Methods for Cytogenetic Chromosome Barcoding and Chromosome Painting in Brachypodium distachyon and Its Relative Species

Idziak-Helmcke, Dominika; Betekhtin, Alexander

doi:10.1007/978-1-4939-7278-4_1

Cited by 4 publications

(4 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The availability of the B. distachyon whole-genome sequence [4] () combined with FISH using low-repeat BAC (bacterial artificial chromosomes) clones as probes [36,37,38] enabled the precise dissection of the chromosome structure at the microscopic level via selective visualization of either their smaller (via CCB) or larger (including entire chromosomes: via CCP) regions. Apart from Brachypodium , similar approaches are limited in plants to a handful of small-genome taxa within Brassicaceae [39,40], Cucumis [41], rice [42], and, recently, also in maize [43].…”

Section: Introductionmentioning

confidence: 99%

Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution

Lusinska

Betekhtin

López-Álvarez

et al. 2019

IJMS

Self Cite

View full text Add to dashboard Cite

The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables the reconstruction of the evolutionary history of individual chromosomes and their segments, allowed us to infer the relationships between putative ancestral karyotypes of extinct species and extant karyotypes of current species. We used over 80 chromosome-specific BAC (bacterial artificial chromosome) clones derived from five reference chromosomes of B. distachyon as probes against the karyotypes of twelve accessions representing five diploid and polyploid Brachypodium perennials. The results showed that descending dysploidy is common in Brachypodium and occurs primarily via nested chromosome fusions. Brachypodium distachyon was rejected as a putative ancestor for allotetraploid perennials and B. stacei for B. mexicanum. We propose two alternative models of perennial polyploid evolution involving either the incorporation of a putative x = 5 ancestral karyotype with different descending dysploidy patterns compared to B. distachyon chromosomes or hybridization of two x = 9 ancestors followed by genome doubling and descending dysploidy. Details of the karyotype structure and evolution in several Brachypodium perennials are revealed for the first time.

show abstract

Section: Introductionmentioning

confidence: 99%

Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution

Lusinska

Betekhtin

López-Álvarez

et al. 2019

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…Mitotic chromosome preparations of the root meristems were made according to a previously described procedure [65] with minor modifications. The seeds of oat-maize addition lines, oat cv.…”

Section: Chromosome Preparationsmentioning

confidence: 99%

“…The in situ hybridization procedure was adopted from [65] with minor modifications. In brief, the slides were pre-treated with RNase, washed several times in a 2× saline sodium citrate (SSC) buffer, dehydrated in an ethanol series (70%, 90%, 100%), and air-dried.…”

Section: Dna Labeling and In Situ Hybridizationmentioning

confidence: 99%

3-D Nucleus Architecture in Oat × Maize Addition Lines

Idziak-Helmcke

Warzecha

Sowa

et al. 2020

IJMS

Self Cite

View full text Add to dashboard Cite

The nucleus architecture of hybrid crop plants is not a well-researched topic, yet it can have important implications for their genetic stability and usefulness in the successful expression of agronomically desired traits. In this work we studied the spatial distribution of introgressed maize chromatin in oat × maize addition lines with the number of added maize chromosomes varying from one to four. The number of chromosome additions was confirmed by genomic in situ hybridization (GISH). Maize chromosome-specific simple sequence repeat (SSR) markers were used to identify the added chromosomes. GISH on 3-D root and leaf nuclei was performed to assess the number, volume, and position of the maize-chromatin occupied regions. We revealed that the maize chromosome territory (CT) associations of varying degree prevailed in the double disomic lines, while CT separation was the most common distribution pattern in the double monosomic line. In all analyzed lines, the regions occupied by maize CTs were located preferentially at the nuclear periphery. A comparison between the tissues showed that the maize CTs in the leaf nuclei are positioned closer to the center of the nucleus than in the root nuclei. These findings shed more light on the processes that shape the nucleus architecture in hybrids.

show abstract

“…The molecular cytogenetic studies advanced greatly with the development of Brachypodium bacterial artificial chromosome (BAC) libraries [29]. These resources coupled with the sequenced genome of Brachypodium provided insight into grass karyotype evolution [30]. Brachypodium shares an extensive synteny among other grasses, so it was a good structural model for the assembly of large genomes [28].…”

Section: Introductionmentioning

confidence: 99%

Reconstruction of evolutionary trajectories of chromosomes unraveled independent genomic repatterning between Triticeae and Brachypodium

Wang

Pan

et al. 2019

BMC Genomics

View full text Add to dashboard Cite

Background After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidization, after which the originally doubled chromosome numbers reduced to different chromosome numbers among them. A telomere-centric reduction model was proposed previously to explain chromosome number reduction. With Brachpodium as an intermediate linking different major lineages of grasses and a model plant of the Pooideae plants, we wonder whether it mediated the evolution from ancestral grass karyotype to Triticeae karyotype. Results By inferring the homology among Triticeae, rice, and Brachpodium chromosomes, we reconstructed the evolutionary trajectories of the Triticeae chromosomes. By performing comparative genomics analysis with rice as a reference, we reconstructed the evolutionary trajectories of Pooideae plants, including Ae. Tauschii (2n = 14, DD), barley (2n = 14), Triticum turgidum (2n = 4x = 28, AABB), and Brachypodium (2n = 10). Their extant Pooidea and Brachypodium chromosomes were independently produced after sequential nested chromosome fusions in the last tens of millions of years, respectively, after their split from rice. More frequently than would be expected by chance, in Brachypodium , the ‘invading’ and ‘invaded’ chromosomes are homoeologs, originating from duplication of a common ancestral chromosome, that is, with more extensive DNA-level correspondence to one another than random chromosomes, nested chromosome fusion events between homoeologs account for three of seven cases in Brachypodium ( P -value≈0.00078). However, this phenomenon was not observed during the formation of other Pooideae chromosomes. Conclusions Notably, we found that the Brachypodium chromosomes formed through exclusively distinctive trajectories from those of Pooideae plants, and were well explained by the telomere-centric model. Our work will contribute to understanding the structural and functional innovation of chromosomes in different Pooideae lineages and beyond. Electronic supplementary material The online version of this article (10.1186/s12864-019-5566-8) contains supplementary material, which is available to authorized users.

show abstract

Methods for Cytogenetic Chromosome Barcoding and Chromosome Painting in Brachypodium distachyon and Its Relative Species

Cited by 4 publications

References 10 publications

Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution

Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution

3-D Nucleus Architecture in Oat × Maize Addition Lines

Reconstruction of evolutionary trajectories of chromosomes unraveled independent genomic repatterning between Triticeae and Brachypodium

Contact Info

Product

Resources

About