Structural evidence for MADS-box type I family expansion seen in new assemblies ofA. arenosaandA. lyrata DOI Creative Commons
Jonathan Bramsiepe, Anders K. Krabberød, Katrine N. Bjerkan

et al.

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

Published: May 31, 2023

Summary Arabidopsis thaliana diverged from A. arenosa and lyrata at least 6 million years ago are identified by genome-wide polymorphisms or morphological traits. The species to a high degree reproductively isolated, but hybridization barriers incomplete. A special type of barrier is based in the triploid endosperm seed, where embryo lethality caused failure support developing embryo. MADS-box I family transcription factors specifically expressed has been proposed play role endosperm-based barriers. gene well known for evolutionary duplication rate, as being regulated genomic imprinting. Here we address evolution genes context hybridization. Using two de-novo assembled annotated chromosome-level genomes ssp. petraea analyzed predict orthologs, copy number structural variation related loci. Our findings were compared expression profiles sampled before after transition cellularization order investigate involvement loci We observed substantial differences type-I between endosperm, suggesting genetic cause hybrid seeds.

Language: Английский

Cycles of satellite and transposon evolution in Arabidopsis centromeres DOI
Piotr Włodzimierz, Fernando A. Rabanal, Robin Burns

et al.

Nature, Journal Year: 2023, Volume and Issue: 618(7965), P. 557 - 565

Published: May 17, 2023

Language: Английский

Citations

91
Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae DOI Creative Commons
Polina Novikova, Uliana Kolesnikova, Alison Scott

et al.

Plant Reproduction, Journal Year: 2022, Volume and Issue: 36(1), P. 125 - 138

Published: Oct. 25, 2022

Abstract Self-incompatibility systems based on self-recognition evolved in hermaphroditic plants to maintain genetic variation of offspring and mitigate inbreeding depression. Despite these benefits diploid plants, for polyploids who often face a scarcity mating partners, self-incompatibility can thwart reproduction. In contrast, self- compatibility provides an immediate advantage: route reproductive viability. Thus, selfing lineages may facilitate the formation new allopolyploid species. Here, we describe mechanism establishment at least four species Brassicaceae ( Arabidopsis suecica , kamchatica, Capsella bursa-pastoris, Brassica napus ), manner dependent prior loss one ancestors. each case, degraded S -locus from parental lineage was dominant over functional outcrossing lineage. Such loss-of-function mutations promote transition allopolyploids their establishment.

Language: Английский

Citations

20
Breakdown of self-incompatibility due to genetic interaction between a specific S-allele and an unlinked modifier DOI Creative Commons
Yan Li,

Ekaterina Mamonova,

Nadja Köhler

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: June 9, 2023

Breakdown of self-incompatibility has frequently been attributed to loss-of-function mutations alleles at the locus responsible for recognition self-pollen (i.e. S-locus). However, other potential causes have rarely tested. Here, we show that self-compatibility S

Language: Английский

Citations

10
Structural evidence for MADS‐box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata DOI Creative Commons
Jonathan Bramsiepe, Anders K. Krabberød, Katrine N. Bjerkan

et al.

The Plant Journal, Journal Year: 2023, Volume and Issue: 116(3), P. 942 - 961

Published: July 30, 2023

Arabidopsis thaliana diverged from A. arenosa and lyrata at least 6 million years ago. The three species differ by genome-wide polymorphisms morphological traits. are to a high degree reproductively isolated, but hybridization barriers incomplete. A special type of barrier is based on the triploid endosperm seed, where embryo lethality caused failure support developing embryo. MADS-box I family transcription factors specifically expressed in has been proposed play role endosperm-based barriers. gene well known for its evolutionary duplication rate, as being regulated genomic imprinting. Here we address evolution genes context hybridization. Using two de-novo assembled annotated chromosome-level genomes ssp. petraea analyzed predict orthologs, copy number, structural variation related loci. Our findings were compared expression profiles sampled before after transition cellularization order investigate involvement loci We observed substantial differences type-I petraea, suggesting genetic cause between petraea.

Language: Английский

Citations

4
Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids DOI Creative Commons
Tianlin Duan, Zebin Zhang, Mathieu Genête

et al.

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

Published: April 18, 2023

Abstract The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants, and has broad effects on trajectories. In Brassicaceae, ability impede controlled by two genes, SCR SRK, tightly linked within S-locus. A series small non-coding RNAs also encoded S-locus regulates transcriptional activity alleles, resulting a linear dominance hierarchy between them. Brassicaceae allopolyploid species are often self-compatible (SC) even when their parents self-incompatible, but causes loss self-incompatibility (SI) polyploid lineages have generally remained elusive. We used synthetic hybrids obtained self-fertilizing Capsella orientalis C. grandiflora test whether breakdown SI species, such as bursa-pastoris , could be explained interactions S-haplotypes inherited parental lineages. After establishing database reference S-allele sequences, we RNA-sequencing data young inflorescences measure allele-specific expression SRK genes diploid tetraploid hybrids. then compared observed alleles with predicted relationship pollen seed set autonomous Our results formally establish that upon hybridization, immediate effect mating system depends relative S-alleles species. They illustrate detailed understanding genetic architecture control essential predict patterns association changes ploidy. Lay summary Polyploidy inheritable condition carrying more than sets chromosomes. It can result within-species genome duplication (auto-polyploidy), or merging chromosomes different following hybridization (allo-polyploidy). Because sexual reproduction individuals levels ploidy not successful, been considered key component establishment success However, reasons why polyploids may differ remains mysterious. plants family, several arose an most cases self-fertilizing. proposed these allopolyploids relationships functional non-functional Here, tested this prediction characterizing at (RNA-seq) phenotypic (estimation production) found matched well phenotypes. Hence, newly formed allotetraploids parents. Overall, our improve mechanisms which alter over course evolution.

Language: Английский

Citations

3
The self‐compatibility is acquired after polyploidization: a case study of Brassica napus self‐incompatible trilinear hybrid breeding system DOI Open Access

Shengwei Dou,

Tong Zhang, Lulin Wang

et al.

New Phytologist, Journal Year: 2023, Volume and Issue: 241(4), P. 1690 - 1707

Published: Nov. 30, 2023

Summary Self‐incompatibility plays a vital role in angiosperms, by preventing inbreeding depression and maintaining genetic diversity within populations. Following polyploidization, many angiosperm species transition from self‐incompatibility to self‐compatibility. Here, we investigated the S ‐locus Brassicaceae identified distinct origins for sRNA loci, SMI SMI2 ( SCR Methylation Inducer 1 2 ), ‐locus. The loci were found be widespread Cruciferae, whereas exclusive Brassica species. Additionally, discovered four major ‐haplotypes BnS‐1 , BnS‐6 BnS‐7 BnS‐1300 ) rapeseed. Overexpression of BnSMI‐1 self‐incompatible napus (‘S‐70 S1300S6 ’) resulted significant increase DNA methylation promoter regions BnSCR‐6 BnSCR‐1300 leading Conversely, overexpressing point mutation BnSmi‐1 ‘S‐70 ’ line, observed lower levels promoters. Furthermore, overexpression BnSMI2‐1300 ‘SI‐326 S7S6 line inhibited expression BnSCR‐7 through transcriptional repression Smi2 haplotype. Our study demonstrates that self‐compatibility rapeseed is determined sRNA‐mediated silencing after which helps further breed or self‐compatible lines, thereby facilitating utilization heterosis.

Language: Английский

Citations

1
Multiple polyploidizations inArabidopsis lyratastabilized by long-range adaptive introgression across Eurasia DOI Creative Commons
Alison Scott, Uliana Kolesnikova, Anna Glushkevich

et al.

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

Published: Aug. 27, 2024

Abstract Abundance of polyploidy varies across lineages, evolutionary time and geography, suggesting both genetics environment play a role in polyploid persistence. Arabidopsis lyrata appears to be the most polyploidy-rich species-complex genus, with multiple origins autotetraploidy. This is revealed by genomic data from over 400 samples Eurasia. We found 30 previously undescribed autotetraploid populations Siberia minimum two separate origins, independent those reported Central Europe. The establishment Siberian tetraploids mediated meiotic adaptation at same genes as European tetraploid A. arenosa, despite high divergence geographical separation. Haplotype analysis based on synthetic long-read assemblies supports long-range introgression adaptive alleles interspecific pool arenosa . Once evolved, promotes new lineages through inter– intraspecific introgression.

Language: Английский

Citations

0
Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure DOI Creative Commons
Michael R. Winter, Adam Taranto, Henok Zemene Yimer

et al.

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

Published: March 23, 2023

Abstract We present the chromosome-scale genome of allopolyploid root-knot nematode Meloidogyne javanica . show that M. is predominantly allotetraploid, comprising two subgenomes, A and B, most likely originated from hybridisation ancestral parental species. The assembly annotated using full-length non-chimeric transcripts, comparison to reference databases, ab initio prediction techniques, subgenomes are phased k-mer spectral analysis. Subgenome B appears greater fission chromosomal contigs, while there substantial synteny between we also identify regions lacking may have diverged in genomes prior or following hybridisation. Indels common both alleles within a subgenome, suggesting exists dynamic hypo-tetraploidy where copy number can vary along chromosome. This forms significant resource for understanding origins genetics these globally important plant pathogens. Author Summary Root-knot nematodes represent one crop parasites globally. Despite their agricultural importance, only rudimentary genomic resources been published date, leaving gap genetic mechanisms driving evolution virulence. Here, used modern bioinformatic approaches create investigate constitution species reproduces by ameiotic parthenogenesis has an among damaging parasitic with large evolving host range. Utilising long-range DNA sequencing bioinformatics approaches, successfully into its constituent first this agriculturally clade. While find landscape mostly syntenic identified minimal similarity, highlight structural divergence subgenomes. demonstrate was originally tetraploid, but insertions deletions major force generating diversity, resulting hypo-tetraploid local variations ploidy.

Language: Английский

Citations

0
Structural evidence for MADS-box type I family expansion seen in new assemblies ofA. arenosaandA. lyrata DOI Creative Commons
Jonathan Bramsiepe, Anders K. Krabberød, Katrine N. Bjerkan

et al.

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

Published: May 31, 2023

Summary Arabidopsis thaliana diverged from A. arenosa and lyrata at least 6 million years ago are identified by genome-wide polymorphisms or morphological traits. The species to a high degree reproductively isolated, but hybridization barriers incomplete. A special type of barrier is based in the triploid endosperm seed, where embryo lethality caused failure support developing embryo. MADS-box I family transcription factors specifically expressed has been proposed play role endosperm-based barriers. gene well known for evolutionary duplication rate, as being regulated genomic imprinting. Here we address evolution genes context hybridization. Using two de-novo assembled annotated chromosome-level genomes ssp. petraea analyzed predict orthologs, copy number structural variation related loci. Our findings were compared expression profiles sampled before after transition cellularization order investigate involvement loci We observed substantial differences type-I between endosperm, suggesting genetic cause hybrid seeds.

Language: Английский

Citations

0