scholarly journals Tracing the Diploid Ancestry of the Cultivated Octoploid Strawberry

2020 ◽  
Author(s):  
Chao Feng ◽  
Jing Wang ◽  
A J Harris ◽  
Kevin M Folta ◽  
Mizhen Zhao ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Gene Order ◽  
Molecular Breeding ◽  
Parental Species ◽  
The Other ◽  
Gene Content ◽  
Fragaria Vesca ◽  
Fragaria Ananassa ◽  
Dated Phylogeny ◽  
Conserved Gene

Abstract The commercial strawberry, Fragaria × ananassa, is a recent allo-octoploid that is cultivated worldwide. However, other than Fragaria vesca, which is universally accepted one of its diploid ancestors, its other early diploid progenitors remain unclear. Here, we performed comparative analyses of the genomes of five diploid strawberries, F. iinumae, F. vesca, F. nilgerrensis, F. nubicola, and F. viridis, of which the latter three are newly sequenced. We found that the genomes of these species share highly conserved gene content and gene order. Using an alignment-based approach, we show that F. iinumae and F. vesca are the diploid progenitors to the octoploid F. × ananassa, whereas the other three diploids that we analyzed in this study are not parental species. We generated a fully resolved, dated phylogeny of Fragaria, and determined that the genus arose ∼6.37 Ma. Our results effectively resolve conflicting hypotheses regarding the putative diploid progenitors of the cultivated strawberry, establish a reliable backbone phylogeny for the genus, and provide genetic resources for molecular breeding.

Actualisation du catalogue des pteridophytes du Nord Ouest Algerien (region de Tlemcen). An update of the cheklist of pteridophytes from Nordwest Algeria (Tlemcen region)

2013 ◽  
Vol 38 ◽  
pp. 33-39 ◽  
Author(s):  
Boumediene Medjahdi ◽  
Assia Ltreuch-Belarouci ◽  
Rémy Prelli
Keyword(s):  
Nous Avons ◽  
Genetic Resources ◽  
Threatened Species ◽  
The Other ◽  
Natural Distribution ◽  
Ecological Characteristics ◽  
Statutory Protection ◽  
Ouest Algérien ◽  
A Site ◽  
Ressources Génétiques

Français. Un inventaire des ptéridophytes a été entrepris dans les forêts de la région de Tlemcen. L’inventaire de ces populations constitue une étape importante pour le développement des stratégies de conservation des ressources génétiques et de la diversité de ces populations sur l’ensemble de leur aire de distribution naturelle. Nous avons ainsi effectué le recensement et l’identification des fougères existantes dans la région de Tlemcen. Au total, plusieurs stations dont les caractéristiques écologiques diffèrent d’un site à un autre ont été prospectées, cela a permis l’identification de 26 taxons (dont 5 exceptionnellement rare). La création de réserves naturelles forestières renforcée par une protection réglementaire des espèces les plus menacées est nécessaire pour le maintien de ces communautés si particulières. English. An inventory of Pteridophyta was begun in the forests of the Tlemcen region. The inventory of these populations constitutes an important stage for the developement of the strategies of preservation of the genetic resources and the diversity of these populations on their whole area of natural distribution. We so made the inventory and the identification of the existing ferns in the region of Tlemcen. On the whole, several stations the ecological characteristics differ from a site in the other one were canvassed; they allowed the identification of 26 taxes (among which 5 exceptionally rare). The creation of forest nature reserves strengthened by a statutory protection of the most threatened species is necessary for the preservation of these particular communities.

scholarly journals Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order

Algorithms ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 160
Author(s):  
Qiaoji Xu ◽  
Lingling Jin ◽  
James H. Leebens-Mack ◽  
David Sankoff
Keyword(s):  
Phylogenetic Tree ◽  
Gene Order ◽  
Evolutionary Process ◽  
Gene Content ◽  
Ancestral Genome ◽  
Maximum Weight ◽  
Ancestral Gene ◽  
Maximum Weight Matching

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

scholarly journals The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yan-Yan Guo ◽  
Jia-Xing Yang ◽  
Ming-Zhu Bai ◽  
Guo-Qiang Zhang ◽  
Zhong-Jian Liu
Keyword(s):  
Gene Order ◽  
Inverted Repeat ◽  
Single Copy ◽  
Gene Content ◽  
Comparative Genomic ◽  
Substitution Rates ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Ideal System ◽  
Small Single Copy

Abstract Background Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Results Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. Conclusions We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

Sexual composition of populations of Fragaria virginiana (Rosaceae) collected from Minnesota and western Wisconsin

1995 ◽  
Vol 73 (9) ◽  
pp. 1457-1463 ◽  
Author(s):  
Margaret M. Stahler ◽  
Peter D. Ascher ◽  
James J. Luby ◽  
Alan P. Roelfs
Keyword(s):  
Plant Communities ◽  
Gender Composition ◽  
Fragaria Vesca ◽  
Fragaria Ananassa ◽  
Northern Forest ◽  
Gender Expression ◽  
Sexual Composition ◽  
Consistent Manner ◽  
Fragaria Virginiana ◽  
Collection Sites

Populations of Fragaria virginiana Miller collected from 39 sites in Minnesota and western Wisconsin were gynodioecious, in that 35% of the plants were pistillate, 65% were hermaphroditic with perfect flowers, and none were staminate, when scored for gender expression in greenhouse or field plantings. Instability of gender expression across environments was apparent in 15% of the collections and these genotypes that appeared to change gender were termed weak hermaphrodites. Variation in gender composition of collections was not related in any consistent manner with the plant communities characterizing the collection sites. The proportions of pistillate plants, total hermaphrodites, strong hermaphrodites, and weak hermaphrodites in collections from the northern forest floristic province in the northeastern part of the region were not significantly different from those of collections from the southwestern prairie-forest floristic region, although collections from the prairie-forest province were more variable for gender composition than populations from the northern forest province. Lack of staminate plants and increased percentages of hermaphrodite plants, relative to reports in the literature, suggest that the gender composition of F. virginiana populations in Minnesota has changed, perhaps as a result of introgression from hermaphroditic Fragaria ×ananassa or Fragaria vesca. Key words: Fragaria chiloensis, Fragaria vesca, Fragaria ×ananassa, dioecy, introgression, evolution.

Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology

2021 ◽  
Author(s):  
Ksenia Juravel ◽  
Luis Porras ◽  
Sebastian Hoehna ◽  
Davide Pisani ◽  
Gert Wörheide
Keyword(s):  
Common Ancestor ◽  
Sister Group ◽  
The Other ◽  
Gene Content ◽  
Statistical Hypothesis ◽  
Phylogenetic Position ◽  
Last Common Ancestor ◽  
Statistical Hypothesis Testing ◽  
Animal Phylogeny ◽  
Phylogenetic Hypotheses

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

scholarly journals Gene Content and Distribution in the Nuclear Genome of Fragaria vesca

2009 ◽  
Vol 2 (1) ◽  
Author(s):  
Ana Clara Pontaroli ◽  
Rebekah L. Rogers ◽  
Qian Zhang ◽  
Melanie E. Shields ◽  
Thomas M. Davis ◽  
...  
Keyword(s):  
Nuclear Genome ◽  
Gene Content ◽  
Fragaria Vesca

scholarly journals Influence of Origin of Laying Hens on the Quality of Their Carcasses and Meat After the First Laying Period

2014 ◽  
Vol 14 (3) ◽  
pp. 685-696 ◽  
Author(s):  
Michał Puchała ◽  
Józefa Krawczyk ◽  
Jolanta Calik
Keyword(s):  
Genetic Resources ◽  
Rhode Island ◽  
New Hampshire ◽  
Broiler Chickens ◽  
Laying Hens ◽  
The Other ◽  
Raw Material ◽  
Breeding Lines ◽  
Dressing Percentage

AbstractThe aim of the study was to assess the quality of carcasses and meat from selected native breeds and breeding lines of hens after using them for laying eggs in terms of their usefulness as raw material in traditional old polish cuisine. hens included in the programme for the protection of genetic resources were the object of this study. they belonged to the following breeds/breeding lines: greenleg partridge (Z-11), rhode Island red (r-11), new hampshire (n-11) and Barred rock (WJ-44) – 30 hens from each line. the hens were kept in a closed hen house under standard raising conditions. eight hens were selected from 56-week-old hens of each line which were subjected to analysis after being slaughtered. as a result of the research conducted, it was found that:– Among the hens under study, heavier layers, i.e. Barred rock (WJ-44), new hampshire (n-11) and rhode Island red (r-11), which are characterized by good muscling and dressing percentage similar to that of broiler chickens, proved to be most suitable for use as meat.– The meat from WJ-44 hens contained most cholesterol and least protein, and the meat from Z-11 birds had the least fat compared to the other lines.– At the end of the laying period, meat and broth from WJ-44, n-11 and r-11 hens obtained better sensory scores than those from the carcasses of Z-11 hens, which makes them an attractive raw material for traditional polish cuisine.

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