Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Aug. 2, 2024

Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing significant role in the cultivation of horticultural, ornamental, medicinal varieties. Whole-genome duplication (WGD) its subsequent post-polyploid diploidization (PPD) process represent most drastic type karyotype evolution, injecting potential for promoting diversity this lineage. However, polyploidization histories, well genome subgenome fractionation following WGD events Lamiales species, are still not investigated. In study, we constructed chromosome-level assembly Lindenbergia philippensis (Orobanchaceae) conducted comparative genomic analyses with 14 other species. L. is positioned closest to parasitic lineage within Orobanchaceae has conserved karyotype. Through combination Ks analysis syntenic depth analysis, reconstructed validated histories Our results indicated that Primulina huaijiensis underwent three rounds γ-WGT event, rather than two reported. Besides, reconfirmed shared common event (L-WGD). Subsequently, Ancestral Karyotype (LAK), 11 proto-chromosomes, elucidated evolutionary trajectory, highlighting flexible reshuffling paleogenome. We identified biased subgenomes L-WGD eight highlighted positive impacts non-WGD genes on gene family expansion. This study provides novel resources insights into polyploidy remodeling essential advancing our understanding diversification evolution.

Language: Английский

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Leaf elemental composition analysis in spider plant [Gynandropsis gynandra L. (Briq.)] differentiates three nutritional groups

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 2, 2022

Understanding the genetic variability within a plant species is paramount in implementing successful breeding program. Spider ( Gynandropsis gynandra ) an orphan leafy vegetable and extraordinary source of vitamins, secondary metabolites minerals, representing important resource for combatting malnutrition. However, evaluation leaf elemental composition, using worldwide germplasm collection to inform programs valorization human nutrition still lacking. The present study aimed profile composition G. depict any potential geographical signature 70 advanced lines derived from accessions originating Asia Eastern, Southern West Africa. was grown greenhouse 9 × 8 alpha lattice design with two replications 2020 2021. Inductively coupled plasma–optical emission spectrometry used nine minerals contents. A significant difference p < 0.05) observed among all minerals. Microelements such as iron, zinc, copper manganese contents ranged 12.59–430.72, 16.98–166.58, 19.04–955.71, 5.39–25.10 mg kg −1 dry weight, respectively, while concentrations macroelements potassium, calcium, phosphorus magnesium varied ranges 9992.27–49854.23, 8252.80–33681.21, 3633.55–14216.16, 2068.03–12475.60 respectively. Significant positive correlations were between iron zinc calcium magnesium. Zinc, phosphorus, copper, magnesium, represented landmark elements genotypes. Eastern African genotypes clustered together group 1 higher than Asian lines, which 2 characterized by An additional outstanding 3 six identified high candidates cultivar release. genotype year interaction variance greater genotypic variance, might translate phenotypic plasticity species. Broad-sense heritability low element-specific. results reveal diversity spider represent baseline minerals-based program nutrition.

Language: Английский

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Speedy stomata of a C₄ plant correlate with enhanced K⁺ channel gating

Plant Cell & Environment, Journal Year: 2023, Volume and Issue: 47(3), P. 817 - 831

Published: Nov. 27, 2023

Stomata are microscopic pores at the surface of plant leaves that facilitate gaseous diffusion to support photosynthesis. The guard cells around each stoma regulate pore aperture. Plants carry out C

Language: Английский

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Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales

Plants, Journal Year: 2024, Volume and Issue: 13(2), P. 280 - 280

Published: Jan. 18, 2024

Oleosins (OLEs) are a class of small but abundant structural proteins that play essential roles in the formation and stabilization lipid droplets (LDs) seeds oil crops. Despite proposal five oleosin clades (i.e., U, SL, SH, T, M) angiosperms, their evolution eudicots has not been well-established. In this study, we employed Brassicales, an economically important order flowering plants possessing lineage-specific T clade, as example to address issue. Three 10 members were identified from species representing eight plant families, which include Caricaceae, Moringaceae, Akaniaceae, Capparaceae, Cleomaceae. Evolutionary reciprocal best hit-based homologous analyses assigned 98 genes into six M, N, T) nine orthogroups U1, U2, SH1, SH2, SH3, T). The newly N clade represents ancient group already appeared basal angiosperm Amborella trichopoda, constitutively expressed tree fruit crop Carica papaya, including pulp fruit. Moreover, similar Clade previously defined M is actually Lauraceae-specific widely distributed diverged before radiation angiosperm. Compared with A. expansion family Brassicales was largely contributed by recent whole-genome duplications (WGDs) well γ event shared all core eudicots. contrast flower-preferential expression transcript profiling revealed apparent seed/embryo/endosperm-predominant pattern most Arabidopsis thaliana C. papaya. structure divergence paralogous pairs frequently observed, good gain intron. These findings provide insights facilitates further functional studies nonmodel such

Language: Английский

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Expanding the Triangle of U: The genome assembly ofHirschfeldia incanaprovides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 18, 2024

ABSTRACT The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event ( Br-α , ∼15.9 million years ago), different lineages species underwent differential chromosomal rearrangements (diploidization) leading to diverse patterns of gene retention loss (fractionation). Lineage diversification genomic changes contributed an array divergence in morphology, biochemistry, physiology underlying photosynthesis-related traits. C 3 Hirschfeldia incana is studied as it displays photosynthetic rates under high-light conditions. We present improved chromosome-level genome assembly for H. (Nijmegen, v2.0) using nanopore chromosome conformation capture (Hi-C) technologies, with 409Mb size N50 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). updated annotation allowed investigate WGT history comparative phylogenomic framework from ancestral blocks related diploidized crops. (x=7) shares extensive collinearity Raphanus sativus (x=9). These two share some commonalities Brassica rapa B. oleracea (A genome, x=10 x=9, respectively) other similarities nigra (B x=8). Phylogenetic analysis revealed that R. form monophyletic clade between A/C B genomes. postulate genomes are results reciprocal hybridization combinations types. Our might explain discrepancy observed studies regarding phylogenetic placement relation “Triangle U” species. Expression retained copies sub-genome expression divergence, likely due neo- or sub-functionalization. Finally, we highlighted genes associated physio-biochemical-anatomical adaptive which facilitate its high-photosynthesis traits light.

Language: Английский

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Tangled webs and spider‐flowers: Phylogenomics, biogeography, and seed morphology inform the evolutionary history of Cleomaceae

American Journal of Botany, Journal Year: 2024, Volume and Issue: 111(9)

Published: Aug. 29, 2024

Abstract Premise Cleomaceae is an important model clade for studies of evolutionary processes including genome evolution, floral form diversification, and photosynthetic pathway evolution. Diversification divergence patterns in remain tangled as research has been restricted by its worldwide distribution, limited genetic sampling species coverage, a lack definitive fossil calibration points. Methods We used target sequence capture the Angiosperms353 probe set to perform phylogenetic study Cleomaceae. estimated times biogeographic analyses explore origin diversification family. Seed morphology across extant taxa was documented with multifocal image‐stacking techniques morphological characters were extracted, analyzed, compared records. Results recovered well‐supported resolved tree generic relationships that includes 236 (~86%) species. identified 11 principal clades confidently placed Cleomella sister rest Our suggested Brassicaceae diverged ~56 mya, began diversify ~53 mya Palearctic Africa. Multiple transatlantic disjunct distributions identified. Seeds imaged from 218 (~80%) family all known Conclusions results represent most comprehensive date. disjunctions proposed explanations these patterns, likely either long‐distance dispersals or contractions latitudinal caused climate change over geological timescales. found seed varied considerably but mostly mirrored relationships.

Language: Английский

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Identifying Agronomic, Nutrition and Leaf Vein Quantitative Trait Loci in the Orphan CropGynandropsis gynandra

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 29, 2024

Abstract A sustainable food supply is vital for addressing the challenges of a growing global population and climate change. Gynandropsis gynandra , nutritious C 4 orphan crop native to Africa Asia, thrives in low-input agricultural systems, making it valuable candidate future security. This also serves as model studying photosynthesis. However, research on its genetic improvement limited. In this study, two mapping populations from diverse parental lines were used identify Quantitative Trait Loci (QTL) linked agronomically relevant traits like plant height, leaf area, flowering time, nutritional content, Fifteen QTL identified, with affecting both size time across populations, which can be applied marker assisted selection improvement. Additionally, photosynthesis provide insights into mechanisms behind pathway. Overall, enhances potential G. climate-resilient crop. One sentence summary Leveraging natural variation associated important traits.

Language: Английский

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Expanding the Triangle of U: Comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits

Annals of Botany, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 24, 2024

Abstract Background and Aims The Brassiceae tribe encompasses many economically important crops exhibits high intra- interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 Mya), differential lineage diversification genomic changes contributed to an array of divergence in morphology, biochemistry physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied because it displays photosynthetic rates high-light conditions. Our aim was elucidate evolution that gave rise genome H. its high-photosynthesis Methods We reconstructed chromosome-level assembly for (Nijmegen, v.2.0) using nanopore chromosome conformation capture (Hi-C) technologies, with 409 Mb size N50 52 (a 10× improvement over previously published scaffold-level v.1.0 assembly). updated annotation were subsequently used investigate WGT history comparative phylogenomic framework from ancestral blocks related diploidized crops. Key Results (x = 7) shares extensive collinearity Raphanus sativus 9). These two share some commonalities Brassica rapa oleracea (A genome, x 10 C 9, respectively) other similarities nigra (B 8). Phylogenetic analysis revealed R. form monophyletic clade between A/C B genomes. postulate genomes are results hybridization or introgression types. might explain discrepancy observed studies regarding phylogenetic placement relationship ‘triangle U’ species. Expression retained gene copies sub-genome expression divergence, probably attributable neo- sub-functionalization. Finally, we highlight genes associated physio-biochemical–anatomical adaptive incana, which likely facilitate traits under light. Conclusions improved assembly, presented this work will be valuable resource future research unravel genetic basis ability maintain efficiency conditions thereby improve photosynthesis enhanced agricultural production.

Language: Английский

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CAM evolution is associated with gene family expansion in an explosive bromeliad radiation

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 3, 2023

1. Abstract The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in plant kingdom and is characterised by repeated evolution Crassulacean Acid Metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many families regarded as a key innovation driver ecological diversification Bromeliaceae. By producing high-quality genome assemblies species pair displaying divergent photosynthetic phenotypes, combining genome-wide investigations synteny, TE dynamics, sequence evolution, gene family temporal differential expression, we were able pinpoint genomic drivers CAM . Several large-scale rearrangements associated with karyotype changes between two genomes highly dynamic landscape shaped However, our analyses show that rewiring metabolism mainly obtained through regulatory rather than coding CAM-related genes are differentially expressed 24-hour cycle species, but no candidates positive selection. Gene orthology reveal manifesting expression underwent accelerated expansion constitutive further supporting view evolution.

Language: Английский

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C4 leaf development and evolution

Current Opinion in Plant Biology, Journal Year: 2023, Volume and Issue: 76, P. 102454 - 102454

Published: Sept. 22, 2023

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