scholarly journals The Overlooked Hybrid: Geographic Distribution and Niche Differentiation Between Spartina Cytotypes (Poaceae) in Wadden Sea Salt Marshes

2021 ◽  
Author(s):  
Dirk Granse ◽  
Mariana Romeiro Motta ◽  
Sigrid Suchrow ◽  
Klaus von Schwartzenberg ◽  
Arp Schnittger ◽  
...  
Keyword(s):  
Salt Marshes ◽  
Wadden Sea ◽  
Elevational Gradient ◽  
Niche Differentiation ◽  
Ploidy Levels ◽  
Evolutionary Forces ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
High Ploidy ◽  
Sea Area

AbstractWhole genome duplications (WGDs) lead to polyploid specimens and are regarded as major drivers for speciation and diversification in plants. One prevalent problem when studying WGDs is that effects of polyploidization in ancient polyploids cannot be disentangled from the consequences of selective evolutionary forces. Cytotypic differences in distribution, phenotypic appearance and in response to surface elevation (determined by HOF-modeling) were identified in a relatively young taxa-group of a hexaploid F1-hybrid (Spartina× townsendii H. Groves & J. Groves, Poaceae) and its dodecaploid descendent (Spartina anglica C.E. Hubbard, Poaceae) using vegetation assessments (1029 plots; 1 × 1 m2) from the European Wadden Sea mainland salt marshes, including elevational and mean high tidal (MHT) data. While the F1-hybrid was mainly present in the eastern part of the Wadden Sea, its dodecaploid descendent occurred in the entire Wadden Sea area. The Spartina cytotypes differed in phenotypes (median of Spartina cover: hexaploid = 25% vs. dodecaploid = 12%) and in elevational niche-optimum (hexaploid = − 49.5 cm MHT vs. dodecaploid = 8.0 cm MHT). High ploidy levels correlated with establishment success in Spartina along geographic gradients but did not seem to increase the capacity to cope with abiotic severity downwards the elevational gradient in salt marshes.

Cytogenetic diversity in the polyploid complex Linum suffruticosum s.l. (Linaceae)

2020 ◽  
Author(s):  
Ana Afonso ◽  
João Loureiro ◽  
Juan Arroyo ◽  
Erika Olmedo-Vicente ◽  
Sílvia Castro
Keyword(s):  
Morphological Variability ◽  
Distribution Patterns ◽  
Flowering Plants ◽  
Whole Genome ◽  
Polyploid Complex ◽  
Chromosome Counts ◽  
Ploidy Levels ◽  
Whole Genome Duplications ◽  
Multiple Origins ◽  
Genome Duplications

Abstract Polyploidy plays a significant role in the evolution and diversification of flowering plants. In several polyploid complexes, high morphological variability and plasticity coupled with cytogenetic diversity make it difficult to disentangle their evolutionary history. The main goal of this study was to gain insights into the role of whole genome duplications as one of the factors shaping the evolution of flowering plants. Linum suffruticosum s.l. has been described as a polyploid complex, with high morphological variability, but nothing is known about current cytogeographical patterns. We investigated cytotype diversity and distribution patterns in 151 populations covering most of the distribution range, in the Iberian Peninsula, south-eastern France, north-western Italy and Morocco, using flow cytometric analyses complemented with chromosome counts. A high cytogenetic diversity was found with five major cytotypes being detected (diploids, tetraploids, hexaploids, octoploids and decaploids) and with new ploidy levels being reported for the first time. The different ploidies were distributed parapatrically, with geographical structure and several contact zones. Most of the populations comprised one cytotype, but a few mixed-ploidy populations were observed. Our results suggest that whole genome duplications are one of the key mechanisms, alone or together with hybridization, governing the diversification of L. suffruticosum s.l. Genome size and/or chromosome counts might be useful tools for identifying specimens of L. suffruticosum s.l. Also, geographical overlap and high cytogenetic diversity suggest multiple origins of the polyploids. The diversity observed here has been mostly neglected to date and should be accounted when studying the biosystematics of this complex.

scholarly journals High KIFC1 expression is associated with poor prognosis in prostate cancer

2021 ◽  
Vol 38 (5) ◽  
Author(s):  
Laurie G. Kostecka ◽  
Athen Olseen ◽  
KiChang Kang ◽  
Gonzalo Torga ◽  
Kenneth J. Pienta ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Poor Prognosis ◽  
Prognostic Indicator ◽  
Tumor Stage ◽  
Ploidy Levels ◽  
Free Survival ◽  
Metastatic Lesions ◽  
High Tumor Stage ◽  
High Ploidy ◽  
Kinesin Family

AbstractKinesins play important roles in the progression and development of cancer. Kinesin family member C1 (KIFC1), a minus end-directed motor protein, is a novel Kinesin involved in the clustering of excess centrosomes found in cancer cells. Recently KIFC1 has shown to play a role in the progression of many different cancers, however, the involvement of KIFC1 in the progression of prostate cancer (PCa) is still not well understood. This study investigated the expression and clinical significance of KIFC1 in PCa by utilizing multiple publicly available datasets to analyze KIFC1 expression in patient samples. High KIFC1 expression was found to be associated with high Gleason score, high tumor stage, metastatic lesions, high ploidy levels, and lower recurrence-free survival. These results reveal that high KIFC1 levels are associated with a poor prognosis for PCa patients and could act as a prognostic indicator for PCa patients as well.

scholarly journals Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1190
Author(s):  
Yuqi Huang ◽  
Minghao Sun ◽  
Lenan Zhuang ◽  
Jin He
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Functional Characterization ◽  
Vertebrate Evolution ◽  
Molecular Phylogenetic Analysis ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Molecular Phylogenetic ◽  
Duplication Events ◽  
Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

scholarly journals Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hua Sun ◽  
Song Cao ◽  
R. Jay Mashl ◽  
Chia-Kuei Mo ◽  
Simone Zaccaria ◽  
...  
Keyword(s):  
Human Tumors ◽  
Multiple Time ◽  
Cancer Treatments ◽  
Whole Genome Duplications ◽  
Patient Derived Xenograft ◽  
Genome Duplications ◽  
Genomic Characterization ◽  
Cancer Types ◽  
Multiple Time Points ◽  
Pdx Models

AbstractDevelopment of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs’ recapitulation of human tumors.

scholarly journals A Diachronic Triangular Perspective on Landscapes: a Conceptual Tool for Research and Management Applied to Wadden Sea Salt Marshes

2021 ◽  
Author(s):  
Mans Schepers ◽  
Erik W. Meijles ◽  
Jan P. Bakker ◽  
Theo Spek
Keyword(s):  
Cultural History ◽  
Salt Marshes ◽  
Cultural Landscape ◽  
Wadden Sea ◽  
Driving Forces ◽  
Landscape Management ◽  
Analytical Framework ◽  
Physical Geography ◽  
Sea Salt ◽  
Conceptual Tool

AbstractStrong disciplinary academic fragmentation and sectoral division in policies lead to problems regarding the management of landscapes. As a result, there is a focus on the preservation and development of either cultural or natural landscapes. We argue that framing landscapes as “natural” or “cultural” will not help sustainable management. The goal of this paper is to show that even what is referred to as nature, virtually always features an intricate combination of physical geography, biology, and cultural history. It provides an analytical framework that visualizes the three forces at play in physical landscapes. Therefore, we introduce a diachronic triangular approach to study and manage landscapes from a holistic point of view, allowing an exchange of different perspectives. To test this approach, we have applied our model to a diachronic case study on Wadden Sea salt marshes. That area has been influenced by physical-geographical, biological, and cultural landscape forces, which are still visible in the landscape to a large extent. By placing different landscape zones in the triangular concept for different time periods, we can identify and visualize these driving forces through time for this specific landscape. These all play their specific roles in the appearance of the landscape over time in a close mutual interconnection. More importantly, we show that the diverse and complex interplay between these forces makes the current-day landscape what it is. We therefore conclude that the diachronic triangular approach provides a conceptual tool to define and operationalize landscape management in the Wadden Sea area. We welcome similar approaches in other landscapes to assess the usefulness of the diachronic triangular landscape approach.

scholarly journals Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon (Acipenser baerii)

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1375
Author(s):  
Larisa S. Biltueva ◽  
Dmitry Yu. Prokopov ◽  
Svetlana A. Romanenko ◽  
Elena A. Interesova ◽  
Manfred Schartl ◽  
...  
Keyword(s):  
Duplication Event ◽  
Siberian Sturgeon ◽  
Genome Duplication Event ◽  
Acipenser Baerii ◽  
Whole Genome Duplications ◽  
Sturgeon Species ◽  
Genome Duplications ◽  
Size Groups ◽  
Genomic Studies ◽  
Syntenic Regions

Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.

scholarly journals On the Expansion of “Dangerous” Gene Repertoires by Whole-Genome Duplications in Early Vertebrates

Cell Reports ◽  
2012 ◽  
Vol 2 (5) ◽  
pp. 1387-1398 ◽  
Author(s):  
Param Priya Singh ◽  
Séverine Affeldt ◽  
Ilaria Cascone ◽  
Rasim Selimoglu ◽  
Jacques Camonis ◽  
...  
Keyword(s):  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Early Vertebrates

scholarly journals Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 563 ◽  
Author(s):  
Anna Szczepaniak ◽  
Michał Książkiewicz ◽  
Jan Podkowiński ◽  
Katarzyna Czyż ◽  
Marek Figlerowicz ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Coenzyme A ◽  
Phylogenetic Inference ◽  
Whole Genome ◽  
Evolutionary Patterns ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Acetyl Coenzyme A Carboxylase

Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.

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