Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge—A Transcriptomics Perspective DOI Open Access
Gaetano Aufiero, Carmine Fruggiero, Davide D’Angelo

et al.

Genes, Journal Year: 2024, Volume and Issue: 15(8), P. 977 - 977

Published: July 24, 2024

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, significant evolutionary process plant kingdom. Transcriptomic analysis provides invaluable insights allopolyploid by elucidating fate duplicated genes, revealing novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how genes have evolved to acquire new functions regulatory roles. This often leads development novel traits adaptive strategies that leverage thrive diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation genetic complexity underlying allopolyploidy but also underscores importance agriculture ecosystem resilience. However, transcriptome profiling is challenging due genomic redundancy, which further complicated presence multiple chromosomes sets variations among homoeologs allelic genes. Prior analysis, sub-genome phasing homoeology inference are essential for obtaining comprehensive view expression. review aims clarify terminology this field, identify most aspects explain inherent difficulties, suggest reliable analytic strategies. Furthermore, bulk RNA-seq highlighted as primary method studying expression, focusing on critical steps like read mapping normalization differential analysis. approach effectively captures from both genomes, facilitating combined profiles. Its sensitivity detecting low-abundance transcripts allows subtle differences between be identified, crucial understanding dynamics balance allopolyploids.

Language: Английский

Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages DOI Creative Commons
Taikui Zhang, Wei‐Chen Huang, Lin Zhang

et al.

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

Published: April 17, 2024

Abstract Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of rho-derived duplicates among lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses 363 grasses covering all 12 subfamilies report nine previously unknown duplications. Furthermore, duplications from single were mapped to multiple nodes on species phylogeny; was likely by woody bamboos with possible gene flow herbaceous bamboos; recent paralogues tetraploid Oryza are implicated tolerance seawater submergence. Moreover, rho showing differential retention include those functions environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β cold responses (Pooideae), SPIRAL1 rapid cell elongation (Bambusoideae), PAI1 drought/cold (Panicoideae). This study presents profile evidence mechanisms that contribute losses.

Language: Английский

Citations

20
Genome of tetraploid sour cherry (Prunus cerasus L.) ‘Montmorency’ identifies three distinct ancestral Prunus genomes DOI Creative Commons
Charity Z. Goeckeritz,

Kathleen E. Rhoades,

Kevin L. Childs

et al.

Horticulture Research, Journal Year: 2023, Volume and Issue: 10(7)

Published: May 10, 2023

Sour cherry (

Language: Английский

Citations

22
Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry DOI Creative Commons
Chao Fang, Ning Jiang, Scott J. Teresi

et al.

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

Published: March 20, 2024

Abstract Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and more highly expressed than those other subgenome(s). However, the molecular mechanisms responsible for remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) cultivated strawberry (2 n = 8 x 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that dominant A contains a greater number total MHSs MHS per gene submissive B/C/D subgenomes. suffers fewer losses MHS-related DNA sequences fragmentations caused by insertions transposable elements. also related to stress response have A. conclude preservation their cognate ACRs, especially responses, play major role establishment octoploid strawberry.

Language: Английский

Citations

6
Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts DOI Creative Commons
Zheng Zheng, Ziqi Sun,

Feiyan Qi

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(9), P. 1975 - 1984

Published: Aug. 13, 2024

Abstract Cultivated peanut ( Arachis hypogaea L.) is a widely grown oilseed crop worldwide; however, the events leading to its origin and diversification are not fully understood. Here by combining chloroplast whole-genome sequence data from large germplasm collection, we show that two subspecies of A. fastigiata ) likely arose distinct allopolyploidization domestication events. Peanut genetic clusters were then differentiated in relation dissemination routes breeding efforts. A combination linkage mapping genome-wide association studies allowed us characterize genes genomic regions related main morpho-agronomic traits, namely flowering pattern, inner tegument color, growth habit, pod/seed weight oil content. Together, our findings shed light on evolutionary history phenotypic peanuts might be broad interest plant breeders.

Language: Английский

Citations

5
Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions DOI Creative Commons
Yuanyuan Zhang, Zhiquan Yang, Yizhou He

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(11), P. 2538 - 2550

Published: Nov. 1, 2024

Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent scale of SV impact across a species remain unknown. In present study, we constructed reference library 334,461 SVs from genome assemblies 16 representative morphotypes neopolyploid Brassica napus accessions detected 258,865 in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, uncovered 285,976 SV-expression quantitative loci (eQTLs) that associate altered 73,580 genes. We developed pipeline for high-throughput joint analyses SV-genome-wide association studies (SV-GWASs) transcriptome-wide phenomic data, eQTLs eQTL-GWAS colocalization, identified 726 SV-gene expression-trait variation associations, some which were verified by transgenics. The pervasive on how reshapes was demonstrated glucosinolate biosynthesis transport pathway. study highlighting genome-wide species-scale provides powerful methodological strategy valuable resources studying evolution, discovery breeding.

Language: Английский

Citations

5
Homoeologous evolution of the allotetraploid genome of Poa annua L. DOI Creative Commons
Christopher W. Benson,

Matthew R. Sheltra,

Peter J. Maughan

et al.

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: June 26, 2023

Poa annua (annual bluegrass) is an allotetraploid turfgrass, agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report chromosome-scale genome assemblies P. annua's diploid progenitors, infirma supina, use multi-omic analyses spanning all three to better understand evolutionary novelty.We find that diploids diverged from their common ancestor 5.5 - 6.3 million years ago hybridized form ≤ 50,000 ago. The genomes are similar in chromosome structure notably distinguished by divergent histories transposable elements, leading a 1.7 × difference size. In annua, biased movement retrotransposons larger (A) subgenome smaller (B) subgenome. We show B preferentially accumulating genes its more highly expressed. Whole-genome resequencing several additional accessions revealed large-scale chromosomal rearrangements characterized extensive TE-downsizing evidence support Genome Balance Hypothesis.The evolutions progenitors played central role conferring onto remarkable phenotypic plasticity. (guided selection drift) elements (mostly guided host immunity) each respond polyploidy unique ways uses whole-genome duplication purge parasitized heterochromatic sequences. findings genomic resources presented here will enable development homoeolog-specific markers for accelerated weed science turfgrass breeding.

Language: Английский

Citations

11
Formation of Different Polyploids Through Disrupting Meiotic Crossover Frequencies Based on cntd1 Knockout in Zebrafish DOI Creative Commons
Yuan Ou, Huilin Li, Juan Li

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(3)

Published: Feb. 29, 2024

Abstract Polyploidy, a significant catalyst for speciation and evolutionary processes in both plant animal kingdoms, has been recognized long time. However, the exact molecular mechanism that leads to polyploid formation, especially vertebrates, is not fully understood. Our study aimed elucidate this phenomenon using zebrafish model. We successfully achieved an effective knockout of cyclin N-terminal domain containing 1 (cntd1) CRISPR/Cas9 technology. This resulted impaired formation meiotic crossovers, leading cell-cycle arrest during metaphase triggering apoptosis spermatocytes testes. Despite these defects, mutant (cntd1−/−) males were still able produce limited amount sperm with normal ploidy function. Interestingly, females, it was capacity egg production altered. haploid, aneuploid, unreduced gametes. alteration enabled us obtain triploid tetraploid from cntd1−/− cntd1−/−/− respectively. Furthermore, tetraploid-heterozygous produced reduced-diploid gametes yielded all-triploid or all-tetraploid offspring when crossed wild-type (WT) zebrafish, Collectively, our findings provide direct evidence supporting crucial role crossover defects process polyploidization. particularly evident generation eggs fish and, potentially, other vertebrate species.

Language: Английский

Citations

4
Rapid formation of stable autotetraploid rice from genome-doubled F1 hybrids of japonica–indica subspecies DOI Creative Commons
Xu Han,

Jiahao Li,

Li Guo

et al.

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

Published: March 31, 2025

Theory predicts that in the absence of selection, a newly formed segmental allopolyploid will become 'autopolyploidized' if homoeologous exchanges (HEs) occur freely. Moreover, because selection against meiotic abnormalities is expected to be strong initial generations, we anticipate HEs uncommon evolved allopolyploids. Here analysed whole-genome composition 202 phenotypically homogeneous and stable rice tetraploid recombinant inbred lines (TRILs) derived from Oryza sativa subsp. japonica indica hybridization/whole-genome doubling. We measured functional traits related growth, development reproductive fitness, chromosomal behaviour TRILs. uncover factors constrain genomic TRILs, including asymmetric parental contribution exclusive uniparental segment retention. Intriguingly, some TRILs have high fertility abiotic stress resilience co-occur with largely stabilized meiosis. Our findings comprise evidence supporting evolutionary possibility HE-catalysed 'allo-to-auto' polyploidy transitions nature, implications for creating new polyploid crops. This study details process duplicated (homoeologous) chromosome 'scrambling' polyploids, indicating natural 'allo-to-autopolyploid' evolution, crop breeding.

Language: Английский

Citations

0
Production, characterization, and potential utility of a newly synthesized allohexaploid wheat Triticum kiharae DOI Creative Commons
Tariq Aslam,

Tianying Zhang,

Taotao Lian

et al.

The Crop Journal, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids DOI Creative Commons
Justin L. Conover, Corrinne E. Grover, Joel Sharbrough

et al.

American Journal of Botany, Journal Year: 2024, Volume and Issue: 111(8)

Published: Aug. 1, 2024

A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting either crossover (homoeologous exchanges) or non-crossover products gene conversion). Homoeologous conversion was first described cotton by comparing SNP patterns sequences from two diploid progenitors with those subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar as conversion, creating uncertainties about reality inferred events.

Language: Английский

Citations

3