Phylogeny and expression of paralogous and orthologous sulphate transporter genes in diploid and hexaploid wheats

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 526-534 ◽  
Author(s):  
Peter Buchner ◽  
Ian M Prosser ◽  
Malcolm J Hawkesford
Keyword(s):  
Sequence Similarity ◽  
Aegilops Tauschii ◽  
Aegilops Speltoides ◽  
Genome Sequences ◽  
D Genome ◽  
B Genome ◽  
Close Relationship ◽  
Genes Encoding ◽  
Intron Structure ◽  
Genome Phylogeny

Twelve genes encoding two closely related subtypes (ST1.1a and ST1.1b) of a sulphate transporter have been identified in the diploid wheats Aegilops tauschii, Triticum urartu, and Aegilops speltoides, as well as the hexaploid Triticum aestivum. Based on phylogenetic comparisons with other plant sulphate transporters, the ST1.1a and 1.1b subtypes aligned with group 1 of the plant sulphate transporter gene family. The exon–intron structure was conserved within the ST1.1a or ST1.1b genes; however, substantial variability in intron sequences existed between the two types. The high overall sequence similarity indicated that ST1.1b represented a duplication of the ST1.1a gene, which must have occurred before the evolution of the ancestral diploid wheat progenitor. In contrast with the close relationship of the T. urartu and Ae. tauschii sequences to the corresponding A and D genome sequences of T. aestivum, the divergence between the Ae. speltoides sequences and the B genome sequences suggested that the B genome ST1.1a gene has been modified by recombination. Transcript analysis revealed predominant expression of the ST1.1a type and an influence of sulphur availability on the level of expression.Key words: genome, phylogeny, progenitor, sulphate transport, wheat.

Phylogenetic analysis of C, M, N, and U genomes and their relationships with Triticum and other related genomes as revealed by LMW-GS genes at Glu-3 loci

Genome ◽  
2011 ◽  
Vol 54 (4) ◽  
pp. 273-284 ◽  
Author(s):  
Shunli Wang ◽  
Xiaohui Li ◽  
Ke Wang ◽  
Xiaozheng Wang ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Aegilops Tauschii ◽  
Cysteine Residue ◽  
Aegilops Speltoides ◽  
Low Molecular Weight ◽  
D Genome ◽  
B Genome ◽  
A Genome ◽  
Study Support

Phylogenetic relationships between the C, U, N, and M genomes of Aegilops species and the genomes of common wheat and other related species were investigated by using three types of low-molecular-weight glutenin subunit (LMW-GS) genes at Glu-3 loci. A total of 20 LMW-GS genes from Aegilops and Triticum species were isolated, including 11 LMW-m type and 9 LMW-i type genes. Particularly, four LMW-m type and three LMW-i type subunits encoded by the genes on the C, N, and U genomes possessed an extra cysteine residue at conserved positions, which could provide useful information for understanding phylogenetic relationships among Aegilops and Triticum genomes. Phylogenetic trees constructed by using either LMW-i or the combination of LMW-m and LMW-s, as well as analysis of all the three types of LMW-GS genes together, demonstrated that the C and U genomes were closely related to the A genome, whereas the N and M genomes were closely related to the D genome. Our results support previous findings that the A genome was derived from Triticum uratu, the B genome was from Aegilops speltoides, and the D genome was from Aegilops tauschii. In addition, phylogenetic relationships among different genomes analysed in this study support the concept that Aegilops is not monophyletic.

Characterization of six wheat × Thinopyrum intermedium derivatives by GISH, RFLP, and multicolor GISH

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 490-495 ◽  
Author(s):  
F P Han ◽  
G Fedak ◽  
A Benabdelmouna ◽  
K Armstrong ◽  
T Ouellet
Keyword(s):  
Genomic Dna ◽  
Aegilops Tauschii ◽  
Rflp Analysis ◽  
Aegilops Speltoides ◽  
Thinopyrum Intermedium ◽  
B Genome ◽  
A Genome ◽  
Genetic Stocks ◽  
Disomic Addition Lines ◽  
Thinopyrum Elongatum

Restriction fragment length polymorphism (RFLP) analysis and multicolor genomic in situ hybridization (GISH) are useful tools to precisely characterize genetic stocks derived from crosses of wheat (Triticum aestivum) with Thinopyrum intermedium and Thinopyrum elongatum. The wheat × Th. intermedium derived stocks designated Z1, Z2, Z3, Z4, Z5, and Z6 were initially screened by multicolor GISH using Aegilops speltoides genomic DNA for blocking and various combinations of genomic DNA from Th. intermedium, Triticum urartu, and Aegilops tauschii for probes. The probing (GISH) results indicated that lines Z1 and Z3 were alien disomic addition lines with chromosome numbers of 2n = 44. Z2 was a substitution line in which chromosome 2D was substituted by a pair of Th. intermedium chromosomes; this was confirmed by RFLP and muticolour GISH. Z4 (2n = 44) contained two pairs of wheat – Th. intermedium translocated chromosomes; one pair involved A-genome chromosomes, the other involved D- and A-genome chromosomes. Z5 (2n = 44) contained one pair of wheat – Th. intermedium translocated chromosomes involving the D- and A-genome chromosomes of wheat. Z6 (2n = 44) contained one pair of chromosomes derived from Th. intermedium plus another pair of translocated chromosomes involving B-genome chromosomes of wheat. Line Z2 was of special interest because it has some resistance to infection by Fusarium graminearum.Key words: wheat, Thinopyrum intermedium, addition, substitution, and translocation lines, GISH, multicolor GISH, RFLP.

Molecular evidence for the origin and evolution of chromosome 4A in polyploidy wheats

1985 ◽  
Vol 27 (2) ◽  
pp. 246-250 ◽  
Author(s):  
A. Lane Rayburn ◽  
B. S. Gill
Keyword(s):  
In Situ Hybridization ◽  
Chinese Spring ◽  
Diploid Species ◽  
Aegilops Speltoides ◽  
Molecular Evidence ◽  
Wheat Evolution ◽  
D Genome ◽  
Origin And Evolution ◽  
B Genome

The chromosomes of polyploid Triticum species and the putative donor diploid species were analyzed by in situ hybridization with a repeated DNA sequence clone pSc 119 isolated from rye and also found in wheat. In Triticum aestivum cv. Chinese Spring, chromosome 4A showed one terminal site in the short arm and one terminal and two interstitial sites of hybridization in the long arm. Triticum turgidum contained a 4A chromosome identical to 'Chinese Spring' with respect to hybridization sites. Chromosome 4A of the timopheevi wheats differed from 4A of 'Chinese Spring' in that the site of the sequence on the short arm was subterminal rather than terminal. Of the A-, B-, and D-genome progenitor species, only potential B-genome donors Aegilops speltoides and Aegilops sharonensis each showed a chromosome with hybridization sites similar to 4A. This suggested that 4A belongs to the B genome. Moreover, with regard to this sequence, chromosome 4A has undergone only minor changes during the evolution of the polyploid wheats.Key words: wheat evolution, in situ hybridization, biotin labeling.

PHYLOGENETIC AFFINITIES IN TRITICINAE STUDIED BY THIN-LAYER CHROMATOGRAPHY

1972 ◽  
Vol 14 (3) ◽  
pp. 703-712 ◽  
Author(s):  
H. C. Dass
Keyword(s):  
Thin Layer ◽  
Thin Layer Chromatography ◽  
Similarity Index ◽  
Aegilops Speltoides ◽  
D Genome ◽  
B Genome ◽  
Genome Donor ◽  
A Genome ◽  
Phylogenetic Affinities ◽  
Layer Chromatography

Thin-layer chromatography was used to assess the phylogenetic affinities in Triticinae. Leaf phenolics of Aegilops speltoides, Ae. bicornis, Ae. squarrosa, Triticum monococcum, T. dicoccoides, T. dicoccum and T. aestivum ssp. spelta were screened on cellulose coated plates. The chromatographic data were analysed statistically and a similarity index (biochemical distance) calculated. This index corresponded most closely with conventional concepts of affinities. T. dicoccoides and T. dicoccum were found to be closer to Ae. bicornis than to Ae. speltoides which suggests that Ae. bicornis is more probably the B genome donor. The contribution of the D genome by Ae. squarrosa was further confirmed. Correlation between the two tetraploids T. dicoccoides and T. dicoccum as well as with T. aestivum was high. Among the Aegilops species studied, Ae. speltoides most closely resembled T. monococcum. Low affinity in terms of the biochemical distance of T. monococcum with emmer wheats and T. aestivum throws doubt upon its direct contribution of the A genome.

scholarly journals Using the synthetic form RS5 to obtain new introgressive lines of common wheat

2021 ◽  
Vol 25 (7) ◽  
pp. 770-777
Author(s):  
R. O. Davoyan ◽  
I. V. Bebyakina ◽  
E. R. Davoyan ◽  
Y. S. Zubanova ◽  
D. M. Boldakov ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Common Wheat ◽  
Yellow Rust ◽  
Aegilops Tauschii ◽  
Genetic Material ◽  
Leaf Rust Resistance ◽  
Wild Relatives ◽  
Aegilops Speltoides ◽  
D Genome ◽  
Synthetic Form

The use of the gene pool of wild relatives, which have a significant reserve of genetic diversity, is of immediate interest for breeding common wheat. The creation and use of synthetic forms as “bridges” is an effective method of transferring valuable genetic material from wild relatives to cultivated wheat. For this purpose, genome addition, genome substitution and recombinant “secondary” synthetic forms have been created in the P.P. Lukyanenko National Center of Grain. The synthetic recombination form RS5 (BBAASDt ), in which the third genome consists of chromosomes of Aegilops speltoides (S) and Aegilops tauschii (Dt ), was obtained from crossing the synthetic forms Avrodes (BBAASS) and M.it./Ae. tauschii (BBAADt Dt ), in which the D genome from Ae. tauschii was added to the BBAA genomes of the durum wheat cultivar Mutico italicum. Introgression lines resistant to leaf rust, yellow rust and powdery mildew have been obtained from backcrosses with the susceptible common wheat cultivars Krasnodarskaya 99, Rostislav and Zhirovka. Twelve resistant lines that additionally have high technological characteristics of grain and flour have been selected. The cytological study (С-banding) has revealed chromosomal modifications in 6 of 8 lines under study. The rearrangements mainly affected the chromosomes of the D genome, 1D, 3D, 4D, 6D and 7D. It was found that in most cases the genetic material from the synthetic form RS5 in the studied lines was represented by substituted chromosomes from Ae. tauschii. In line 5791p17, the substitution of chromosomes 6D from Ae. tauschii and 7D from Ae. speltoides was revealed. Substitutions 4D(4Dt ), 6D(6Dt ) from Ae. tauschii and 7D(7S) from Ae. speltoides were obtained for the first time. Molecular analysis of 12 lines did not reveal effective leaf rust resistance genes, presumably present in synthetic forms of M.it./Ae. tauschii and Avrodes. It is assumed that the lines may carry previously unidentified genes for fungal disease resistance, in particular for resistance to leaf rust, from Ae. tauschii and Ae. speltoides.

scholarly journals Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium

2020 ◽  
Vol 6 (9) ◽  
Author(s):  
Albin Teulet ◽  
Djamel Gully ◽  
Zoe Rouy ◽  
Alicia Camuel ◽  
Ralf Koebnik ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Effector Proteins ◽  
Secretion Systems ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
Sumo Proteases ◽  
Genes Encoding

Bradyrhizobium are abundant soil bacteria and the major symbiont of legumes. The recent availability of Bradyrhizobium genome sequences provides a large source of information for analysis of symbiotic traits. In this study, we investigated the evolutionary dynamics of the nodulation genes (nod) and their relationship with the genes encoding type III secretion systems (T3SS) and their effectors among bradyrhizobia. Based on the comparative analysis of 146 Bradyrhizobium genome sequences, we identified six different types of T3SS gene clusters. The two predominant cluster types are designated RhcIa and RhcIb and both belong to the RhcI-T3SS family previously described in other rhizobia. They are found in 92/146 strains, most of them also containing nod genes. RhcIa and RhcIb gene clusters differ in the genes they carry: while the translocon-encoding gene nopX is systematically found in strains containing RhcIb, the nopE and nopH genes are specifically conserved in strains containing RhcIa, suggesting that these last two genes might functionally substitute nopX and play a role related to effector translocation. Phylogenetic analysis suggests that bradyrhizobia simultaneously gained nod and RhcI-T3SS gene clusters via horizontal transfer or subsequent vertical inheritance of a symbiotic island containing both. Sequence similarity searches for known Nop effector proteins in bradyrhizobial proteomes revealed the absence of a so-called core effectome, i.e. that no effector is conserved among all Bradyrhizobium strains. However, NopM and SUMO proteases were found to be the main effector families, being represented in the majority of the genus. This study indicates that bradyrhizobial T3SSs might play a more significant symbiotic role than previously thought and provides new candidates among T3SS structural proteins and effectors for future functional investigations.

scholarly journals Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1333
Author(s):  
Jana Gregorova ◽  
Petra Vychytilova-Faltejskova ◽  
Sabina Sevcikova
Keyword(s):  
Histone Modifications ◽  
Sequence Similarity ◽  
Tumor Development ◽  
Hematologic Malignancies ◽  
Seed Region ◽  
Cancer Therapies ◽  
Rna Molecules ◽  
Physiological Processes ◽  
Close Relationship ◽  
Aberrant Dna Methylation

MicroRNAs are small non-coding single-stranded RNA molecules regulating gene expression on a posttranscriptional level based on the seed sequence similarity. They are frequently clustered; thus, they are either simultaneously transcribed into a single polycistronic transcript or they may be transcribed independently. Importantly, microRNA families that contain the same seed region and thus target related signaling proteins, may be localized in one or more clusters, which are in a close relationship. MicroRNAs are involved in basic physiological processes, and their deregulation is associated with the origin of various pathologies, including solid tumors or hematologic malignancies. Recently, the interplay between the expression of microRNA clusters and families and epigenetic machinery was described, indicating aberrant DNA methylation or histone modifications as major mechanisms responsible for microRNA deregulation during cancerogenesis. In this review, the most studied microRNA clusters and families affected by hyper- or hypomethylation as well as by histone modifications are presented with the focus on particular mechanisms. Finally, the diagnostic and prognostic potential of microRNA clusters and families is discussed together with technologies currently used for epigenetic-based cancer therapies.

scholarly journals A Microsatellite Map of Wheat

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2007-2023 ◽  
Author(s):  
Marion S Röder ◽  
Victor Korzun ◽  
Katja Wendehake ◽  
Jens Plaschke ◽  
Marie-Hélène Tixier ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Reference Population ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
D Genome ◽  
B Genome ◽  
Microsatellite Map ◽  
A Genome ◽  
Polymorphic Microsatellite ◽  
Primer Sets

Abstract Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

scholarly journals Identification of Epidemiological Traits by Analysis of SARS−CoV−2 Sequences

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 764
Author(s):  
Bohu Pan ◽  
Zuowei Ji ◽  
Sugunadevi Sakkiah ◽  
Wenjing Guo ◽  
Jie Liu ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Host Age ◽  
Hierarchical Clustering Analysis ◽  
Genome Sequences ◽  
Geographic Patterns ◽  
Rapid Spread ◽  
Pairwise Sequence Similarity ◽  
Sequence Similarity Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS−CoV−2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS−CoV−2. Pairwise sequence similarity analysis demonstrated that SARS−CoV−2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS−CoV−2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS−CoV−2 and to facilitate the development of effective vaccines and therapeutics against the virus.

scholarly journals Genetic Investigation of the Catabolic Pathway for Degradation of Abietane Diterpenoids by Pseudomonas abietaniphilaBKME-9

2000 ◽  
Vol 182 (13) ◽  
pp. 3784-3793 ◽  
Author(s):  
Vincent J. J. Martin ◽  
William W. Mohn
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Ring Cleavage ◽  
Catabolic Pathway ◽  
Transcriptional Fusion ◽  
Abietane Diterpenoids ◽  
Genes Encoding ◽  
Dna Fragment ◽  
Reading Frames

ABSTRACT We have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by Pseudomonas abietaniphila BKME-9. Thedit gene cluster is located on a 16.7-kb DNA fragment containing 13 complete open reading frames (ORFs) and 1 partial ORF. The genes ditA1A2A3 encode the α and β subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8,13-abietadien acid. The dioxygenase mutant strain BKME-941 (ditA1::Tn5) did not grow on nonaromatic abietanes, and transformed palustric and abietic acids to 7-oxodehydroabietic acid in cell suspension assays. Thus, nonaromatic abietanes are aromatized prior to further degradation. Catechol 2,3-dioxygenase activity of xylEtranscriptional fusion strains showed induction of ditA1and ditA3 by abietic, dehydroabietic, and 7-oxodehydroabietic acids, which support the growth of strain BKME-9, as well as by isopimaric and 12,14-dichlorodehydroabietic acids, which are diterpenoids that do not support the growth of strain BKME-9. In addition to the aromatic-ring-hydroxylating dioxygenase genes, thedit cluster includes ditC, encoding an extradiol ring cleavage dioxygenase, and ditR, encoding an IclR-type transcriptional regulator. Although ditR is not strictly required for the growth of strain BKME-9 on abietanes, aditR::Kmr mutation in aditA3::xylE reporter strain demonstrated that it encodes an inducer-dependent transcriptional activator of ditA3. An ORF with sequence similarity to genes encoding permeases (ditE) is linked with genes involved in abietane degradation.

Sign in / Sign up

Export Citation Format

Share Document