scholarly journals Convergent evolution of polyploid genomes from across the eukaryotic tree of life

2021 ◽  
Author(s):  
Yue Hao ◽  
Jonathon Fleming ◽  
Joanna Petterson ◽  
Eric Lyons ◽  
Patrick P. Edger ◽  
...  
Keyword(s):  
High Frequency ◽  
Gene Loss ◽  
Relative Rate ◽  
Duplicate Gene ◽  
Single Copy ◽  
Selective Constraint ◽  
Diploid Hybrid ◽  
Hybrid Species ◽  
Evolutionary Forces ◽  
Modern Species

By modeling the homoeologous gene losses that occurred in fifty genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes or yeasts. The models suggest these events were nearly all allopolyploidies, with two distinct progenitors contributing to the modern species. We show that many of the events show a relative rate of duplicate gene loss prior to the first post-polyploidy speciation that is significantly higher than in later phases of their evolution. The relatively low selective constraint seen for the single-copy genes these losses produced lead us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate post-polyploid period. We also find ongoing and extensive reciprocal gene losses (RGL; alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is therefore possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass RGL barriers.

scholarly journals Meiotic effects of MSH4 copy number variation support an adaptive role for post-polyploidy gene loss

2018 ◽  
Author(s):  
Adrián Gonzalo ◽  
Marie-Odile Lucas ◽  
Catherine Marquis ◽  
Andrew Lloyd ◽  
Eric Jenczewski
Keyword(s):  
Chromosome Segregation ◽  
Meiotic Recombination ◽  
Copy Number ◽  
Gene Loss ◽  
Duplicate Gene ◽  
Single Copy ◽  
Homologous Chromosomes ◽  
Evolutionary Forces ◽  
Copy Numbers ◽  
Number Variation

ABSTRACTMany eukaryotes descend from polyploid ancestors that experienced massive duplicate gene loss. This genomic erosion is particularly strong for duplicated (meiotic) recombination genes that return to a single copy more rapidly than genome average following polyploidy. To better understand the evolutionary forces underlying duplicate loss, we analysed how varying copy numbers of MSH4, an essential meiotic recombination gene, influences crossover formation in allotetraploid Brassica napus. We show that faithful chromosome segregation and crossover frequencies between homologous chromosomes are unchanged with MSH4 duplicate loss; by contrast, crossovers between homoeologous chromosomes (which result in genomic rearrangements) decrease with reductions in MSH4 copy number. We also found that inter-homoeologue crossovers originate almost exclusively from the MSH4-dependent crossover pathway. Limiting the efficiency of this pathway by decreasing the copy number of key meiotic recombination genes could therefore contribute to adaptation to polyploidy, by promoting regular chromosome segregation and genomic stability.

scholarly journals Transcriptional regulation of ribosomal proteins during a nutritional upshift in Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (7) ◽  
pp. 2429-2435 ◽  
Author(s):  
D M Donovan ◽  
N J Pearson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Proteins ◽  
Protein Gene ◽  
Relative Rate ◽  
Ribosomal Protein Gene ◽  
Single Copy ◽  
Protein Product ◽  
Yeast Genome ◽  
Base Pairs ◽  
Beta Galactosidase

The relative rates of synthesis of Saccharomyces cerevisiae ribosomal proteins increase coordinately during a nutritional upshift. We constructed a gene fusion which contained 528 base pairs of sequence upstream from and including the TATA box of ribosomal protein gene rp55-1 (S16A-1) fused to a CYC1-lacZ fusion. This fusion was integrated in single copy at the rp55-1 locus in the yeast genome. During a nutritional upshift, in which glucose was added to cells growing in an ethanol-based medium, we found that the increase in the relative rate of synthesis of the beta-galactosidase protein product followed the same kinetics as the change in relative rates of synthesis of several ribosomal proteins measured in the same experiment. This demonstrates that the nontranscribed sequences upstream from the rp55-1 gene, which are present in the fusion, are sufficient to mediate the change in rates of synthesis characteristic of ribosomal proteins under these conditions. The results also suggest that a change in transcription rates is mainly responsible for the increase in relative rates of synthesis of ribosomal proteins during a nutritional upshift in S. cerevisiae.

scholarly journals Codon usage bias and dinucleotide preference in 29 Drosophila species

2021 ◽  
Author(s):  
Prajakta P Kokate ◽  
Stephen M Techtmann ◽  
Thomas Werner
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Single Copy ◽  
Biochemical Properties ◽  
Extensive Study ◽  
Drosophila Species ◽  
Phylogenetic Distance ◽  
Interesting Phenomenon ◽  
Evolutionary Forces ◽  
Usage Patterns

Abstract Codon usage bias, where certain codons are used more frequently than their synonymous counterparts, is an interesting phenomenon influenced by three evolutionary forces: mutation, selection, and genetic drift. To better understand how these evolutionary forces affect codon usage bias, an extensive study to detect how codon usage patterns change across species is required. This study investigated 668 single-copy orthologous genes independently in 29 Drosophila species to determine how the codon usage patterns change with phylogenetic distance. We found a strong correlation between phylogenetic distance and codon usage bias and observed striking differences in codon preferences between the two subgenera Drosophila and Sophophora. As compared to the subgenus Sophophora, species of the subgenus Drosophila showed reduced codon usage bias and a reduced preference specifically for codons ending with C, except for codons with G in the second position. We found that codon usage patterns in all species were influenced by the nucleotides in the codon's 2nd and 3rd positions rather than the biochemical properties of the amino acids encoded. We detected a concordance between preferred codons and preferred dinucleotides (at positions 2 and 3 of codons). Furthermore, we observed an association between speciation, codon preferences, and dinucleotide preferences. Our study provides the foundation to understand how selection acts on dinucleotides to influence codon usage bias.

scholarly journals Comparative genome analysis revealed gene inversions, boundary expansion and contraction, and gene loss in Stemona sessilifolia (Miq.) Miq. chloroplast genome

2021 ◽  
Author(s):  
Jingting Liu ◽  
Mei Jiang ◽  
Haimei Chen ◽  
Yu Liu ◽  
Chang Liu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gene Loss ◽  
Herbal Medicines ◽  
Single Copy ◽  
Asparagus Officinalis ◽  
Accurate Identification ◽  
Protein Coding ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Next Generation Sequencing Technology

AbstractStemona sessilifolia (Miq.) Miq., commonly known as Baibu, is one of the most popular herbal medicines in Asia. In Chinese Pharmacopoeia, Baibu has multiple authentic sources, and there are many homonym herbs sold as Baibu in the herbal medicine market. The existence of the counterfeits of Baibu brings challenges to its identification. To assist the accurate identification of Baibu, we sequenced and analyzed the complete chloroplast genome of Stemona sessilifolia using next-generation sequencing technology. The genome was 154,039 bp in length, possessing a typical quadripartite structure consisting of a pair of inverted repeats (IRs: 27,094 bp) separating by a large single copy (LSC: 81,950 bp) and a small single copy (SSC: 17,901 bp). A total of 112 unique genes were identified, including 80 protein-coding, 28 transfer RNA, and four ribosomal RNA genes. Besides, 45 tandem, 27 forward, 23 palindromic, and 72 simple sequence repeats were detected in the genome by repeat analysis. Compared with its counterfeits (Asparagus officinalis and Carludovica palmate), we found that IR expansion and SSC contraction events of Stemona sessilifolia resulted in two copies of the rpl22 gene in the IR regions and partial duplication of the ndhF gene in the SSC region. Secondly, an approximately 3-kb-long inversion was identified in the LSC region, leading to the petA and cemA gene presented in the complementary strand of the chloroplast DNA molecule. Comparative analysis revealed some highly variable regions, including trnF-GAA_ndhJ, atpB_rbcL, rps15_ycf1, trnG-UCC_trnR-UCU, ndhF_rpl32. Finally, gene loss events were investigated in the context of phylogenetic relationships. In summary, the complete plastome of Stemona sessilifolia will provide valuable information for the molecular identification of Baibu and assist in elucidating the evolution of Stemona sessilifolia.

scholarly journals High frequency repeat-induced point mutation (RIP) is not associated with efficient recombination in Neurospora.

Genetics ◽  
1994 ◽  
Vol 138 (4) ◽  
pp. 1093-1103 ◽  
Author(s):  
J T Irelan ◽  
A T Hagemann ◽  
E U Selker
Keyword(s):  
Point Mutation ◽  
Dna Sequences ◽  
High Frequency ◽  
Recombination Frequency ◽  
Single Copy ◽  
Sexual Cycle ◽  
Base Pairs ◽  
Copy Gene ◽  
The Relationship ◽  
Repeat Induced Point Mutation

Abstract Duplicated DNA sequences in Neurospora crassa are efficiently detected and mutated during the sexual cycle by a process named repeat-induced point mutation (RIP). Linked, direct duplications have previously been shown to undergo both RIP and deletion at high frequency during premeiosis, suggesting a relationship between RIP and homologous recombination. We have investigated the relationship between RIP and recombination for an unlinked duplication and for both inverted and direct, linked duplications. RIP occurred at high frequency (42-100%) with all three types of duplications used in this study, yet recombination was infrequent. For both inverted and direct, linked duplications, recombination was observed, but at frequencies one to two orders of magnitude lower than RIP. For the unlinked duplication, no recombinants were seen in 900 progeny, indicating, at most, a recombination frequency nearly three orders of magnitude lower than the frequency of RIP. In a direct duplication, RIP and recombination were correlated, suggesting that these two processes are mechanistically associated or that one process provokes the other. Mutations due to RIP have previously been shown to occur outside the boundary of a linked, direct duplication, indicating that RIP might be able to inactivate genes located in single-copy sequences adjacent to a duplicated sequence. In this study, a single-copy gene located between elements of linked duplications was inactivated at moderate frequencies (12-14%). Sequence analysis demonstrated that RIP mutations had spread into these single-copy sequences at least 930 base pairs from the boundary of the duplication, and Southern analysis indicated that mutations had occurred at least 4 kilobases from the duplication boundary.

Excision and transposition of Tn5 upon insertion in the hha gene of Escherichia coli

1994 ◽  
Vol 40 (7) ◽  
pp. 597-601 ◽  
Author(s):  
C. Badenas ◽  
C. Madrid ◽  
A. Juárez
Keyword(s):  
Escherichia Coli ◽  
High Frequency ◽  
Chromosomal Location ◽  
Single Copy

We report the occurrence of Tn5 secondary transpositions in Escherichia coli HB101 hha::Tn5(pANN202-312). Tn5-induced hha mutants (hemolysin oveiproducers) segregated at high frequency either hemolysin-negative clones or clones showing the parental hemolytic phenotype (reduced hemolysin production). Secondary transpositions of Tn5 appeared to be responsible for the phenotypes of both types of derivatives. The hemolysin-negative clones no longer harboured Tn5 in the hha gene, but rather Tn5 was in the hly genes of the hemolytic plasmid pANN202-312. The derivatives that recovered the parental hemolytic phenotype contained a single copy of Tn5 in a chromosomal location different from that of hha. Both kinds of transpositional events appeared to restore the function of the hha gene.Key words: Tn5, transposition, Escherichia coli, excision.

scholarly journals Formation of an inverted duplication can be an initial step in gene amplification.

1988 ◽  
Vol 8 (10) ◽  
pp. 4302-4313 ◽  
Author(s):  
J C Ruiz ◽  
G M Wahl
Keyword(s):  
Gene Amplification ◽  
High Frequency ◽  
Integration Site ◽  
Initial Step ◽  
Single Copy ◽  
Growth Conditions ◽  
Drug Selection ◽  
Gene Insertion ◽  
Inverted Duplication ◽  
Extrachromosomal Elements

We have developed a gene transfer approach to facilitate the identification and isolation of chromosomal regions which are prone to high-frequency gene amplification. Such regions are identified by assaying for transformants which show high-frequency resistance to PALA and/or methotrexate by amplification of a vector containing the genes which encode the enzyme targets of these antiproliferative agents. We identified 2 of 47 transformants which displayed high-frequency amplification of the transfected genes, and in this report we describe the analysis of one of them (L46). Molecular analysis of the integration site in transformant L46 revealed that the donated genes were at the center of an inverted duplication which spanned more than 70 kilobase pairs and consisted largely of host DNA. The data suggest that integration of the transfected sequences generates a submicroscopic molecule containing the inverted duplication and at least 750 kilobases of additional sequences. The donated sequences and the host sequences were readily amplified and lost in exponentially growing cultures in the absence of drug selection, which suggests that the extrachromosomal elements are acentric. In contrast to the instability of this region following gene insertion, the preinsertion site was maintained at single copy level under growth conditions which produced copy number heterogeneity in L46. The implications of our results for mechanisms of genetic instability and mammalian gene amplification are discussed.

scholarly journals DIPLOID HETEROZYGOUS HYBRIDS FROM MATINGS BETWEEN ESCHERICHIA COLI AND SALMONELLA TYPHOSA

1960 ◽  
Vol 112 (2) ◽  
pp. 361-372 ◽  
Author(s):  
L. S. Baron ◽  
Walter M. Spilman ◽  
Warren F. Carey
Keyword(s):  
High Frequency ◽  
Carbon Sources ◽  
Low Frequency ◽  
Diploid Hybrid ◽  
Hybrid Form ◽  
Biochemical Characteristics ◽  
Cultural Form ◽  
E Coli ◽  
Unstable Type ◽  
K 12

An Hfr strain of E. coli K-12 has been shown to mate at low frequency with a number of strains of S. typhosa. The hybrids, selected as lactose positives, retained all other antigenic and biochemical manifestations of the S. typhosa parent. A Lac+ hybrid, S. typhosa strain 643L+ was remated with the E. coli Hfr and plated on minimal media containing L-arabinose, D-xylose, L-rhamnose, or L-fucose as the sole carbon sources. Hybrids of the remated strain appeared at high frequency on the plates containing L-arabinose, and could be detected at lower frequencies on plates containing D-xylose, L-rhamnose, and L-fucose. Those selected for D-xylose or L-rhamnose utilization possessed the attributes of segregating diploid heterozygotes being highly unstable and continually segregating a cultural form typical of the S. typhosa parent. The unstable type exhibited most of the biochemical characteristics of the E. coli parent including the ability to produce indol, and also reacted with antiserum to both the E. coli and S. typhosa parent strains, owing to the acquisition of a thermolabile antigen from the E. coli parent. The parent and hybrid strains were examined in detail for changes in patterns of phage susceptibility and virulence. Acquisition of susceptibility to a number of the T phages, a characteristic of the E. coli parent, was observed in one of the hybrid types. A decrease in virulence of the diploid hybrid form of S. typhosa in the mouse virulence test was found.

High frequency of single-copy T-DNA transformants produced by floral dip inCRE-expressing Arabidopsis plants

2009 ◽  
Vol 59 (4) ◽  
pp. 517-527 ◽  
Author(s):  
Annelies De Paepe ◽  
Sylvie De Buck ◽  
Katleen Hoorelbeke ◽  
Jonah Nolf ◽  
Ingrid Peck ◽  
...  
Keyword(s):  
High Frequency ◽  
Single Copy ◽  
Floral Dip

Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

2008 ◽  
Vol 33 (3) ◽  
pp. 589-597 ◽  
Author(s):  
Elizabeth A. Friar ◽  
Linda M. Prince ◽  
Jennifer M. Cruse-Sanders ◽  
Mitchell E. McGlaughlin ◽  
Charles A. Butterworth ◽  
...  
Keyword(s):  
Single Copy ◽  
Nuclear Genes ◽  
Hybrid Origin ◽  
Internal Transcribed Spacer Region ◽  
Hybrid Species ◽  
Cytogenetic Data ◽  
Molecular Phylogenetic ◽  
Distinct Lineage ◽  
Phylogenetic Hypotheses ◽  
Genomic Regions

Incongruence among different estimates of species relationships in plants, from different molecules, cytogenetic data, biogeographic data, morphological/anatomical data or other sources, has been used frequently as an indication of introgression, hybrid species origin, or chloroplast (cp) capture. In plants, these incongruences are most often seen between data derived from the nuclear vs. the cp genomes and the nuclear markers used for comparison usually have been from the nuclear ribosomal (nr) internal transcribed spacer region (ITS). The amount of genomic material shared between introgressing species can be highly variable. In some of these cases, other nuclear genomic regions have moved between species without leaving a signature on the nrITS. An example of well-supported phylogenetic incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA); evolutionary hypotheses for D. scabra based on molecular as opposed to cytogenetic data are strongly discordant. In this paper, we test these two conflicting phylogenetic hypotheses regarding the evolutionary relationships of Dubautia scabra using evidence from six low-copy nuclear genes, as well as multiple chloroplast noncoding regions and nrITS. The nrITS region is also examined for the presence of multiple copy types. Incongruence between inferred relationships based on nuclear chromosomal arrangements and molecular phylogenetic data from chloroplast DNA and nrITS is resolved in favor of a hypothesis of ancient hybridization rather than cytogenetic homoplasy involving dysploidy. Most single-copy nuclear genes track histories of D. scabra compatible with cytogenetic data whereas chloroplast and nrITS data track a common, different history that appears to reflect hybridization with a chromosomally distinct lineage that also occurs on Maui Nui and Hawai'i (the Big Island).

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