scholarly journals Genome Duplication Events and Functional Reduction of Ploidy Levels in Sturgeon (Acipenser, Huso and Scaphirhynchus)

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 1203-1215
Author(s):  
Arne Ludwig ◽  
Natalia M Belfiore ◽  
Christian Pitra ◽  
Victor Svirsky ◽  
Ingo Jenneckens
Keyword(s):  
Genome Duplication ◽  
Chromosomal Rearrangements ◽  
Diploid Species ◽  
Ploidy Levels ◽  
Sturgeon Species ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene ◽  
Duplication Events ◽  
Functional Reduction ◽  
Multiple Levels

Abstract Sturgeon (order Acipenserformes) provide an ideal taxonomic context for examination of genome duplication events. Multiple levels of ploidy exist among these fish. In a novel microsatellite approach, data from 962 fish from 20 sturgeon species were used for analysis of ploidy in sturgeon. Allele numbers in a sample of individuals were assessed at six microsatellite loci. Species with ∼120 chromosomes are classified as functional diploid species, species with ∼250 chromosomes as functional tetraploid species, and with ∼500 chromosomes as functional octaploids. A molecular phylogeny of the sturgeon was determined on the basis of sequences of the entire mitochondrial cytochrome b gene. By mapping the estimated levels of ploidy on this proposed phylogeny we demonstrate that (I) polyploidization events independently occurred in the acipenseriform radiation; (II) the process of functional genome reduction is nearly finished in species with ∼120 chromosomes and more active in species with ∼250 chromosomes and ∼500 chromosomes; and (III) species with ∼250 and ∼500 chromosomes arose more recently than those with ∼120 chromosomes. These results suggest that gene silencing, chromosomal rearrangements, and transposition events played an important role in the acipenseriform genome formation. Furthermore, this phylogeny is broadly consistent with previous hypotheses but reveals a highly supported oceanic (Atlantic-Pacific) subdivision within the Acipenser/Huso complex.

scholarly journals Artificial whole genome duplication in paleopolyploid sturgeons yields highest documented chromosome number in vertebrates

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ievgen Lebeda ◽  
Petr Ráb ◽  
Zuzana Majtánová ◽  
Martin Flajšhans
Keyword(s):  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Mitotic Division ◽  
Chromosome Count ◽  
Whole Genome ◽  
Acipenser Baerii ◽  
Ploidy Levels ◽  
Duplication Events ◽  
C Value

AbstractCritically endangered sturgeons, having undergone three whole genome duplication events, represent an exceptional example of ploidy plasticity in vertebrates. Three extant ploidy groups, combined with autopolyploidization, interspecific hybridization and the fertility of hybrids are important issues in sturgeon conservation and aquaculture. Here we demonstrate that the sturgeon genome can undergo numerous alterations of ploidy without severe physiological consequences, producing progeny with a range of ploidy levels and extremely high chromosome numbers. Artificial suppression of the first mitotic division alone, or in combination with suppression of the second meiotic division of functionally tetraploid zygotes (4n, C-value = 4.15) of Siberian sturgeon Acipenser baerii and Russian sturgeon A. gueldenstaedtii resulted in progeny of various ploidy levels—diploid/hexaploid (2n/6n) mosaics, hexaploid, octoploid juveniles (8n), and dodecaploid (12n) larvae. Counts between 477 to 520 chromosomes in octoploid juveniles of both sturgeons confirmed the modal chromosome numbers of parental species had been doubled. This exceeds the highest previously documented chromosome count among vertebrates 2n ~ 446 in the cyprinid fish Ptychobarbus dipogon.

Evolution of Tandemly Arranged Repetitive DNAs in Three Species of Cyprinoidei with Different Ploidy Levels

2021 ◽  
pp. 1-11
Author(s):  
Ali Bishani ◽  
Dmitry Y. Prokopov ◽  
Svetlana A. Romanenko ◽  
Anna S. Molodtseva ◽  
Polina L. Perelman ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genome Duplication ◽  
Diploid Species ◽  
Duplication Event ◽  
Repetitive Elements ◽  
Genomic Locus ◽  
Genome Duplication Event ◽  
Ploidy Levels ◽  
Genomic Markers ◽  
Tench Tinca Tinca

Polyploid species represent a challenge for both cytogenetic and genomic studies due to their high chromosome numbers and the morphological similarity between their paralogous chromosomes. This paper describes the use of low-coverage high-throughput sequencing to identify the 14 most abundant tandemly arranged repetitive elements in the paleotetraploid genome of the crucian carp (Carassius carassius, 2n = 100). These repetitive elements were then used for molecular cytogenetic studies of a closely related functionally triploid form of the Prussian carp (Carassius gibelio, 3n = 150 + Bs) and a relatively distant diploid species, the tench (Tinca tinca, 2n = 48). According to their distribution on the chromosomes of the 3 aforementioned species, the repetitive elements here identified can be divided into 5 groups: (1) those specific to a single genomic locus in both Carassius species, despite the recent carp-specific genome duplication; (2) those located in a single genomic locus of T. tinca, but amplified in one or both Carassius species; (3) those massively amplified in the B chromosomes of C. gibelio; (4) those located in a single locus in C. gibelio, but amplified in many blocks in C. carassius; and (5) those located in multiple pericentromeric loci in both Carassius species. Our data indicate that some of the repetitive elements are highly conserved in cyprinoid species and may serve as good cytogenetic and genomic markers for discriminating paralogous chromosomes, while others are evolutionarily recent, and their amplification may be related to the last whole-genome duplication event.

scholarly journals Whole-genome duplication and host genotype affect rhizosphere microbial communities

2019 ◽  
Author(s):  
Julian C. B. Ponsford ◽  
Charley J. Hubbard ◽  
Joshua G. Harrison ◽  
Lois Maignien ◽  
C. Alex Buerkle ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ploidy Level ◽  
Bacterial Communities ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Plant Traits ◽  
Whole Genome ◽  
Host Genotype ◽  
Ploidy Levels ◽  
Duplication Events

AbstractThe composition of complex microbial communities found in association with plants is influenced in part by host phenotype. Yet, the salient genetic architecture is often unknown. Genome duplication events are common in the evolutionary history of plants, influence many important plant traits, and may affect associated microbial communities. Using experimentally induced whole genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis thaliana. Specifically, we performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genotypes (Columbia vs. Landsberg) and ploidy levels (diploid vs. tetraploid). We modeled abundances of individual bacterial taxa by utilizing a hierarchical Bayesian framework, based on the Dirichlet and multinomial distributions. We found that host genotype and host ploidy level affected rhizosphere community composition, for instance, the microbiome of the tetraploid Columbia genotype differed from that of other host genotypes. We then tested to what extent microbiomes derived from a given host genotype or ploidy level affected plant performance by inoculating sterile seedlings of each genotype with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genotypes. The findings suggest that while both host genotype and ploidy affect microbial community assembly, bacterial communities found in association with only some host genotypes may affect growth of subsequent plant generations.ImportancePlants influence the composition of their associated microbial communities; yet the underlying host genetic factors are often unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits, including the quality and quantity of compounds exuded into the root zone, which can affect root-bound microbes. In Arabidopsis thaliana, we characterized how whole-genome duplication affected the composition of rhizosphere bacterial communities, and how bacterial communities associated with two host plant genotypes and ploidy levels affected subsequent plant growth. We observed an interaction in which ploidy level within one host genotype affected both bacterial community composition and function. This research reveals how genome duplication, a widespread genetic feature of both wild and crop plant species, influences the coexistence of bacterial taxa and affects plant growth.

scholarly journals Discovery of a new mammal species (Soricidae: Eulipotyphla) from Narcondam volcanic island, India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Manokaran Kamalakannan ◽  
Chandrakasan Sivaperuman ◽  
Shantanu Kundu ◽  
Govindarasu Gokulakrishnan ◽  
Chinnadurai Venkatraman ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Genetic Distances ◽  
Medium Size ◽  
Mitochondrial Cytochrome ◽  
Volcanic Island ◽  
Mammal Species ◽  
Molecular Approaches ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene

AbstractWe discovered a new Crocidura species of shrew (Soricidae: Eulipotyphla) from Narcondam Island, India by using both morphological and molecular approaches. The new species, Crocidura narcondamica sp. nov. is of medium size (head and body lengths) and has a distinct external morphology (darker grey dense fur with a thick, darker tail) and craniodental characters (braincase is rounded and elevated with weak lambdoidal ridges) in comparison to other close congeners. This is the first discovery of a shrew from this volcanic island and increases the total number of Crocidura species catalogued in the Indian checklist of mammals to 12. The newly discovered species shows substantial genetic distances (12.02% to 16.61%) to other Crocidura species known from the Indian mainland, the Andaman and Nicobar Archipelago, Myanmar, and from Sumatra. Both Maximum-Likelihood and Bayesian phylogenetic inferences, based on mitochondrial (cytochrome b) gene sequences showed distinct clustering of all included soricid species and exhibit congruence with the previous evolutionary hypothesis on this mammalian group. The present phylogenetic analyses also furnished the evolutionary placement of the newly discovered species within the genus Crocidura.

Patterns of genome duplication within the Brassica napus genome

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 291-303 ◽  
Author(s):  
I A.P Parkin ◽  
A G Sharpe ◽  
D J Lydiate
Keyword(s):  
Brassica Napus ◽  
Genome Duplication ◽  
Chromosomal Rearrangements ◽  
Centric Fusion ◽  
Linkage Groups ◽  
Gross Chromosomal Rearrangements ◽  
A Genome ◽  
C Genome ◽  
Homologous Locus ◽  
Duplicate Loci

The progenitor diploid genomes (A and C) of the amphidiploid Brassica napus are extensively duplicated with 73% of genomic clones detecting two or more duplicate sequences within each of the diploid genomes. This comprehensive duplication of loci is to be expected in a species that has evolved through a polyploid ancestor. The majority of the duplicate loci within each of the diploid genomes were found in distinct linkage groups as collinear blocks of linked loci, some of which had undergone a variety of rearrangements subsequent to duplication, including inversions and translocations. A number of identical rearrangements were observed in the two diploid genomes, suggesting they had occurred before the divergence of the two species. A number of linkage groups displayed an organization consistent with centric fusion and (or) fission, suggesting this mechanism may have played a role in the evolution of Brassica genomes. For almost every genetically mapped locus detected in the A genome a homologous locus was found in the C genome; the collinear arrangement of these homologous markers allowed the primary regions of homoeology between the two genomes to be identified. At least 16 gross chromosomal rearrangements differentiated the two diploid genomes during their divergence from a common ancestor.Key words: genome evolution, Brassicaeae, polyploidy, homoeologous linkage groups.

scholarly journals Phenotypic diversity of bread wheat lines with introgressions from the diploid cereal Aegilops speltoides for technological properties of grain and f lour

2020 ◽  
Vol 24 (7) ◽  
pp. 738-746
Author(s):  
L. V. Shchukina ◽  
I. F. Lapochkina ◽  
T. A. Pshenichnikova
Keyword(s):  
Genetic Diversity ◽  
Bread Wheat ◽  
Phenotypic Diversity ◽  
Chromosomal Rearrangements ◽  
Diploid Species ◽  
Aegilops Speltoides ◽  
Technological Properties ◽  
Gluten Content ◽  
Spring Variety ◽  
Growing Conditions

The creation of varieties adapted to changing environmental conditions, resistant to various pathogens, and satisfying various grain purposes is impossible without using the genetic diversity of wheat. One of the ways to expand the genetic diversity of wheat is to introduce new variants of genes from the genetic pool of congeners and wild relatives into the genotypes of existing varieties. In this study, we used 10 lines from the Arsenal collection created on the genetic basis of the spring variety ‘Rodina’ and the diploid species Aegilops speltoides in the Federal Research Center “Nemchinovka” in 1994. The lines were previously characterized for the presence of translocations and chromosomal rearrangements cytologically and using molecular markers. Technological analyses were performed on grain obtained in Western Siberia and Moscow region. The aim of this study was to establish the possibilities of expanding the phenotypic diversity for technological properties of grain and flour as a result of such hybridization of bread wheat and the diploid cereal Aegilops speltoides. The variety ‘Rodina’ forms a vitreous grain with a high gluten content in Siberia, but has low physical properties of flour and dough. Five derived lines were found to have significantly higher protein and gluten content in grain. The highest values under both growing conditions were found in lines 73/00i, 82/00i, and 84/00i. Two lines (69/00i and 76/00i) showed a high flour strength and dough elasticity, characterizing the lines as strong and valuable in quality. These lines can be used for baking bread. Line 82/00i inherited from Ae. speltoides a soft-grain endosperm, which indicates the introgression of the Ha-Sp gene, homoeoallelic to the Ha gene of bread wheat, into ‘Rodina’. Flour of this line is suitable for the manufacture of confectionery without the use of technological additives. The lines generally retained their characteristics in different growing conditions. They can be attracted as donors of new alleles of genes that determine the technological properties of grain and resistance to biotic stresses.

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