scholarly journals Ancient gene duplications, rather than polyploidization, facilitate diversification of petal pigmentation patterns in Clarkia gracilis (Onagraceae)

2021 ◽  
Author(s):  
Rong-Chien Lin ◽  
Mark D. Rausher
Keyword(s):  
Gene Tree ◽  
Diploid Species ◽  
Gene Duplications ◽  
Loss Of Function ◽  
Expression Domain ◽  
Evolutionary Changes ◽  
The Common ◽  
Morphological Novelties ◽  
Polyploidization Event ◽  
Ancient Gene

AbstractIt has been suggested that gene duplication and polyploidization create opportunities for the evolution of novel characters. However, the connections between the effects of polyploidization and morphological novelties have rarely been examined. In this study, we investigated whether petal pigmentation patterning in an allotetraploid Clarkia gracilis has evolved as a result of polyploidization. C. gracilis is thought to be derived through a recent polyploidization event with two diploid species, C. amoena huntiana and an extinct species that is closely related to C. lassenensis. We reconstructed phylogenetic relationships of the R2R3-MYBs (the regulators of petal pigmentation) from two subspecies of C. gracilis and the two purported progenitors, C. a. huntiana and C. lassenensis. The gene tree reveals that these R2R3-MYB genes have arisen through duplications that occurred before the divergence of the two progenitor species, i.e., before polyploidization. After polyploidization and subsequent gene loss, only one of the two orthologous copies inherited from the progenitors was retained in the polyploid, turning it to diploid inheritance. We examined evolutionary changes in these R2R3-MYBs and in their expression, which reveals that the changes affecting patterning (including expression domain contraction, loss-of-function mutation, cis-regulatory mutation) occurred after polyploidization within the C. gracilis lineages. Our results thus suggest that polyploidization itself is not necessary in producing novel petal color patterns. By contrast, duplications of R2R3-MYB genes in the common ancestor of the two progenitors have apparently facilitated diversification of petal pigmentation patterns.

The domino gene of Drosophila encodes novel members of the SWI2/SNF2 family of DNA-dependent ATPases, which contribute to the silencing of homeotic genes

Development ◽  
2001 ◽  
Vol 128 (8) ◽  
pp. 1429-1441 ◽  
Author(s):  
M.L. Ruhf ◽  
A. Braun ◽  
O. Papoulas ◽  
J.W. Tamkun ◽  
N. Randsholt ◽  
...  
Keyword(s):  
Polytene Chromosomes ◽  
Gene Mutations ◽  
Polycomb Group ◽  
Protein Isoforms ◽  
Homeotic Genes ◽  
Loss Of Function ◽  
Trithorax Group ◽  
A Subunit ◽  
The Common ◽  
Hematopoietic Disorders

The Drosophila domino gene has been isolated in a screen for mutations that cause hematopoietic disorders. Generation and analysis of loss-of-function domino alleles show that the phenotypes are typical for proliferation gene mutations. Clonal analysis demonstrates that domino is necessary for cell viability and proliferation, as well as for oogenesis. domino encodes two protein isoforms of 3202 and 2498 amino acids, which contain a common N-terminal region but divergent C termini. The common region includes a 500 amino acid DNA-dependent ATPase domain of the SWI2/SNF2 family of proteins, which function via interaction with chromatin. We show that, although domino alleles do not exhibit homeotic phenotypes by themselves, domino mutations enhance Polycomb group mutations and counteract Trithorax group effects. The Domino proteins are present in large complexes in embryo extracts, and one isoform binds to a number of discrete sites on larval polytene chromosomes. Altogether, the data lead us to propose that domino acts as a repressor by interfering with chromatin structure. This activity is likely to be performed as a subunit of a chromatin-remodeling complex.

scholarly journals Hepatica transsilvanica Fuss (Ranunculaceae) is an Allotetraploid Relict of the Tertiary Flora in Europe – Molecular Phylogenetic Evidence

2020 ◽  
Vol 89 (3) ◽  
Author(s):  
Levente Laczkó ◽  
Gábor Sramkó
Keyword(s):  
Parental Species ◽  
Gene Tree ◽  
Diploid Species ◽  
Nuclear Gene ◽  
Hybrid Origin ◽  
Distribution Area ◽  
Recent Common Ancestor ◽  
Term Survival ◽  
Quaternary Glaciation ◽  
Eastern Carpathians

The <em>Hepatica </em>section <em>Angulosa </em>consists of mainly tetraploid (2<em>n </em>= 28) species that are distributed disjunctly throughout Eurasia. Karyological evidence proves the hybrid origin of the polyploid species of this section. <em>Hepatica transsilvanica </em>is a member of this species group with a conspicuous distribution restricted to the Eastern Carpathians. Based on genome size and cytotypes, the paternal parent of <em>H. transsilvanica </em>is described to be the only diploid species in section <em>Angulosa</em>, <em>H. falconeri</em>. The maternal species is hypothesized to be <em>H. nobilis</em>, a European species with entirely lobed leaves and a wider distribution area. Although the hybrid origin of <em>H. transsilvanica </em>is well documented by karyological evidence, the time of hybridization has never been studied. By using sequences of both the nuclear and plastid genome, we reconstructed the phylogenetic relationships and divergence times of <em>H. transsilvanica </em>and its parental species. The identity of the parental species is corroborated by discordant gene tree topologies of the nrITS and plastid sequences. Moreover, both gene copies of the parental species could be identified with the low-copy nuclear gene, <em>MLH1</em>. Divergence dating analysis using Bayesian phylogenetic methods strongly supported the long-term survival of <em>H. transsilvanica </em>in the Southeastern Carpathians, as the most recent common ancestor of the hybrid and parent species existed not later than the beginning of the Pleistocene, ca. 3 million years ago. These results not only highlight the biogeographic importance of the Southeastern Carpathians in the Quaternary glaciation periods, but also emphasize that Tertiary lineages could have survived in a Central European cryptic refugium.

scholarly journals A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa

2019 ◽  
Vol 10 (2) ◽  
pp. 811-826 ◽  
Author(s):  
Albert Erives ◽  
Bernd Fritzsch
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Families ◽  
Single Copy ◽  
Gene Duplications ◽  
Nervous Systems ◽  
Evolutionary Diversification ◽  
Transmembrane Channel ◽  
Sensory Epithelia ◽  
Protein X ◽  
Ancient Gene

The evolutionary diversification of animals is one of Earth’s greatest marvels, yet its earliest steps are shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) vs. Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the Max-like protein X (MLX and MLXIP) family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplicated gene pair that is sister to the single-copy gene maintained in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.

scholarly journals Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae

2020 ◽  
Vol 10 (12) ◽  
pp. 4387-4398
Author(s):  
Dhanushya Ramachandran ◽  
Michael R. McKain ◽  
Elizabeth A. Kellogg ◽  
Jennifer S. Hawkins
Keyword(s):  
Insertional Mutagenesis ◽  
Evolutionary Dynamics ◽  
Diploid Species ◽  
Duplicate Gene ◽  
Plant Genome ◽  
Abiotic Stress Response ◽  
Repeat Content ◽  
Gene Copies ◽  
Polyploidization Event ◽  
Plant Genome Evolution

Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.

Ancient gene duplications and the root(s) of the tree of life

PROTOPLASMA ◽  
2005 ◽  
Vol 227 (1) ◽  
pp. 53-64 ◽  
Author(s):  
Olga Zhaxybayeva ◽  
Pascal Lapierre ◽  
J. Peter Gogarten
Keyword(s):  
Tree Of Life ◽  
Gene Duplications ◽  
Ancient Gene

scholarly journals PhyloBrain atlas: a cortical brain MRI atlas following a phylogenetic approach

2020 ◽  
Author(s):  
M Zhernovaia ◽  
M Dadar ◽  
S. Mahmoud ◽  
Y Zeighami ◽  
Maranzano
Keyword(s):  
Brain Mri ◽  
Regions Of Interest ◽  
Human Cortex ◽  
Middle Temporal ◽  
Functional Regions ◽  
Lingual Gyrus ◽  
Evolutionary Changes ◽  
Anatomical Nomenclature ◽  
Functional Features ◽  
The Common

ABSTRACTCortical atlases constitute a consistent division of the human cortex into areas that have common structural as well as meaningful and distinctive functional characteristics. The most widely used atlases follow the cytoarchitectonic and myeloarchitectonic characteristics of the cortex and have been combined to the standard anatomical nomenclature of gyri and sulci. More recently, common functional features depicted by resting state functional MRI have also guided the division of the cortical brain in functional regions of interest. However, to date, there are no atlases that divide the cortex considering the common evolutionary changes experienced by the mammalian cortex.Hence, the present study proposes the division of cortical areas into five main regions of interest (ROIs) following a phylogenetic approach: 1- archicortex, 2- paleocortex, 3- peri-archicortex, 4- proisocortex, 5-neocortex, and twelve neocortical sub-ROIs: 5.1.temporopolar, 5.2.post-central, 5.3.pre-central, 5.4.pericalcarine, 5.5.superior temporal, 5.6.middle temporal, 5.7.precuneus, 5.8.insular, 5.9.inferior parietal, 5.10.caudal anterior, 5.11.posterior cingulate, and 5.12.lingual gyrus.The segmentations were done using the T1-weighted MNI-ICBM152 non-linear 6th generation symmetric average brain MRI model.

scholarly journals EVIDENCE FOR DUPLICATION OF THE STRUCTURAL GENES CODING PLASTID AND CYTOSOLIC ISOZYMES OF TRIOSE PHOSPHATE ISOMERASE IN DIPLOID SPECIES OF CLARKIA

Genetics ◽  
1983 ◽  
Vol 105 (2) ◽  
pp. 421-436
Author(s):  
E Pichersky ◽  
L D Gottlieb
Keyword(s):  
Diploid Species ◽  
Triose Phosphate Isomerase ◽  
Gene Duplications ◽  
Structural Genes ◽  
Diploid Plant ◽  
Triose Phosphate ◽  
Gene Coding ◽  
The Family ◽  
Entire Plant ◽  
Number Of Individuals

ABSTRACT Formal genetic analyses of the mode of inheritance of the multiple plastid and cytosolic isozymes of triose phosphate isomerase (TPI, EC 5.3.1.1) in annual diploid species of Clarkia (Onagraceae), native to California, suggest that each set of isozymes is specified by duplicate structural genes. In contrast, most diploid plant species possess one plastid and one cytosolic TPI isozyme each coded by a single locus. Linkage tests revealed that the two genes coding the plastid TPIs assort independently. Although the number of individuals sampled per species was small, the plastid isozymes were electrophoretically more variable than the cytosolic isozymes. The two gene duplications are the first reported that characterize an entire plant genus. Initial electrophoretic surveys of TPI in other genera of Onagraceae revealed that the duplication of the gene coding the plastid isozyme is apparently restricted to Clarkia, whereas that of the gene coding the cytosolic isozyme is present in most genera of the family. The separate phylogenetic distributions of the two duplications suggest that the processes that gave rise to them were unrelated.

scholarly journals foxc1a genetically interacts with ripply1 to regulate mesp-ba expression and somitogenesis in the zebrafish embryo

2016 ◽  
Author(s):  
Rotem Lavy ◽  
W. Ted Allison ◽  
Fred B. Berry
Keyword(s):  
Regulatory Network ◽  
Zebrafish Embryo ◽  
Temporal Order ◽  
Regulatory Mechanisms ◽  
Loss Of Function ◽  
Expression Domain ◽  
Somite Formation ◽  
Opposing Effects ◽  
Expression Loss ◽  
Time Point

AbstractSomitogenesis is a fundamental segmentation process that forms the vertebrate body plan. A network of transcription factors is essential in establishing the spatial temporal order of this process. One such transcription factor is mesp-ba which has an important role in determining somite boundary formation. Its expression in somitogenesis is tightly regulated by the transcriptional activator Tbx6 and the repressor Ripply1 via a feedback regulatory network. Loss of foxc1a function in zebrafish leads to lack of anterior somite formation and reduced mesp-ba expression. Here we examine how foxc1a interacts with the tbx6-ripply1 network to regulate mesp-ba expression. In foxc1a morphants, anterior somites did not form at 12.5 hours post fertilization (hpf). At 22 hpf posterior somites formed, whereas anterior somites remained absent. In ripply1 morphants, no somites were observed at any time point. The expression of mesp-ba was reduced in the foxc1a morphants and expanded anteriorly in ripply1 morphants. The tbx6 expression domain was smaller and shifted anteriorly in the foxc1a morphants. Double knockdown of foxc1a and ripply1 resulted in absence of anterior somite formation while posterior somites did form, suggesting a partial rescue of the ripply1 phenotype. However, unlike the single foxc1a morphants, expression of mesp-ba was restored in the anterior PSM. Expression of tbx6 was expanded anteriorly in the double morphants. In conclusion, both foxc1a and ripply1 morphants displayed defects in somitogenesis, but their individual loss of function had opposing effects on mesp-ba expression. Loss of ripply1 appears to have rescued the mesp-ba expression in the foxc1a morphant, suggesting that intersection of these parallel regulatory mechanisms is required for normal mesp-ba expression and somite formation.

scholarly journals Spatial specification of mammalian eye territories by reciprocal transcriptional repression of Pax2 and Pax6

Development ◽  
2000 ◽  
Vol 127 (20) ◽  
pp. 4325-4334 ◽  
Author(s):  
M. Schwarz ◽  
F. Cecconi ◽  
G. Bernier ◽  
N. Andrejewski ◽  
B. Kammandel ◽  
...  
Keyword(s):  
Visual System ◽  
Transcriptional Repression ◽  
Ectopic Expression ◽  
Pax6 Gene ◽  
Loss Of Function ◽  
Pax6 Expression ◽  
Expression Domain ◽  
Enhancer Activity ◽  
Optic Stalk ◽  
Optic Cup

We have studied the molecular basis of the Pax2 and Pax6 function in the establishment of visual system territories. Loss-of-function mutants have revealed crucial roles for Pax2 in the generation of the optic stalk and for Pax6 in the development of the optic cup. Ectopic expression of Pax6 in the optic stalk under control of Pax2 promoter elements resulted in a shift of the optic cup/optic stalk boundary indicated by the presence of retinal pigmented cells on the optic stalk. By studying mouse embryos at early developmental stages we detected an expansion of Pax2 expression domain in the Pax6(−/−) mutant and of Pax6 expression domain in the Pax2(−/−) embryo. These results suggest that the position of the optic cup/optic stalk boundary depends on Pax2 and Pax6 expression, hinting at a possible molecular interaction. Using gel shift experiments, we confirmed the presence of Pax2- and Pax6-binding sites on the retina enhancer of the Pax6 gene and on the Pax2 upstream control region, respectively. Co-transfection experiments revealed a reciprocal inhibition of Pax2 promoter/enhancer activity by Pax6 protein and vice versa. Based on our findings, we propose a model for Pax gene regulation that establishes the proper spatial regionalization of the mammalian visual system.

scholarly journals A screen for gene paralogies delineating evolutionary branching order of early Metazoa

2019 ◽  
Author(s):  
Albert Erives ◽  
Bernd Fritzsch
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Families ◽  
Single Copy ◽  
Gene Duplications ◽  
Nervous Systems ◽  
Evolutionary Diversification ◽  
Transmembrane Channel ◽  
Sensory Epithelia ◽  
Ancient Gene ◽  
Early Metazoan

The evolutionary diversification of animals is one of Earth’s greatest triumphs, yet its origins are still shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) versus Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the MLX/MLXIP family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplication, absent in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.

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