scholarly journals Molecular-cytogenetic analysis of diploid wheatgrass Thinopyrum bessarabicum (Savul. and Rayss) A. Löve

2019 ◽  
Vol 13 (4) ◽  
pp. 389-402 ◽  
Author(s):  
Ekaterina D. Badaeva ◽  
Sergei A. Surzhikov ◽  
Alexander V. Agafonov
Keyword(s):  
Cytogenetic Analysis ◽  
Tandem Repeats ◽  
Diploid Species ◽  
Gene Families ◽  
The Other ◽  
Rrna Gene ◽  
Agropyron Elongatum ◽  
Molecular Cytogenetic ◽  
Rdna Loci ◽  
Thinopyrum Bessarabicum

Thinopyrum bessarabicum (T. Săvulescu & T. Rayss, 1923) A. Löve, 1980 is diploid (2n=2x=14, JJ or EbEb), perennial self-fertilizing rhizomatous maritime beach grass, which is phylogenetically close to another diploid wheatgrass species, Agropyron elongatum (N. Host, 1797) P. de Beauvois, 1812. The detailed karyotype of Th. bessarabicum was constructed based on FISH with six DNA probes representing 5S and 45S rRNA gene families and four tandem repeats. We found that the combination of pAesp_SAT86 (= pTa-713) probe with pSc119.2 or pAs1/ pTa-535 allows the precise identification of all J-genome chromosomes. Comparison of our data with the results of other authors showed that karyotypically Th. bessarabicum is distinct from A. elongatum. On the other hand, differences between the J-genome chromosomes of Th. bessarabicum and the chromosomes of hexaploid Th. intermedium (N. Host, 1797) M. Barkworth & D.R. Dewey, 1985 and decaploid Th. ponticum (J. Podpěra, 1902) Z.–W. Liu & R.–C. Wang, 1993 in the distribution of rDNA loci and hybridization patterns of pSc119.2 and pAs1 probes could be an indicative of (1) this diploid species was probably not involved in the origin of these polyploids or (2) it could has contributed the J-genome to Th. intermedium and Th. ponticum, but it was substantially modified over the course of speciation

Cytogenetics of Hybrids Among Perennial Species of Glycine Subgenus Glycine

1979 ◽  
Vol 27 (6) ◽  
pp. 713 ◽  
Author(s):  
E Putievsky ◽  
P Broue
Keyword(s):  
Cytogenetic Analysis ◽  
Diploid Species ◽  
The Other ◽  
F1 Hybrids ◽  
Pollen Stainability ◽  
Perennial Species ◽  
Tetraploid Form ◽  
Other Hand ◽  
Self Fertilization

A cytogenetic analysis based on F1 hybrids of some of the perennial species of Glycine subgenus Glycine Verdc. shows that G. clandestina and G. canescens are closely related and further, that either one of these diploid species could have provided one genome for the tetraploid form of G. tomentella. On the other hand, it appears that G. falcata and G. tabacina are distinctive species which are not closely related to the other three species. The tetraploid form of G. tomentella is genetically heterogeneous and crosses between certain types yield F1s with low pollen stainability which fail to set seed under conditions of self-fertilization.

Capnocytophaga periodontitidis sp. nov., isolated from subgingival plaque of periodontitis patient

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Yifei Zhang ◽  
Dan Qiao ◽  
Wenyu Shi ◽  
Danni Wu ◽  
Man Cai
Keyword(s):  
Genomic Analysis ◽  
Gene Families ◽  
Core Gene ◽  
The Other ◽  
Specific Gene ◽  
Rrna Gene ◽  
Subgingival Plaque ◽  
Content Type ◽  
Periodontitis Patient ◽  
Link Type

Two carbon dioxide-requiring, gliding, Gram-stain-negative strains, designated p1a2T and 051621, were isolated from subgingival plaque in association with severe periodontitis. The 16S rRNA gene sequence analysis revealed that they represented members of the genus Capnocytophaga and had less than 96.4 % pairwise similarity with species with validly published names in this genus. The whole-genome sequences of those strains had less than 91.9 % average nucleotide identity and 48.4 % digital DNA–DNA hybridization values with the other type strains of species of the genus Capnocytophaga , both below the species delineation threshold. The results of pan-genomic analysis indicated that p1a2T and 051621 shared 765 core gene families with the other ten species in this genus, and the numbers of strain-specific gene families were 493 and 455, respectively. The major fatty acids were iso-C15 : 0 and C16 : 0. A combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicate that p1a2T and 051621 should be considered to represent a novel species of the genus Capnocytophaga , for which the name Capnocytophaga periodontitidis sp. nov. is proposed. The type strain is p1a2T (=CGMCC 1.17337T=JCM 34126T).

scholarly journals Intragenomic Polymorphism of the ITS 1 Region of 35S rRNA Gene in the Group of Grasses with Two-Chromosome Species: Different Genome Composition in Closely Related Zingeria Species

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1647
Author(s):  
Alexander V. Rodionov ◽  
Alexander A. Gnutikov ◽  
Nikolai N. Nosov ◽  
Eduard M. Machs ◽  
Yulia V. Mikhaylova ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Diploid Species ◽  
Morphological Difference ◽  
The Other ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Genome Composition ◽  
Genomic Constitution ◽  
The Relationship ◽  
Small Genus

Zingeria (Poaceae) is a small genus that includes Z. biebersteiniana, a diploid species with the lowest chromosome number known in plants (2n = 4) as well as hexaploid Z. kochii and tetraploid Z. pisidica, and/or Z. trichopoda species. The relationship between these species and the other low-chromosomes species Colpodium versicolor are unclear. To explore the intragenomic polymorphism and genome composition of these species we examined the sequences of the internal transcribed spacer 1 of the 35S rRNA gene via NGS approach. Our study revealed six groups of ribotypes in Zingeria species. Their distribution confirmed the allopolyploid nature of Z. kochii, whose probable ancestors were Colpodium versicolor and Z. pisidica. Z. pisidica has 98% of rDNA characteristic only for this species, and about 0.3% of rDNA related to that of Z. biebersteiniana. We assume that hexaploid Z. kochii is either an old allopolyploid or a homodiploid that has lost most of the rRNA genes obtained from Z. biebersteiniana. In Z. trichopoda about 81% of rDNA is related to rDNA of Z. biebersteiniana and 19% of rDNA is derived from Poa diaphora sensu lato. The composition of the ribotypes of the two plants determined by a taxonomy specialist as Z. pisidica and Z. trichopoda is very different. Two singleton species are proposed on this base with ribotypes as discriminative characters. So, in all four studied Zingeria species, even if the morphological difference among the studied species was modest, the genomic constitution was significantly different, which suggests that these are allopolyploids that obtained genomes from different ancestors.

scholarly journals First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lampet Wongsaroj ◽  
Ratmanee Chanabun ◽  
Naruemon Tunsakul ◽  
Pinidphon Prombutara ◽  
Somsak Panha ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Organic Fertilizer ◽  
The Other ◽  
Organic Fertilizers ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Physiochemical Properties ◽  
Nutrient Profiles ◽  
Soil Recovery ◽  
Local Farmers

AbstractNortheastern Thailand relies on agriculture as a major economic activity, and has used high levels of agrochemicals due to low facility, and salty sandy soil. To support soil recovery and sustainable agriculture, local farmers have used organic fertilizers from farmed animal feces. However, knowledge about these animal fecal manures remains minimal restricting their optimal use. Specifically, while bacteria are important for soil and plant growth, an abundance and a diversity of bacterial composition in these animal fecal manures have not been reported to allow selection and adjustment for a more effective organic fertilizer. This study thereby utilized metagenomics combined with 16S rRNA gene quantitative PCR (qPCR) and sequencing to analyze quantitative microbiota profiles in association with nutrients (N, P, K), organic matters, and the other physiochemical properties, of the commonly used earthworm manure and other manures from livestock animals (including breed and feeding diet variations) in the region. Unlike the other manures, the earthworm manure demonstrated more favorable nutrient profiles and physiochemical properties for forming fertile soil. Despite low total microbial biomass, the microbiota were enriched with maximal OTUs and Chao richness, and no plant pathogenic bacteria were found based on the VFDB database. The microbial metabolic potentials supported functions to promote crop growth, such as C, N and P cyclings, xenobiotic degradation, and synthesis of bioactive compounds. Pearson’s correlation analyses indicated that the quantitative microbiota of the earthworm manure were clustered in the same direction as N, and conductivity, salinity, and water content were essential to control the microbiota of animal manures.

scholarly journals Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Liuyang Fu ◽  
Qian Wang ◽  
Lina Li ◽  
Tao Lang ◽  
Junjia Guo ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Tandem Repeats ◽  
Genetic Research ◽  
Diploid Species ◽  
Reference Sequence ◽  
A Genome ◽  
Genome Map ◽  
Chromosomal Variants

Abstract Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

scholarly journals Camelina neglecta (Brassicaceae, Camelineae), a new diploid species from Europe

PhytoKeys ◽  
2019 ◽  
Vol 115 ◽  
pp. 51-57 ◽  
Author(s):  
Jordan R. Brock ◽  
Terezie Mandáková ◽  
Martin A. Lysak ◽  
Ihsan A. Al-Shehbaz
Keyword(s):  
New Species ◽  
Diploid Species ◽  
The Other

Camelinaneglecta is described as a new diploid species and its relationship to the other diploids of the genus and to the somewhat superficially similar tetraploid C.rumelica and hexaploid C.microcarpa, are discussed. SEM of seed and stem trichomes of the new species are presented.

Molecular cytogenetic analysis of feline leukemia virus insertions in cat lymphoid tumor cells

2010 ◽  
Vol 163 (2) ◽  
pp. 344-352 ◽  
Author(s):  
Yasuhito Fujino ◽  
Hitoshi Satoh ◽  
Koichi Ohno ◽  
Hajime Tsujimoto
Keyword(s):  
Tumor Cells ◽  
Cytogenetic Analysis ◽  
Leukemia Virus ◽  
Feline Leukemia Virus ◽  
Lymphoid Tumor ◽  
Molecular Cytogenetic

Perinatal findings and molecular cytogenetic analysis ofde novo partial trisomy 16q (16q22.1?qter) and partial monosomy 20q (20q13.3?qter)

2005 ◽  
Vol 25 (2) ◽  
pp. 112-118 ◽  
Author(s):  
Chih-Ping Chen ◽  
Shuan-Pei Lin ◽  
Chyi-Chyang Lin ◽  
Yueh-Chun Li ◽  
Schu-Rern Chern ◽  
...  
Keyword(s):  
Cytogenetic Analysis ◽  
Partial Trisomy ◽  
Partial Monosomy ◽  
Molecular Cytogenetic

A Centromeric Tandem Repeat Family Originating From a Part of Ty3/gypsy-Retroelement in Wheat and Its Relatives

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 665-672 ◽  
Author(s):  
Zhi-Jun Cheng ◽  
Minoru Murata
Keyword(s):  
In Situ Hybridization ◽  
Tandem Repeats ◽  
Diploid Species ◽  
Upstream Region ◽  
Aegilops Speltoides ◽  
Repeat Family ◽  
B Genome ◽  
Intervening Sequences ◽  
Wild Diploid Species

AbstractFrom a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that ∼250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity (∼53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

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