scholarly journals Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata

2017 ◽  
Author(s):  
Hollie Putnam ◽  
Diane Adams ◽  
Ehud Zelzion ◽  
Nicole Wagner ◽  
Huan Qiu ◽  
...  
Keyword(s):  
Dna Markers ◽  
Sequence Variation ◽  
Marker Gene ◽  
Genomic Data ◽  
Single Copy ◽  
Rdna Repeat ◽  
Montipora Capitata ◽  
Sperm Bundle ◽  
Limited Variation ◽  
A Minor

We investigated intra and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2-3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.

scholarly journals Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3319 ◽  
Author(s):  
Hollie M. Putnam ◽  
Diane K. Adams ◽  
Ehud Zelzion ◽  
Nicole E. Wagner ◽  
Huan Qiu ◽  
...  
Keyword(s):  
Dna Markers ◽  
Sequence Variation ◽  
Marker Gene ◽  
Genomic Data ◽  
Single Copy ◽  
Rdna Repeat ◽  
Montipora Capitata ◽  
Sperm Bundle ◽  
Limited Variation ◽  
A Minor

We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.

scholarly journals Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata

2017 ◽  
Author(s):  
Hollie Putnam ◽  
Diane Adams ◽  
Ehud Zelzion ◽  
Nicole Wagner ◽  
Huan Qiu ◽  
...  
Keyword(s):  
Dna Markers ◽  
Sequence Variation ◽  
Marker Gene ◽  
Genomic Data ◽  
Single Copy ◽  
Rdna Repeat ◽  
Montipora Capitata ◽  
Sperm Bundle ◽  
Limited Variation ◽  
A Minor

We investigated intra and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2-3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.

scholarly journals Transcriptional Regulation and Organization of thedcuA and dcuB Genes, Encoding Homologous Anaerobic C4-Dicarboxylate Transporters inEscherichia coli

1998 ◽  
Vol 180 (24) ◽  
pp. 6586-6596 ◽  
Author(s):  
Paul Golby ◽  
David J. Kelly ◽  
John R. Guest ◽  
Simon C. Andrews
Keyword(s):  
Degradation Products ◽  
Single Copy ◽  
Northern Blotting ◽  
Primer Extension ◽  
Receptor Protein ◽  
Primary Role ◽  
Homologous Proteins ◽  
Dicarboxylate Transport ◽  
Genes Encoding ◽  
A Minor

ABSTRACT The dcuA and dcuB genes ofEscherichia coli encode homologous proteins that appear to function as independent and mutually redundant C4-dicarboxylate transporters during anaerobiosis. ThedcuA gene is 117 bp downstream of, and has the same polarity as, the aspartase gene (aspA), whiledcuB is 77 bp upstream of, and has the same polarity as, the anaerobic fumarase gene (fumB). To learn more about the respective roles of the dcu genes, the environmental and regulatory factors influencing their expression were investigated by generating and analyzing single-copy dcuA- anddcuB-lacZ transcriptional fusions. The results show thatdcuA is constitutively expressed whereas dcuBexpression is highly regulated. The dcuB gene is strongly activated anaerobically by FNR, repressed in the presence of nitrate by NarL, and subject to cyclic AMP receptor protein (CRP)-mediated catabolite repression. In addition, dcuB is strongly induced by C4-dicarboxylates, suggesting thatdcuB is under the control of an uncharacterized C4-dicarboxylate-responsive gene regulator. Northern blotting confirmed that dcuA (and aspA) is expressed under both aerobic and anaerobic conditions and thatdcuB (and fumB) is induced anaerobically. Major monocistronic transcripts were identified for aspA anddcuA, as well as a minor species possibly corresponding to an aspA-dcuA cotranscript. Five major transcripts were observed for dcuB and fumB: monocistronic transcripts for both fumB and dcuB; adcuB-fumB cotranscript; and two transcripts, possibly corresponding to dcuB-fumB and fumB mRNA degradation products. Primer extension analysis revealed independent promoters for aspA, dcuA, and dcuB, but surprisingly no primer extension product could be detected forfumB. The expression of dcuB is entirely consistent with a primary role for DcuB in mediating C4-dicarboxylate transport during anaerobic fumarate respiration. The precise physiological purpose of DcuA remains unclear.

scholarly journals The miR-430 locus with extreme promoter density is a transcription body organizer, which facilitates long range regulation in zygotic genome activation

2021 ◽  
Author(s):  
Yavor Hadzhiev ◽  
Lucy Wheatley ◽  
Ledean Cooper ◽  
Federico Ansaloni ◽  
Celina Whalley ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Gene Cluster ◽  
Core Promoter ◽  
Single Copy ◽  
Early Embryo ◽  
Zygotic Genome Activation ◽  
Pol Ii ◽  
A Minor ◽  
Genome Activation ◽  
Zygotic Genome

In anamniote embryos the major wave of zygotic genome activation (ZGA) starts during the mid-blastula transition. This major wave of ZGA is facilitated by several mechanisms, including dilution of repressive maternal factors and accumulation of activating transcription factors during the fast cell division cycles preceding the mid-blastula transition. However, a set of genes escape global genome repression and are activated substantially earlier, during what is called, the minor wave of genome activation. While the mechanisms underlying the major wave of genome activation have been studied extensively, the minor wave of genome activation is little understood. In zebrafish the earliest expressed RNA polymerase II (Pol II) transcribed genes are activated in a pair of large transcription bodies depleted of chromatin, abundant in elongating Pol II and nascent RNAs (Hadzhiev et al., 2019; Hilbert et al., 2021). This transcription body includes the miR-430 gene cluster required for maternal mRNA clearance. Here we explored the genomic, chromatin organisation and cis-regulatory mechanisms of the minor wave of genome activation occurring in the transcription body. By long read genome sequencing we identified a remarkable cluster of miR-430 genes with over 300 promoters and spanning 0.6 Mb, which represent the highest promoter density of the genome. We demonstrate that the miR-430 gene cluster is required for the formation of the transcription body and acts as a transcription organiser for minor wave activation of a set of zinc finger genes scattered on the same chromosome arm, which share promoter features with the miR-430 cluster. These promoter features are shared among minor wave genes overall and include the TATA-box and sharp transcription start site profile. Single copy miR-430 promoter transgene reporter experiments indicate the importance of promoter-autonomous mechanisms regulating escape from global repression of the early embryo. These results together suggest that formation of the transcription body in the early embryo is the result of high promoter density coupled to a minor wave-specific core promoter code for transcribing key minor wave ZGA genes, which are required for the overhaul of the transcriptome during early embryonic development.

scholarly journals Species and Recombination Effects on DNA Variability in the Tomato Genus

Genetics ◽  
2001 ◽  
Vol 158 (4) ◽  
pp. 1725-1735 ◽  
Author(s):  
Emmanuelle Baudry ◽  
Carole Kerdelhué ◽  
Hideki Innan ◽  
Wolfgang Stephan
Keyword(s):  
Mating System ◽  
Recombination Rate ◽  
Sequence Variation ◽  
Single Copy ◽  
Recombination Rates ◽  
Dna Sequence Variation ◽  
Incompatibility Alleles ◽  
Selection For ◽  
Weak Influence ◽  
Selfing Species

Abstract Population genetics theory predicts that strong selection for rare, beneficial mutations or against frequent, deleterious mutations reduces polymorphism at linked neutral (or weakly selected) sites. The reduction of genetic variation is expected to be more severe when recombination rates are lower. In outbreeding species, low recombination rates are usually confined to certain chromosomal regions, such as centromeres and telomeres. In contrast, in predominantly selfing species, the rarity of double heterozygotes leads to a reduced effective recombination rate in the whole genome. We investigated the effects of restricted recombination on DNA polymorphism in these two cases, analyzing five Lycopersicon species with contrasting mating systems: L. chilense, L. hirsutum, L. peruvianum, L. chmielewskii, and L. pimpinellifolium, of which only the first three species have self-incompatibility alleles. In each species, we determined DNA sequence variation of five single-copy genes located in chromosomal regions with either high or low recombination rate. We found that the mating system has a highly significant effect on the level of polymorphism, whereas recombination has only a weak influence. The effect of recombination on levels of polymorphism in Lycopersicon is much weaker than in other well-studied species, including Drosophila. To explain these observations, we discuss a number of hypotheses, invoking selection, recombination, and demographic factors associated with the mating system. We also provide evidence that L. peruvianum, showing a level of polymorphism (almost 3%) that is comparable to the level of divergence in the whole genus, is the ancestral species from which the other species of the genus Lycopersicon have originated relatively recently.

scholarly journals Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

2018 ◽  
Author(s):  
Ella T Sieradzki ◽  
Jed A Fuhrman ◽  
Sara Rivero-Calle ◽  
Laura Gómez-Consarnau
Keyword(s):  
Marker Gene ◽  
Single Copy ◽  
Oxygenic Photosynthesis ◽  
Sampling Location ◽  
Pr Genes ◽  
Surface Ocean ◽  
San Pedro ◽  
Accessory Function ◽  
The Pacific ◽  
The Pacific Ocean

The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (< 1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65-104% of the genomes as estimated by single-copy recA), followed by PSI (5-104%) and AAnP (5-32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average±standard deviation 26.2±8.4 vs. 11±9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013±0.02). We demonstrate that rhodopsin expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-aconcentrations (< 0.25 µg/L). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.

scholarly journals Identification of a Pi9-Containing Rice Germplasm with a Newly Developed Robust Marker

2016 ◽  
Vol 106 (8) ◽  
pp. 871-876 ◽  
Author(s):  
Klaus Konrad Scheuermann ◽  
Yulin Jia
Keyword(s):  
Dna Markers ◽  
Sequence Variation ◽  
Blast Resistance ◽  
Blast Disease ◽  
Rice Germplasm ◽  
Oryza Minuta ◽  
Dna Sequence Variation ◽  
Aa Genome ◽  
Dna Primers ◽  
New Cultivars

The Pi9 gene in rice, originating from Oryza minuta, is an effective resistance gene for controlling rice blast disease. However, currently available linked DNA markers do not accurately identify the function of Pi9, thus hindering its efficient incorporation into new cultivars through marker-assisted selection (MAS). In addition, no known Pi9-containing rice germplasm is available to breeders. In the present study, DNA sequence variation of Pi9 alleles and their family members was analyzed in 40 diverse rice germplasm accessions from the AA genome to develop a robust Pi9 marker. In total, 29 DNA primers of 20 to 23 nucleotides were designed and each possible combination of primer pairs was used to detect Pi9. Only one combination of DNA primers, KS28/KS6, was identified to specifically detect Pi9 in the monogenic line IRBL9-W. The presence of Pi9 was verified with the predicted Pi9-specific blast reaction. Subsequently, 201 genetically diverse mini-core rice accessions from 114 countries were screened with KS28/KS6. One germplasm, IR 9660-48-1-1-2, was identified to carry Pi9 and the function of Pi9 was verified with pathogenicity assays. This robust Pi9 marker and a rice germplasm, IR9660-48-1-1-2 (GSOR310687), carrying Pi9 can be used to improve blast resistance with a MAS approach.

scholarly journals Establishment of Agrobacterium tumefaciens-Mediated Transformation of an Oleaginous Fungus, Mortierella alpina 1S-4, and Its Application for Eicosapentaenoic Acid Producer Breeding

2009 ◽  
Vol 75 (17) ◽  
pp. 5529-5535 ◽  
Author(s):  
Akinori Ando ◽  
Yosuke Sumida ◽  
Hiroaki Negoro ◽  
Dian Anggraini Suroto ◽  
Jun Ogawa ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Agrobacterium Tumefaciens ◽  
Eicosapentaenoic Acid ◽  
Marker Gene ◽  
Auxotrophic Mutant ◽  
Single Copy ◽  
Mortierella Alpina ◽  
Chromosomal Dna ◽  
Total Fatty Acids

ABSTRACT Gene manipulation tools for an arachidonic-producing filamentous fungus, Mortierella alpina 1S-4, have not been sufficiently developed. In this study, Agrobacterium tumefaciens-mediated transformation (ATMT) was investigated for M. alpina 1S-4 transformation, using the uracil-auxotrophic mutant (ura5 − strain) of M. alpina 1S-4 as a host strain and the homologous ura5 gene as a selectable marker gene. Furthermore, the gene for ω3-desaturase, catalyzing the conversion of n-6 fatty acid to n-3 fatty acid, was overexpressed in M. alpina 1S-4 by employing the ATMT system. As a result, we revealed that the frequency of transformation surpassed 400 transformants/108 spores, most of the integrated T-DNA appeared as a single copy at a random position in chromosomal DNA, and most of the transformants (60 to 80%) showed mitotic stability. Moreover, the accumulation of n-3 fatty acid in transformants was observed under the conditions of optimal ω3-desaturase gene expression. In particular, eicosapentaenoic acid (20:5n-3), an end product of n-3 fatty acids synthesized in M. alpina 1S-4, reached a maximum of 40% of total fatty acids. In conclusion, the ATMT system was found to be effective and suitable for the industrial strain Mortierella alpina 1S-4 and will be a useful tool for basic mutagenesis research and for industrial breeding of this strain.

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