scholarly journals Recombination Events Generating a Novel Rp1 Race Specificity

2005 ◽  
Vol 18 (3) ◽  
pp. 220-228 ◽  
Author(s):  
Shavannor M. Smith ◽  
Scot H. Hulbert
Keyword(s):  
Rust Resistance ◽  
The Novel ◽  
Gene Recombination ◽  
Sequence Comparisons ◽  
Parental Haplotype ◽  
Resistance Specificity ◽  
Race Specificity

Genes at the maize Rpl rust resistance complex often mispair in meiosis, which allows genes to recombine unequally, creating recombinant haplotypes. Four recombinant haplotypes were identified from progeny of an Rpl-D/Rpl-I heterozygote that conferred a nonparental resistance specificity designated Rpl-I*. Sequence comparisons of paralogs in the recombinant and parental haplotypes demonstrated that all four recombinants were derived from intergenic (between gene) recombination events. The sequence of paralogs in the HRpl-I parental haplotype indicated this haplotype includes 41 or more rpl genes, at least 31 of which are transcribed. The results indicate that most of the novel resistance specificities that have arisen spontaneously at Rp1 are the result of reassortment of existing Rpl genes.

scholarly journals A Novel Cardiotropic Murine Adenovirus Representing a Distinct Species of Mastadenoviruses

2009 ◽  
Vol 83 (11) ◽  
pp. 5749-5759 ◽  
Author(s):  
Boris Klempa ◽  
Detlev H. Krüger ◽  
Brita Auste ◽  
Michal Stanko ◽  
Adalbert Krawczyk ◽  
...  
Keyword(s):  
Distinct Species ◽  
Heart Tissue ◽  
Amino Acid Sequences ◽  
Phylogenetic Distance ◽  
The Novel ◽  
Sequence Comparisons ◽  
Cytopathic Effects ◽  
Cell Culture Isolation ◽  
Genomic Regions ◽  
Type 3

ABSTRACT During cell culture isolation experiments to recover Dobrava hantavirus from a suspension of liver from a striped field mouse (Apodemus agrarius), an unknown virus was coisolated. Atypically for hantaviruses, it had extensive cytopathic effects. Using a random PCR approach, it was identified as a novel murine adenovirus, MAdV-3 (for MAdV type 3). A plaque-purified virus clone was prepared and further characterized. The complete genome sequence of MAdV-3 was determined to be 30,570 bp in length. Sequence comparisons to other adenovirus species revealed highest similarity to MAdV-1, the representative of the murine adenovirus A species. However, substantial differences were found in the E1, E3, and E4 genomic regions. The phylogenetic distance of MAdV-3 amino acid sequences for pVIII, protease, polymerase, and hexon from MAdV-1 is markedly higher than 0.1 exchange per position, and, based on our cross-neutralization experiments, MAdV-3 and MAdV-1 can be regarded as different serotypes. Therefore, we propose to classify MAdV-3 as the first isolate of a novel adenovirus species, designated murine adenovirus C (MAdV-C). The novel MAdV-3 virus is not only genetically and serologically distinct from MAdV-1 but also shows a unique organ tropism in infected mice. In contrast to MAdV-1, the virus was not detectable in brain but predominantly infected heart tissue. Thus, infection of mice with cardiotropic MAdV-3 might be an interesting animal model of adenovirus-induced myocarditis.

Roseomonas riguiloci sp. nov., isolated from wetland freshwater

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3024-3029 ◽  
Author(s):  
Keun Sik Baik ◽  
Seong Chan Park ◽  
Han Na Choe ◽  
Se Na Kim ◽  
Jae-Hak Moon ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach

A non-motile, coccobacillus-shaped and pink pigmented bacterium, designated strain 03SU10-PT, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram reaction-negative and catalase- and oxidase-positive. The major fatty acids (>10 % of total) were C18 : 1ω7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The predominant respiratory lipoquinone was Q-10. The DNA G+C content was 68 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Spermidine, putrescine and 1,3-diaminopropane were the major polyamines. A phylogenetic tree based on 16S rRNA gene sequence comparisons showed that strain 03SU10-PT formed an evolutionary lineage within the radiation enclosing the members of the genus Roseomonas . The nearest neighbour to the novel strain was Roseomonas stagni HS-69T (96.3 % gene sequence similarity). The evidence provided by the polyphasic taxonomic approach used in this study indicated that strain 03SU10-PT could not be assigned to any recognized species; therefore a novel species is proposed, Roseomonas riguiloci sp. nov., with 03SU10-PT ( = KCTC 23339T = JCM 17520T) as the type strain.

An anchored AFLP- and retrotransposon-based map of diploid Avena

Genome ◽  
2000 ◽  
Vol 43 (5) ◽  
pp. 736-749 ◽  
Author(s):  
Gong-Xin Yu ◽  
Roger P Wise
Keyword(s):  
Resistance Gene ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Rust Resistance ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Crown Rust ◽  
Crown Rust Resistance ◽  
Resistance Specificity ◽  
Specific Amplification

A saturated genetic map of diploid oat was constructed based on a recombinant inbred (RI) population developed from a cross between Avena strigosa (Cereal Introduction, C.I. 3815) and A. wiestii (C.I. 1994). This 513-locus map includes 372 AFLP (amplified fragment length polymorphism) and 78 S-SAP (sequence-specific-amplification polymorphism) markers, 6 crown-rust resistance loci, 8 resistance-gene analogs (RGAs), one morphological marker, one RAPD (random amplified polymorphic DNA) marker, and is anchored by 45 grass-genome RFLP (restriction fragment length polymorphism) markers. This new A. strigosa × A. wiestii RI map is colinear with a diploid Avena map from an A. atlantica × A. hirtula F2 population. However, some linkage blocks were rearranged as compared to the RFLP map derived from the progenitor A. strigosa × A. wiestii F2 population. Mapping of Bare-1-like sequences via sequence-specific AFLP indicated that related retrotransposons had considerable heterogeneity and widespread distribution in the diploid Avena genome. Novel amplified fragments detected in the RI population suggested that some of these retrotransposon-like sequences are active in diploid Avena. Three markers closely linked to the Pca crown-rust resistance cluster were identified via AFLP-based bulk-segregant analysis. The derived STS (sequence-tagged-site) marker, Agx4, cosegregates with Pc85, the gene that provides resistance specificity to crown-rust isolate 202 at the end of the cluster. This framework map will be useful in gene cloning, genetic mapping of qualitative genes, and positioning QTL (quantitative trait loci) of agricultural importance.Key words: AFLP, Bare-1 retrotransposon, sequence-specific-amplification polymorphism (S-SAP), resistance-gene analog, crown-rust resistance, Pca, Gramineae, grass anchor probe.

scholarly journals Robiginitomaculum antarcticum gen. nov., sp. nov., a member of the family Hyphomonadaceae, from Antarctic seawater

2007 ◽  
Vol 57 (11) ◽  
pp. 2595-2599 ◽  
Author(s):  
Kiyoung Lee ◽  
Hong Kum Lee ◽  
Tae-Hwan Choi ◽  
Jang-Cheon Cho
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Fatty Acid Content ◽  
Salinity Range ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Sequence Comparisons ◽  
The Family ◽  
The Antarctic

A seawater bacterium, designated IMCC3195T, was isolated from the Antarctic coast. Cells of the novel strain were Gram-negative, rusty-coloured, strictly aerobic, chemoheterotrophic, non-budding and non-motile rods or vibrioids that possessed a thin prostheca. Based on 16S rRNA gene sequence comparisons, the novel strain was most closely related to the genera Hyphomonas (89.4–90.9 %), Maricaulis (90.1–90.4 %), Hirschia (89.0 %) and Oceanicaulis (87.9 %) of the family Hyphomonadaceae. Phylogenetic analyses also showed the Antarctic isolate to be only distantly related to the genera of stalked bacteria of marine origin in the family Hyphomonadaceae. The DNA G+C content of the novel strain was 60.3 mol% and the predominant cellular fatty acids were C18 : 1 ω7c (41.9 %), C17 : 1 ω8c (21.4 %) and C17 : 0 (14.3 %). The major quinone was Q-10. Several phenotypic and chemotaxonomic characteristics, including optimum temperature and salinity range for growth, cell morphology, pigmentation and fatty acid content, differentiated the novel strain from other related genera in the family Hyphomonadaceae. From the taxonomic evidence collected in this study, it is suggested that strain IMCC3195T (=KCCM 42687T=NBRC 103098T) represents a new genus and novel species in the family Hyphomonadaceae, for which the name Robiginitomaculum antarcticum gen. nov., sp. nov. is proposed.

scholarly journals High prevalence, genetic diversity and a potentially novel genotype of Sapelovirus A (Picornaviridae) in enteric and respiratory samples in Hungarian swine farms

2020 ◽  
Vol 101 (6) ◽  
pp. 609-621 ◽  
Author(s):  
Ákos Boros ◽  
Zoltán László ◽  
Péter Pankovics ◽  
András Marosi ◽  
Mihály Albert ◽  
...  
Keyword(s):  
Faecal Sample ◽  
Virus Isolation ◽  
Viral Metagenomics ◽  
The Novel ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Swine Farms ◽  
High Prevalence ◽  
Single Genotype

All of the known porcine sapeloviruses (PSVs) currently belong to a single genotype in the genus Sapelovirus (family Picornaviridae). Here, the complete genome of a second, possibly recombinant, genotype of PSV strain SZ1M-F/PSV/HUN2013 (MN807752) from a faecal sample of a paraplegic pig in Hungary was characterized using viral metagenomics and RT-PCR. This sapelovirus strain showed only 64 % nucleotide identity in the VP1 region to its closest PSV-1 relative. Complete VP1 sequence-based epidemiological investigations of PSVs circulating in Hungary showed the presence of diverse strains found in high prevalence in enteric and respiratory samples collected from both asymptomatic and paraplegic pigs from 12 swine farms. Virus isolation attempts using PK-15 cell cultures were successful in 3/8 cases for the classic but not the novel PSV genotype. Sequence comparisons of faeces and isolate strains derived VP1 showed that cultured PSV strains not always represent the dominant PSVs found in vivo.

scholarly journals Functional Analysis of Alkane Hydroxylases from Gram-Negative and Gram-Positive Bacteria

2002 ◽  
Vol 184 (6) ◽  
pp. 1733-1742 ◽  
Author(s):  
Theo H. M. Smits ◽  
Stefanie B. Balada ◽  
Bernard Witholt ◽  
Jan B. van Beilen
Keyword(s):  
Functional Analysis ◽  
The Novel ◽  
Alkane Hydroxylase ◽  
Sequence Comparisons ◽  
Gram Positive Bacteria ◽  
Sequence Identity ◽  
Medium Chain Length ◽  
Protein Sequence Identity ◽  
Alkane Hydroxylases ◽  
Host Strains

ABSTRACT We have cloned homologs of the Pseudomonas putida GPo1 alkane hydroxylase from Pseudomonas aeruginosa PAO1, Pseudomonas fluorescens CHA0, Alcanivorax borkumensis AP1, Mycobacterium tuberculosis H37Rv, and Prauserella rugosa NRRL B-2295. Sequence comparisons show that the level of protein sequence identity between the homologs is as low as 35%, and that the Pseudomonas alkane hydroxylases are as distantly related to each other as to the remaining alkane hydroxylases. Based on the observation that rubredoxin, an electron transfer component of the GPo1 alkane hydroxylase system, can be replaced by rubredoxins from other alkane hydroxylase systems, we have developed three recombinant host strains for the functional analysis of the novel alkane hydroxylase genes. Two hosts, Escherichia coli GEc137 and P. putida GPo12, were equipped with pGEc47ΔB, which encodes all proteins necessary for growth on medium-chain-length alkanes (C6 to C12), except a functional alkane hydroxylase. The third host was an alkB knockout derivative of P. fluorescens CHA0, which is no longer able to grow on C12 to C16 alkanes. All alkane hydroxylase homologs, except the Acinetobacter sp. ADP1 AlkM, allowed at least one of the three hosts to grow on n-alkanes.

scholarly journals Recombination Between Paralogues at the rp1 Rust Resistance Locus in Maize

Genetics ◽  
2001 ◽  
Vol 158 (1) ◽  
pp. 423-438 ◽  
Author(s):  
Qing Sun ◽  
Nicholas C Collins ◽  
Michael Ayliffe ◽  
Shavannor M Smith ◽  
Jeff Drake ◽  
...  
Keyword(s):  
Rust Resistance ◽  
Crossing Over ◽  
Resistance Locus ◽  
Leucine Rich Repeat ◽  
Partial Loss ◽  
Sequence Comparisons ◽  
Truncated Protein ◽  
Coding Regions ◽  
Lrr Domain ◽  
Recombination Breakpoints

Abstract Rp1 is a complex rust resistance locus of maize. The HRp1-D haplotype is composed of Rp1-D and eight paralogues, seven of which also code for predicted nucleotide binding site-leucine rich repeat (NBS-LRR) proteins similar to the Rp1-D gene. The paralogues are polymorphic (DNA identities 91-97%), especially in the C-terminal LRR domain. The remaining family member encodes a truncated protein that has no LRR domain. Seven of the nine family members, including the truncated gene, are transcribed. Sequence comparisons between paralogues provide evidence for past recombination events between paralogues and diversifying selection, particularly in the C-terminal half of the LRR domain. Variants selected for complete or partial loss of Rp1-D resistance can be explained by unequal crossing over that occurred mostly within coding regions. The Rp1-D gene is altered or lost in all variants, the recombination breakpoints occur throughout the genes, and most recombinant events (9/14 examined) involved the same untranscribed paralogue with the Rp1-D gene. One recombinant with a complete LRR from Rp1-D, but the aminoterminal portion from another homologue, conferred the Rp1-D specificity but with a reduced level of resistance.

scholarly journals Molecular Mapping of the Stripe Rust Resistance Gene Yr69 on Wheat Chromosome 2AS

Plant Disease ◽  
2016 ◽  
Vol 100 (8) ◽  
pp. 1717-1724 ◽  
Author(s):  
Liyuan Hou ◽  
Juqing Jia ◽  
Xiaojun Zhang ◽  
Xin Li ◽  
Zujun Yang ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Expressed Sequence Tag ◽  
Molecular Mapping ◽  
Puccinia Striiformis ◽  
Dominant Gene ◽  
Introgression Line ◽  
Stripe Rust Resistance ◽  
Resistance Specificity

Wheat is one of the major food crops in the world. Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an economically important disease that affects wheat worldwide. The discovery of novel resistance genes and the deployment of effectively resistant cultivars are important for the ongoing control of wheat stripe rust and the maintenance of the agricultural productivity of wheat. CH7086, a new stripe rust-resistant wheat introgression line, was selected by crossing susceptible cultivars with the resistant Thinopyrum ponticum-derived partial amphiploid Xiaoyan 7430. The resistance of CH7086 is effective against all current Chinese P. striiformis f. sp. tritici races. CH7086 was crossed with the stripe rust-susceptible cultivars to develop F1, F2, F3, and BC1 populations for genetic analysis. Segregation in the F2 and BC1 populations and F2:3 lines were tested for resistance against the P. striiformis f. sp. tritici race CYR32. This test showed that CH7086 carries a single dominant gene for stripe rust resistance, which was temporarily designated YrCH86. The closest of the eight simple sequence repeat (SSR) and expressed sequence tag-SSR markers flanking the locus were X2AS33, which is 1.9 cM distal, and Xmag3807, which is 3.1 cM proximal. The resistance gene and its polymorphic markers were placed in deletion bin 2AS-0.78-1.00 using the ‘Chinese Spring’ nullisomic-tetrasomic, ditelosomic, and deletion lines. The tests of both allelism and resistance specificity suggested that the resistance gene found in CH7086 was not Yr17, which was the only current formally named Yr gene on chromosome 2AS. Thus, YrCH86 appeared to be a new locus and was permanently designated Yr69.

scholarly journals Mycoplasma iguanae sp. nov., from a green iguana (Iguana iguana) with vertebral disease

2006 ◽  
Vol 56 (4) ◽  
pp. 761-764 ◽  
Author(s):  
D. R. Brown ◽  
D. L. Demcovitz ◽  
D. R. Plourdé ◽  
S. M. Potter ◽  
M. E. Hunt ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Western Blots ◽  
Iguana Iguana ◽  
A Cell ◽  
Green Iguanas

Strain 2327T, first cultured from vertebral abscesses of green iguanas (Iguana iguana) collected in Florida, USA, was readily distinguished from all previously described mollicutes by 16S rRNA gene sequence comparisons. Strain 2327T lacks a cell wall, ferments glucose, does not hydrolyse arginine, aesculin or urea and is sensitive to digitonin. Western blots distinguished the novel isolate serologically from the most closely related members of the Mycoplasma neurolyticum cluster. On the basis of these data, the isolate represents a novel species for which the name Mycoplasma iguanae sp. nov. is proposed. The type strain is strain 2327T (=ATCC BAA-1050T=NCTC 11745T).

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