Excessive and asymmetrical removal of heterozygous sites by maxSH biases downstream population genetic inference: Implications for hybridization between two primroses DOI Open Access
Jie Zhang, Francisco Pina‐Martins,

Zu‐Shi Jin

et al.

Journal of Systematics and Evolution, Journal Year: 2022, Volume and Issue: 61(5), P. 906 - 918

Published: Nov. 3, 2022

Abstract Techniques of reduced‐representation sequencing (RRS) have revolutionized ecological and evolutionary genomics studies. Precise establishment orthologs is a critical challenge for RRS, especially when reference genome absent. The proportion shared heterozygous sites across samples an alternative criterion filtering paralogs. In the prevailing pipeline variant calling RRS data – PYRAD/IPYRAD, maxSH often overlooked parameter with implications to detecting paralogs according heterozygosity. Using empirical genotyping by two primroses ( Primula alpicola Stapf florindae Ward) their putative hybrids, extra sets Californian golden cup oaks, we explore impact on further downstream analyses. Our study sheds light simultaneous validity risk using , its significant effects analyses outlier detection, population assignment, demographic modeling, emphasizing importance attention detail during bioinformatic processes. mutual confirmation between results assignment modeling in this suggested = 0.10 has potentially excessive asymmetrical effect removal truly as These indicate that hybridization origin hypotheses hybrids represented 0.25 0.50 are more credible. conclusion, revealed hazard filtration sharing heterozygosity at first, so propose use specific protocols, rather than filter potential closely related lineages.

Language: Английский

Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat DOI
Jeffrey A. Fawcett, Ryoma Takeshima, Shinji Kikuchi

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(8), P. 1236 - 1251

Published: Aug. 10, 2023

Language: Английский

Citations

23
Convergent evolutionary patterns of heterostyly across angiosperms support the pollination-precision hypothesis DOI Creative Commons
Violeta I. Simón‐Porcar, Marcial Escudero, Rocío Santos‐Gally

et al.

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

Published: Feb. 9, 2024

Since the insights by Charles Darwin, heterostyly, a floral polymorphism with morphs bearing stigmas and anthers at reciprocal heights, has become model system for study of natural selection. Based on his archetypal heterostylous flower, including regular symmetry, few stamens tube, Darwin hypothesised that heterostyly evolved to promote outcrossing through efficient pollen transfer between involving different areas pollinator's body, thus proposing seminal pollination-precision hypothesis. Here we update number other style-length polymorphic taxa 247 genera belonging 34 families, notably expanding known cases 20%. Using phylogenetic comparative analyses across angiosperms, show numerous independent origins associated actinomorphic, tubular flowers low sex organs, fused corolla, pollination long-tongued insects. These associations provide support Darwinian hypothesis as basis convergent evolution angiosperms.

Language: Английский

Citations

12
Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level DOI Creative Commons
Juanita Gutiérrez‐Valencia, Marco Fracassetti, Emma L. Berdan

et al.

Current Biology, Journal Year: 2022, Volume and Issue: 32(20), P. 4360 - 4371.e6

Published: Sept. 9, 2022

Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding their origins and evolution remains incomplete. The reciprocal placement stigmas anthers pin thrum floral morphs distylous species constitutes an iconic example balanced polymorphism governed by supergene, the distyly S-locus. Recent studies have shown that Primula Turnera supergenes are both hemizygous thrums, but it unknown whether hemizygosity is pervasive among S-loci. As has major consequences for supergene loss, clarifying this genetic architecture shared critical. Here, we characterized Linum generating chromosome-level genome assembly tenue, followed identification S-locus using population genomic data. We show thrum-specific expression S-linked genes, including pistil-expressed candidate gene style length, features Structural variation likely instrumental recombination suppression, although non-recombining dominant haplotype accumulated transposable elements, genes not under relaxed purifying selection. Our findings reveal remarkable convergence independently derived supergenes, provide counterexample to classic inversion-based shed new light on origin maintenance polymorphism.

Language: Английский

Citations

38
Genomic analyses elucidate S‐locus evolution in response to intra‐specific losses of distyly in Primula vulgaris DOI Creative Commons
Emiliano Mora‐Carrera, Rebecca L. Stubbs, Giacomo Potente

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(3)

Published: March 1, 2024

Distyly, a floral dimorphism that promotes outcrossing, is controlled by hemizygous genomic region known as the

Language: Английский

Citations

6
Genomic evidence supports the genetic convergence of a supergene controlling the distylous floral syndrome DOI
Zhongtao Zhao, Yu Zhang, Miaomiao Shi

et al.

New Phytologist, Journal Year: 2022, Volume and Issue: 237(2), P. 601 - 614

Published: Oct. 14, 2022

Heterostyly, a plant sexual polymorphism controlled by the S-locus supergene, has evolved numerous times among angiosperm lineages and represents classic example of convergent evolution in form function. Determining whether underlying molecular convergence occurs could provide insights on constraints to floral evolution. Here, we investigated genes distylous Gelsemium (Gelsemiaceae) determine there is evidence with unrelated species. We used several approaches, including anatomical measurements sex-organ development transcriptome whole-genome sequencing, identify components supergene. also performed evolutionary analysis candidate compared them those reported Primula Turnera. The supergene contained four genes, which three appear have originated from gene duplication events within Gelsemiaceae. style-length GeCYP CYP734A50 likely arose same gene, CYP734A1. Three out elegans were hemizygous, as previously genomic genetic distyly distantly related help illuminate architecture involved heterostyly.

Language: Английский

Citations

25
Haplotype‐resolved genome assembly provides insights into the evolution of S‐locus supergene in distylous Nymphoides indica DOI Open Access
Jingshan Yang, Haoran Xue, Zhizhong Li

et al.

New Phytologist, Journal Year: 2023, Volume and Issue: 240(5), P. 2058 - 2071

Published: Sept. 17, 2023

Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture single diallelic locus (S-locus) supergene, linkage group functionally associated genes, and explore how it may have distylous Nymphoides indica, lineage flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) locate S-locus co-expression network analysis gene networks underpinning development distyly, comparative genomic analyses origins supergene. identified three linked candidate genes - NinBAS1, NinKHZ2, NinS1 that were only evident short-styled morph hemizygous. Co-expression suggested brassinosteroids contribute dimorphic sex organs morph. Comparative indicated supergene likely via stepwise duplications affected by transposable element activities. Our provides novel insight into structure, regulation, evolution governing distyly N. indica. It also high-quality resources for future research on mechanisms underlying striking evolutionary convergence form function across heterostylous taxa.

Language: Английский

Citations

14
Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis DOI
Franziska Saul, Mathias Scharmann, Takanori Wakatake

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(12), P. 2000 - 2015

Published: Nov. 23, 2023

Language: Английский

Citations

11
PfPIN5 promotes style elongation by regulating cell length in Primula forbesii Franch DOI Open Access
Ying Liu,

Weijia Si,

Sitong Fu

et al.

Annals of Botany, Journal Year: 2024, Volume and Issue: 133(3), P. 473 - 482

Published: Jan. 8, 2024

Abstract Background and Aims Style dimorphism is one of the polymorphic characteristics flowers in heterostylous plants, which have two types flowers: pin morph, with long styles shorter anthers, thrum short longer anthers. The formation dimorphic has received attention plant world. Previous studies showed that CYP734A50 Primula determined style length limited elongation brassinosteroid metabolic pathway was involved regulation length. However, it unknown whether there are other factors affecting Primula. Methods Differentially expressed genes highly morph were screened based on forbesii transcriptome data. Virus-induced gene silencing used to silence these genes, anatomical changes observed 20 days after injection. Key Results PfPIN5 styles. When silenced, shortened long-homostyle plants by shortening cells. Moreover, increased expression level significantly, increased. results indicated PfPIN5, an auxin efflux transporter gene, contributed P. forbesii. Conclusions implied might also be forbesii, providing a new for elucidating molecular mechanism

Language: Английский

Citations

4
A hemizygous supergene controls homomorphic and heteromorphic self-incompatibility systems in Oleaceae DOI
Pauline Raimondeau,

Sayam Ksouda,

William Marande

et al.

Current Biology, Journal Year: 2024, Volume and Issue: 34(9), P. 1977 - 1986.e8

Published: April 15, 2024

Language: Английский

Citations

4
Rapid detection of RNase‐based self‐incompatibility in Lysimachia monelli (Primulaceae) DOI Creative Commons
Karolis Ramanauskas, Francisco Javier Jiménez‐López, Mercedes Sánchez‐Cabrera

et al.

American Journal of Botany, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 13, 2025

Abstract Premise Primroses famously employ a system that simultaneously expresses distyly and filters out self‐pollen. Other species in the Primulaceae family, including Lysimachia monelli (blue pimpernel), also express self‐incompatibility (SI), but involving with distinct features an unknown molecular genetic basis. Methods We utilize candidate‐based transcriptome sequencing (RNA‐seq) approach, relying on candidate T2/S‐RNase Class III S‐linked F‐box‐motif‐containing genes harnessing unusual evolutionary of SI, to examine whether RNase‐based mechanism underlies SI L. . term this approach "SI detection RNA‐seq" (SIDR). Results The results sequencing, crossing, population genetics, each support causal association linking recovered genotypes phenotypes. finding (Ericales) all cements long‐held view was present ancestral pentapetal eudicot, whose descendants now comprise two‐thirds angiosperms. It significantly narrows plausible maximum age for heterostyly evolution within family. Conclusions SIDR is powerful, flexible, inexpensive, most critically enables work often‐neglected species. may be used or without close enormous gaps understanding basis history breeding evolution.

Language: Английский

Citations

0