CAM evolution is associated with gene family expansion in an explosive bromeliad radiation DOI Creative Commons
Clara Groot Crego, Jaqueline Hess, Gil Yardeni

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(10), P. 4109 - 4131

Published: April 30, 2024

The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in plant kingdom and is characterized 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, transposable element (TE) dynamics, sequence evolution, gene family temporal differential expression, we were able pinpoint genomic drivers CAM Tillandsia. Several large-scale rearrangements associated with karyotype changes between 2 genomes highly dynamic TE landscape shaped However, our analyses show that rewiring mainly obtained through regulatory rather than coding CAM-related genes are differentially expressed 24-h cycle but not candidates positive selection. Gene orthology reveal manifesting expression underwent accelerated expansion constitutive species, further supporting view evolution.

Language: Английский

Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome DOI Creative Commons
Ryan C. Lynch, Lillian K. Padgitt‐Cobb, Andrea R. Garfinkel

et al.

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

Published: May 24, 2024

Cannabis sativa is a globally significant seed-oil, fiber, and drug-producing plant species. However, century of prohibition has severely restricted legal breeding germplasm resource development, leaving potential hemp-based nutritional fiber applications unrealized. Existing cultivars are highly heterozygous lack competitiveness in the overall grain markets, relegating hemp to less than 200,000 hectares globally1. The relaxation drug laws recent decades generated widespread interest expanding reincorporating cannabis into agricultural systems, but progress been impeded by limited understanding genomics potential. No studies date have examined genomic diversity evolution populations using haplotype-resolved, chromosome-scale assemblies from publicly available germplasm. Here we present pangenome, constructed with 181 new 12 previously released genomes total 156 biological samples both male (XY) female (XX) plants, including 42 trio phased 36 assemblies. We discovered regions pangenome that surprisingly diverse for single species, high levels genetic structural variation, propose novel population structure hybridization history. Conversely, cannabinoid synthase genes contain very low diversity, despite being embedded within variable region containing multiple pseudogenized paralogs distinct transposable element arrangements. Additionally, identified variants acyl-lipid thioesterase (ALT) associated fatty acid chain length variation production rare cannabinoids, tetrahydrocannabinol varin (THCV) cannabidiol (CBDV). conclude gene pool only partially characterized, existence wild relatives Asia remains likely, while its as crop species largely

Language: Английский

Citations

13
A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence DOI Creative Commons
Mario Ivanković, Jeremias N. Brand, Luca Pandolfini

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 18, 2024

Language: Английский

Citations

12
Unlocking saponin biosynthesis in soapwort DOI Creative Commons
Seohyun Jo, Amr El‐Demerdash, Charlotte Owen

et al.

Nature Chemical Biology, Journal Year: 2024, Volume and Issue: unknown

Published: July 23, 2024

Abstract Soapwort ( Saponaria officinalis ) is a flowering plant from the Caryophyllaceae family with long history of human use as traditional source soap. Its detergent properties are because production polar compounds (saponins), which oleanane-based triterpenoid saponins, saponariosides A and B, major components. saponins have anticancer also interest endosomal escape enhancers for targeted tumor therapies. Intriguingly, these share common structural features vaccine adjuvant QS-21 and, thus, represent potential alternative supply saponin precursors. Here, we sequence S . genome through mining combinatorial expression, identify 14 enzymes that complete biosynthetic pathway to saponarioside B. These include noncanonical cytosolic GH1 (glycoside hydrolase 1) transglycosidase required addition d- quinovose. Our results open avenues accessing engineering natural new-to-nature pharmaceuticals, drug delivery agents immunostimulants.

Language: Английский

Citations

11
Structural variation in the pangenome of wild and domesticated barley DOI Creative Commons
Murukarthick Jayakodi, Qiongxian Lu, Hélène Pidon

et al.

Nature, Journal Year: 2024, Volume and Issue: 636(8043), P. 654 - 662

Published: Nov. 13, 2024

Pangenomes are collections of annotated genome sequences multiple individuals a species

Language: Английский

Citations

10
The Silene latifolia genome and its giant Y chromosome DOI
Carol Moraga, Catarina Branco, Quentin Rougemont

et al.

Science, Journal Year: 2025, Volume and Issue: 387(6734), P. 630 - 636

Published: Feb. 6, 2025

In many species with sex chromosomes, the Y is a tiny chromosome. However, dioecious plant Silene latifolia has giant ~550-megabase chromosome, which remained unsequenced so far. We used long- and short-read hybrid approach to obtain high-quality male genome. Comparative analysis of chromosomes their homologs in outgroups showed that highly rearranged degenerated. Recombination suppression between X extended several steps triggered massive accumulation repeats on as well nonrecombining pericentromeric region X, leading chromosomes. Using phenotype mutants, we identified candidate sex-determining genes locations consistent favoring recombination events 11 5 million years ago.

Language: Английский

Citations

2
A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium DOI Creative Commons

Kate E. Jaggi,

Karol Krak, Helena Štorchová

et al.

The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)

Published: Feb. 28, 2025

Abstract The genus Chenopodium L. is characterized by its wide geographic distribution and ecological adaptability. Species such as quinoa ( Willd.) have served domesticated staple crops for centuries. Wild species exhibit diverse niche adaptations are important genetic reservoirs beneficial agronomic traits, including disease resistance climate hardiness. To harness the potential of wild taxa crop improvement, we developed a pangenome through assembly comparative analyses 12 that encompass eight known genome types (A–H). Six new chromosome‐scale assemblies, many polyploids; thus, total 20 genomes were included in analyses. We show vary dramatically size with D being smallest (∼370 Mb) B largest (∼700 was correlated independent expansions Copia Gypsy LTR retrotransposon families, suggesting transposable elements played critical role evolution genomes. annotated 33,457 pan‐ gene which ∼65% classified shell (2% private). Phylogenetic analysis clarified evolutionary relationships among lineages, notably resolving taxonomic placement F while highlighting uniqueness A Western Hemisphere. These genomic resources particularly understanding secondary tertiary pools available improvement chenopods furthering our complexity within genus.

Language: Английский

Citations

2
Solanum pan-genetics reveals paralogues as contingencies in crop engineering DOI Creative Commons
Matthias Benoit, Katharine M. Jenike, James W. Satterlee

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

Language: Английский

Citations

2
Analysis of 30 chromosome-level Drosophila genome assemblies reveals dynamic evolution of centromeric satellite repeats DOI Creative Commons
Daniel Gebert, Amir D. Hay,

Jennifer P. Hoang

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 18, 2025

Abstract Background The Drosophila genus is ideal for studying genome evolution due to its relatively simple chromosome structure and small size, with rearrangements mainly restricted within arms, such as Muller elements. However, work on the rapidly evolving repetitive genomic regions, composed of transposons tandem repeats, have been hampered by lack genus-wide chromosome-level assemblies. Results Integrating long-read sequencing capture technology, here we produce annotate 30 assemblies genus. Based this dataset, reveal evolutionary dynamics across phylogeny, including identification regions that show comparatively high structural stability throughout evolution. Moreover, ananassae subgroup, uncover emergence new conformations rapid expansion novel satellite DNA sequence families, which form large continuous pericentromeric domains higher-order repeat structures are reminiscent those observed in human Arabidopsis genomes. Conclusions These present a valuable resource future research, power demonstrated our analysis In addition, based findings, propose subgroup an model system centromere structure.

Language: Английский

Citations

1
Adaptation repeatedly uses complex structural genomic variation DOI
Zachariah Gompert, Jeffrey L. Feder, Thomas L. Parchman

et al.

Science, Journal Year: 2025, Volume and Issue: 388(6744)

Published: April 17, 2025

Structural elements are widespread across genomes, but their complexity and role in repeatedly driving local adaptation remain unclear. In this work, we use phased genome assemblies to show that adaptive divergence cryptic color pattern a stick insect is underlain by structural variation, not simple chromosomal inversion. We found populations of insects on two mountains associated with translocations have also been inverted. These differ size origin each mountain, they overlap partially involve some the same gene regions. Moreover, variation subject divergent selection arose without introgression between species. Our results how provides mechanism for repeated bouts adaptation.

Language: Английский

Citations

1
New whole-genome alignment tools are needed for tapping into plant diversity DOI Creative Commons
Baoxing Song, Edward S. Buckler, Michelle C. Stitzer

et al.

Trends in Plant Science, Journal Year: 2023, Volume and Issue: 29(3), P. 355 - 369

Published: Sept. 23, 2023

Genome alignment is one of the most foundational methods for genome sequence studies. With rapid advances in sequencing and assembly technologies, these newly assembled genomes present challenges tools to meet increased complexity scale. Plant technologically challenging because frequent whole-genome duplications (WGDs) as well chromosome rearrangements fractionation, high nucleotide diversity, widespread structural variation, transposable element (TE) activity causing large proportions repeat elements. We summarize classical pairwise multiple (MGA) methods, highlight techniques that are widely used or being developed by plant research community. also outline remaining precise interpretation results plants.

Language: Английский

Citations

19