Hybrids involving wheat relatives and autotetraploid Triticum umbellulatum

Genome ◽  
1989 ◽  
Vol 32 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Gordon Kimber ◽  
Yang Yen
Keyword(s):  
Numerical Methods ◽  
Chromosome Pairing ◽  
Genome Analysis ◽  
Reliable Method ◽  
Genomic Analysis ◽  
Conclusive Evidence ◽  
Diploid Progenitor ◽  
Substantial Evidence ◽  
Evolutionary Pathways ◽  
Specific Pairing

Genomic analysis based on chromosome pairing is perhaps the most reliable method of determining the major evolutionary pathways in allopolyploid series. Difficulties can arise when genomes have become modified, since then they will not correspond exactly to the genomes used as analysers. Some resolution of this type of problem is possible when the interpretation of meiotic data is enhanced by numerical methods. However, providing conclusive evidence of which chromosomes are pairing rather than just how many remains a problem unless specific chromosomes can be recognized. One possible solution is to make hybrids between natural polyploids and autotetraploids of the putative diploid progenitors. The recognition of specific pairing patterns in such hybrids will provide substantial evidence of which chromosomes are pairing at metaphase I. Hybrids between an autotetraploid Triticum umbellulatum and the natural U-genome polyploids T. kotschyi, T. neglecta, T. ovatum, T. macrochaetum, T. columnare, T. triunciale, and T. juvenale demonstrate that the U-genome of most of them is very closely related to the U-genome of the diploid T. umbellulatum. The U-genome in four hybrids in two accessions of T. ovatum does differ from its diploid progenitor, T. columnare shows some heterogeneity, and T. juvenale may show differentiation.Key words: autotetraploid, evolution, genome analysis, Triticum species, pivotal–differential evolution.

Genomic Analysis of Citrobacter Portucalensis Sb-2 Identifies a Phage Predation Driven Metalloid Resistance

2021 ◽  
Author(s):  
Yanshuang Yu ◽  
Zhenchen Xie ◽  
Jigang Yang ◽  
Jinxuan Liang ◽  
YuanPing Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Significant Role ◽  
Genome Analysis ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Resistant Bacterium ◽  
Bacterial Adaptation ◽  
Resistance Determinants

Abstract Bacterial adaptation to extreme environments is often mediated by horizontal gene transfer (HGT). At the same time, phage mediated HGT for conferring bacterial arsenite and antimonite resistance has not been documented before. In this study, a highly arsenite and antimonite resistant bacterium, C. portucalensis strain Sb-2, was isolated and subsequent genome analysis showed that putative arsenite and antimonite resistance determinants were flanked or embedded by prophages. We predict these phage-mediated resistances play a significant role in maintaining genetic diversity within the genus of Citrobacter and are responsible for endowing the corresponding resistances to C. portucalensis strain Sb-2.

Estimating meiotic chromosome pairing and recombination parameters in telocentric trisomics

Genome ◽  
2007 ◽  
Vol 50 (11) ◽  
pp. 1014-1028 ◽  
Author(s):  
J. Sybenga ◽  
H. Verhaar ◽  
D.G.A. Botje
Keyword(s):  
Gene Transfer ◽  
Chromosome Pairing ◽  
Genome Analysis ◽  
Meiotic Chromosome ◽  
Chiasma Formation ◽  
Chromosome Morphology ◽  
Test Material ◽  
Gene Localization ◽  
Maximum Information ◽  
Chromosome 1R

Telocentric trisomics (telotrisomics; one arm of a metacentric chromosome present in addition to two complete genomes) are used in theoretical studies of pairing affinities and chiasma formation in competitive situations and applied in genome analysis, gene localization, gene transfer, and breakage of close linkages. These applications require knowledge of the recombination characteristics of telotrisomics. Appropriate cytological and molecular markers and favorable chromosome morphology are not always available or applicable for quantitative analyses. We developed new mathematical models for extracting the maximum information from simple metaphase I observations. Two types of telotrisomics of the short arm of chromosome 1R of rye ( Secale cereale ), including several genotypes, were used as test material. In simple telotrisomics, pairing between morphologically identical complete chromosomes was more frequent than pairing between the telocentric and either of the normal chromosomes. In the telocentric substitution, morphologically identical telocentrics paired less frequently with each other than either one with the normal chromosome. Pairing partner switch was significant. Interaction between the two arms was variable. Variation within plants was considerable. Telotrisomics without markers are suitable for analyzing pairing preferences, for gene localization and gene transfer, and for breaking tight linkages, but less so for genome analysis.

scholarly journals First Steps in the Analysis of Prokaryotic Pan-Genomes

2020 ◽  
Vol 14 ◽  
pp. 117793222093806
Author(s):  
Sávio Souza Costa ◽  
Luís Carlos Guimarães ◽  
Artur Silva ◽  
Siomar Castro Soares ◽  
Rafael Azevedo Baraúna
Keyword(s):  
Genome Analysis ◽  
Core Genome ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Specific Group ◽  
The Core ◽  
Pan Genome ◽  
Research Areas ◽  
Key Concepts

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

scholarly journals Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P[4] human rotavirus strains

2011 ◽  
Vol 92 (9) ◽  
pp. 2201-2208 ◽  
Author(s):  
Souvik Ghosh ◽  
Noriaki Adachi ◽  
Zipporah Gatheru ◽  
James Nyangao ◽  
Dai Yamamoto ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Human Rotavirus ◽  
Genotype Constellation ◽  
Common Causes

Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1–5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.

Use of meiotic analysis to describe genomic affinities in Medicago

1984 ◽  
Vol 26 (6) ◽  
pp. 679-681 ◽  
Author(s):  
S. E. Smith
Keyword(s):  
Numerical Analysis ◽  
Numerical Methods ◽  
Chromosome Pairing ◽  
Meiotic Analysis

Numerical methods of meiotic analysis were used to describe genomic affinities in triploid Medicago hybrids. No differences in affinity were observed among the genomes of M. sativa subsp. sativa, M. sativa subsp. caerulea, and M. falcata. This study establishes the feasibility of using meiotic analysis in cytotaxonomic studies in Medicago.Key words: alfalfa, chromosome pairing, cytotaxonomy, numerical analysis.

scholarly journals Web-Based Genome Analysis of Bacterial Meningitis Pathogens for Public Health Applications Using the Bacterial Meningitis Genomic Analysis Platform (BMGAP)

2020 ◽  
Vol 11 ◽  
Author(s):  
Sean A. Buono ◽  
Reagan J. Kelly ◽  
Nadav Topaz ◽  
Adam C. Retchless ◽  
Hideky Silva ◽  
...  
Keyword(s):  
Public Health ◽  
Bacterial Meningitis ◽  
Sensitivity And Specificity ◽  
Genome Analysis ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Public Health Response ◽  
Analysis Platform

Effective laboratory-based surveillance and public health response to bacterial meningitis depends on timely characterization of bacterial meningitis pathogens. Traditionally, characterizing bacterial meningitis pathogens such as Neisseria meningitidis (Nm) and Haemophilus influenzae (Hi) required several biochemical and molecular tests. Whole genome sequencing (WGS) has enabled the development of pipelines capable of characterizing the given pathogen with equivalent results to many of the traditional tests. Here, we present the Bacterial Meningitis Genomic Analysis Platform (BMGAP): a secure, web-accessible informatics platform that facilitates automated analysis of WGS data in public health laboratories. BMGAP is a pipeline comprised of several components, including both widely used, open-source third-party software and customized analysis modules for the specific target pathogens. BMGAP performs de novo draft genome assembly and identifies the bacterial species by whole-genome comparisons against a curated reference collection of 17 focal species including Nm, Hi, and other closely related species. Genomes identified as Nm or Hi undergo multi-locus sequence typing (MLST) and capsule characterization. Further typing information is captured from Nm genomes, such as peptides for the vaccine antigens FHbp, NadA, and NhbA. Assembled genomes are retained in the BMGAP database, serving as a repository for genomic comparisons. BMGAP’s species identification and capsule characterization modules were validated using PCR and slide agglutination from 446 bacterial invasive isolates (273 Nm from nine different serogroups, 150 Hi from seven different serotypes, and 23 from nine other species) collected from 2017 to 2019 through surveillance programs. Among the validation isolates, BMGAP correctly identified the species for all 440 isolates (100% sensitivity and specificity) and accurately characterized all Nm serogroups (99% sensitivity and 98% specificity) and Hi serotypes (100% sensitivity and specificity). BMGAP provides an automated, multi-species analysis pipeline that can be extended to include additional analysis modules as needed. This provides easy-to-interpret and validated Nm and Hi genome analysis capacity to public health laboratories and collaborators. As the BMGAP database accumulates more genomic data, it grows as a valuable resource for rapid comparative genomic analyses during outbreak investigations.

The interspecific and evolutionary relationships of Triticum ovatum

Genome ◽  
1988 ◽  
Vol 30 (2) ◽  
pp. 218-221 ◽  
Author(s):  
Gordon Kimber ◽  
P. J. Sallee ◽  
M. M. Feiner
Keyword(s):  
Genome Analysis ◽  
Evolutionary Relationships ◽  
New Combinations ◽  
Diploid Progenitor ◽  
Meiotic Analysis ◽  
Theory Of Evolution ◽  
Substantial Modification ◽  
Wheat Group ◽  
M Genome

Meiotic analysis of 13 hybrids, 3 of which are new combinations, shows that the M genome of Triticum ovatum has undergone substantial modification. The pivotal U genome is much closer to its diploid progenitor, Triticum umbellulatum. However, the possibility exists that it too has been somewhat modified. If this is substantiated, then some reconsideration of the pivotal–differential theory of evolution in the wheat group may be required.Key words: genome analysis, meiosis, Aegilops, wheat.

Genome analysis of Elymus alatavicus and E. batalinii (Poaceae: Triticeae)

1986 ◽  
Vol 28 (5) ◽  
pp. 770-776 ◽  
Author(s):  
Kevin B. Jensen ◽  
Douglas R. Dewey ◽  
Kay H. Asay
Keyword(s):  
Chromosome Pairing ◽  
Genome Analysis ◽  
Taxonomic Classification ◽  
Meiotic Behaviour ◽  
Pseudoroegneria Spicata ◽  
Mode Of Reproduction ◽  
The Relationship ◽  
Partial Fertility ◽  
Metaphase I

Elymus alatavicus (Drob.) A. Love and E. batalinii (Krasn.) A. Love were studied to determine (i) meiotic behaviour, (ii) the mode of reproduction, (iii) the relationship between the two species, (iv) genomic constitutions, and (v) the most logical taxonomic classification of both species. A series of F1 hybrids between E. alatavicus, E. batalinii, and six "analyzer" species were developed. Chromosome pairing was studied at metaphase I to identify genomic similarities or differences. The results showed that E. alatavicus and E. batalinii are caespitose, self-fertile allohexaploids (2n = 42) with the same genomic formula SSYYXX. The F1 hybrids between E. alatavicus and E. batalinii had complete pairing (21 bivalents) at metaphase I in 7% of the cells and almost complete pairing in the remaining cells. High chromosome pairing and partial fertility (4 seeds/plant) in the F1 hybrids shows that the two species are closely related. Hybrids were obtained between E. alatavicus or E. batalinii and the following "analyzer" species with known genomic formulas: Pseudoroegneria spicata (Pursh) A. Love, 2n = 14, SS; P. cognata (Hack.) A. Love, 2n = 14, SS; E. lanceolatus (Scribn. &Smith) Gould, 2n = 28, SSHH; E. trachycaulus1 (Link) Gould ex Shinners, 2n = 28, SSHH; E. mutabilis (Drob.) Tzvelev, 2n = 28, SSHH; and E. drobovii (Nevski) Tzvelev, 2n = 42, SSHHYY. Chromosome pairing in this series of hybrids demonstrated that E. alatavicus and E. batalinii contain an S and probably a Y genome plus an unknown genome, X, that may have been derived from Psathryostachys huashanica Keng or from Agropyron. Elymus alatavicus and E. batalinii are correctly classified in the genus Elymus.Key words: cytotaxonomy, Agropyron, meiosis, chromosome.

Chromosome pairing in triploid and tetraploid hybrids in Elytrigia (Triticeae; Poaceae)

1984 ◽  
Vol 26 (5) ◽  
pp. 519-522 ◽  
Author(s):  
Patrick E. McGuire
Keyword(s):  
Chromosome Pairing ◽  
Genome Analysis ◽  
Triploid Hybrid ◽  
Pollen Mother Cells ◽  
Tetraploid Hybrid ◽  
A Genome ◽  
Mother Cells ◽  
Metaphase I

Mean chromosome pairing of 5.14I + 1.28II (rod) + 3.86II (ring) + 1.47III + 0.11IV (open) + 0.11V was observed in pollen mother cells at metaphase I in the triploid hybrid Elytrigia scirpea (K. Presl) Holub, 2n = 4x = 28 × E. bessarabica (Savul. et Rayss) Dubrovik, 2n = 4x = 14. Mean chromosome pairing of 3.71I + 2.29II (rod) + 1.82II (ring) + 2.64III + 0.29IV (open) was observed in the triploid hybrid E. curvifolia (Lange) Holub, 2n = 4x = 28 × E. bessarabica. Mean chromosome pairing of 3.00I + 0.93II (rod) + 1.57II (ring) + 1.36III + 1.79IV (open) + 1.I4IV (closed) + 0.79V was observed in the tetraploid hybrid E. junceiformis Löve et Löve, 2n = 4x = 28 × E. curvifolia. The first hybrid provides the first evidence by genome analysis that E. bessarabica possesses a genome (designated Eb) which is closely related to the genomes of E. scirpea (ES and ESC) and hence to the E genome of E. elongata (Host) Nevski, 2n = 2x = 14. The second and third hybrids provide the first evidence that the two genomes of E. curvifolia (designated EC and ECU) are related to the Eb genome of E. bessarabica and thus to the E genome of E. elongata.Key words: Elytrigia, homoeology, Triticum, phylogeny, triploid, tetraploid.

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