Chromosome counts in the genusAlchemilla (Rosaceae) from SW Europe

Hayirhoglu-Ayaz, Sema; İnceer, Hüseyin; Frost‐Olsen, Peter

doi:10.1007/bf02904946

Cited by 6 publications

(5 citation statements)

References 5 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similar patterns, often attributed to hybridization and allopolyploidy, have been detected in other genera of Fragariinae (Lundberg 2009;Eriksson et al 2015;Gehrke et al 2016 Dickinson et al 2007;Lundberg et al, 2009). Ploidy levels have been well documented in Eualchemilla that shows only polyploid species (2n = 64 to 220-224; octoploid to 28-ploid; e.g., Turesson 1943;Izmailow 1981;Walters and Bozman, 1967;Hayirhoǧlu-Ayaz et al 2006). Aphanes has mainly diploid species (2n = 16), with the exception of Aphanes arvensis that is an hexaploid (2n = 48;Montgomery et al 1997).…”

supporting

confidence: 56%

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events inAlchemillas.l. (Rosaceae)

Morales‐Briones

Gehrke

Huang

et al. 2020

Preprint

View full text Add to dashboard Cite

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci. Common approaches for processing paralogs in target enrichment datasets include removal, random selection, and manual pruning of loci that show evidence of paralogy. These approaches can introduce errors in orthology inference, and sometimes significantly reduce the number of loci, especially in groups experiencing whole-genome duplication (WGD) events. Here we used an automated approach for paralog processing in a target enrichment dataset of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested the polyploid origin of the group. However, putative parental lineages remain unknown. By taking paralogs into consideration, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach we established the autopolyploidy origin of the entire Alchemilla s.l. and the nested allopolyploidy origin of four clades within the group. Here we showed the utility of automated orthology methods, commonly used in genomic or transcriptomic datasets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment datasets.

show abstract

supporting

confidence: 56%

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events inAlchemillas.l. (Rosaceae)

Morales‐Briones

Gehrke

Huang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Notwithstanding, circumscription within the genus remain poorly understood due to hybridization, autonomous apomixes, and polyploidization dominant in Alchemilla species ( Izmailow, 1982 ; Czapik, 1996 ; Gehrke et al, 2008 ). The genus Alchemilla is commonly used as perfect example of apomictic traits combined with morphological polymorphism in Rosaceae ( Czapik, 1996 ; Bicknell and Koltunow, 2004 ; Hayirhoglu-Ayaz et al, 2006 ; Salamone et al, 2013 ). This has resulted in the existence of diverse micro-species and species complexes with variable indumentum, unstable flower characteristic structure, and heteroblastic plasticity, making Alchemilla a taxonomically difficult group ( Hörandl, 2004 ; Hayirhoglu-Ayaz et al, 2006 ; Lundberg et al, 2009 ).…”

Section: Introductionmentioning

confidence: 99%

“…The genus Alchemilla is commonly used as perfect example of apomictic traits combined with morphological polymorphism in Rosaceae ( Czapik, 1996 ; Bicknell and Koltunow, 2004 ; Hayirhoglu-Ayaz et al, 2006 ; Salamone et al, 2013 ). This has resulted in the existence of diverse micro-species and species complexes with variable indumentum, unstable flower characteristic structure, and heteroblastic plasticity, making Alchemilla a taxonomically difficult group ( Hörandl, 2004 ; Hayirhoglu-Ayaz et al, 2006 ; Lundberg et al, 2009 ). This necessitated the need for complete cp genome in the genus Alchemilla to help resolve the taxonomic and phylogenetic uncertainties between its species.…”

Section: Introductionmentioning

confidence: 99%

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

et al. 2020

View full text Add to dashboard Cite

The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.

show abstract

“…High intraspecific variability of morphological characters and the indistinctness of microspecies was also described by Sepp andPaal (1998, 2001). The latest studies concerning Alchemilla have mainly been cytotaxonomic and floristic (e.g., Thiel 2004;Hayirlioğlu-Ayaz et al 2006) or pharmacological (e.g., Shivastava et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Environmentally Dependent Morphological Variability in Seven Apomictic Microspecies from Alchemilla L. (Rosaceae)

et al. 2009

View full text Add to dashboard Cite

Apomictic microspecies, for example those of the genus Alchemilla, are often difficult to distinguish. Still, their differences are thought to be persistent due to apomixis. Apomicts are argued to have general-purpose genotypes. The present study aims to assess the variation of morphological characters of Alchemilla depending on environmental conditions both in nature and experimentally; to evaluate the efficacy of characters for identifying the different microspecies; to assess the similarity of different microspecies; and to determine if Alchemilla microspecies have general-purpose genotypes that are not dependent on environmental conditions. The variability of selected characters in seven microspecies of Alchemilla was studied in nature and five microspecies were grown in a common garden experiment. The growing conditions of the latter were subjected to various manipulations (fertilization, shading and irrigation). Typical natural habitats of Alchemilla exhibited only small differences. Environmental conditions therefore had little effect on morphological characters. Neither cultivation in the common garden nor manipulation of conditions therein had a significant impact on the discrimination of microspecies. However, the metric characters were larger in the garden relative to those observed in nature, particularly under fertilization. Fertilization affected most characters, whereas shading and irrigation did not. The most effective characters for discriminating between microspecies were the ratios of the metric characters. Two species pairs: A. vulgaris and A. micans, as well as A. glaucescens and A. hirsuticaulis were morphologically close; however, the species within these pairs could still be distinguished. The morphological characters of Alchemilla microspecies were only slightly dependent on the environmental conditions.

show abstract

Chromosome counts in the genusAlchemilla (Rosaceae) from SW Europe

Cited by 6 publications

References 5 publications

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events inAlchemillas.l. (Rosaceae)

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events inAlchemillas.l. (Rosaceae)

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

Environmentally Dependent Morphological Variability in Seven Apomictic Microspecies from Alchemilla L. (Rosaceae)

Contact Info

Product

Resources

About