to accumulation of various types of transposable elements. We did not detect either genetic system in other heterodichogamous genera within Juglandaceae, suggesting that additional genetic systems for heterodichogamy may yet remain undiscovered.
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Affiliation(s)
- Jeffrey S Groh
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
| | - Diane C Vik
- Department of Evolution and Ecology, University of California, Davis
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis
- Department of Computer Science, University of California, Davis
| | - Patrick J Brown
- Department of Plant Sciences, University of California, Davis
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
| | - Graham Coop
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
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Lipánová V, Kabátová KN, Zeisek V, Kolář F, Chrtek J. Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates. Mol Phylogenet Evol 2023; 189:107940. [PMID: 37820762 DOI: 10.1016/j.ympev.2023.107940] [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: 01/16/2023] [Revised: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
One of the major goals of contemporary evolutionary biology is to elucidate the relative roles of allopatric and ecological differentiation and polyploidy in speciation. In this study, we address the taxonomically intricate Sabulina verna group, which has a disjunct Arctic-alpine postglacial range in Europe and occupies a broad range of ecological niches, including substrates toxic to plants. Using genome-wide ddRAD sequencing combined with morphometric analyses based on extensive sampling of 111 natural populations, we aimed to disentangle internal evolutionary relationships and examine their correspondence with the pronounced edaphic and ploidy diversity within the group. We identified two spatially distinct groups of diploids: a widespread Arctic-alpine group and a spatially restricted yet diverse Balkan group. Most tetraploids exhibited a considerably admixed ancestry derived from both these groups, suggesting their allopolyploid origin. Four genetic clusters in congruence with geography and mostly supported by morphological traits were recognized in the diploid Arctic-alpine group. Tetraploids are split into two distinct and geographically vicariant groups, indicating their repeated polytopic origin. Furthermore, our results also revealed at least five-fold parallel colonization of toxic substrates (serpentine and metalliferous), altogether demonstrating a complex interaction between geography, challenging substrates and polyploidy in the evolution of the group. Finally, we propose a new taxonomic treatment of this complex.
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Affiliation(s)
- Veronika Lipánová
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | | | - Vojtěch Zeisek
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Jindřich Chrtek
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic.
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