scholarly journals Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yumin Huang ◽  
Wei Huang ◽  
Zhuang Meng ◽  
Guilherme Tomaz Braz ◽  
Yunfei Li ◽  
...  
Keyword(s):  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Nucleolus Organizer ◽  
Evolutionary Forces ◽  
Large Size ◽  
Modern Maize ◽  
Evolutionary Variation ◽  
Suppressed Recombination ◽  
Maize Domestication ◽  
Environmental Fitness

Abstract Background Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation. Results In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement. Conclusions These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the “fossil” structure variations during genome evolution and speciation.

scholarly journals Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

2016 ◽  
Author(s):  
Sanzhen Liu ◽  
Jun Zheng ◽  
Pierre Migeon ◽  
Jie Ren ◽  
Ying Hu ◽  
...  
Keyword(s):  
Copy Number ◽  
Organizer Region ◽  
Repetitive Sequences ◽  
Nucleolus Organizer Region ◽  
Nucleolus Organizer ◽  
45S Rdna ◽  
Specific Expression ◽  
Rdna Sequences ◽  
Rdna Expression ◽  
Maize Domestication

AbstractThe major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere repeats, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Previously unknown genotype specific 45S rDNA sequences were discovered. The B73-specific 45S rDNA is not only located on the nucleolus organizer region (NOR) on chromosome 6 but also dispersed on all the chromosomes in B73, indicating the relatively recent spread of 45S rDNA from the NOR. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that dosage compensation operates for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 double haploids (DHs), genomic locations showing differential repetitive contents were genetically mapped. Analysis of WGS sequences of HapMap2 lines, including maize wild progenitor teosintes, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere repeats, 45S rDNA, knob, and retrotransposon sequences were found between teosinte and maize lines, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.

Mapping of the nucleolus organizer region on chromosome 4 inArabidopsis thaliana

1996 ◽  
Vol 250 (1) ◽  
pp. 123-128
Author(s):  
Georg Haberer ◽  
Thilo C. Fischer ◽  
Ramón A. Torres-Ruiz
Keyword(s):  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Nucleolus Organizer ◽  
Chromosome 4

Hybrid ape offspring of a mating of gibbon and siamang

Science ◽  
1979 ◽  
Vol 205 (4403) ◽  
pp. 308-310 ◽  
Author(s):  
RH Myers ◽  
DA Shafer
Keyword(s):  
Parental Species ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Structural Rearrangement ◽  
Female Offspring ◽  
Nucleolus Organizer ◽  
Single Chromosome ◽  
Symphalangus Syndactylus ◽  
Hylobates Moloch ◽  
Lesser Apes

The serendipitous mating of a male gibbon, Hylobates moloch, and a female siamang, Symphalangus syndactylus, has produced two female offspring born 1 year apart. The hybrid karyotype of 47 chromosomes comprises the haploid complements of the parental species, 22 for the gibbon and 25 for the siamang. Chromosomal G and C banding comparisons revealed no clear homologies between the parental karyotypes except for the single chromosome in each species containing the nucleolus organizer region. The lack of homology suggests that the structural rearrangement of chromosomes has played a major role in the process of speciation for these lesser apes.

scholarly journals The relationship between position and expression of genes on the kangaroo X chromosome suggests a tissue-specific spread of inactivation from a single control site

1988 ◽  
Vol 51 (2) ◽  
pp. 103-109 ◽  
Author(s):  
Jennifer A. Marshall Graves ◽  
Garey W. Dawson
Keyword(s):  
Alternative Hypothesis ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Control Site ◽  
Specific Pattern ◽  
Nucleolus Organizer ◽  
Tissue Specific ◽  
Expression Of Genes ◽  
Control Locus ◽  
The Relationship

SummaryIn marsupials, X chromosome inactivation is paternal and incomplete. The tissue-specific pattern of inactivation of X-linked loci (G6PD, PGK, GLA) has been attributed to a piecemeal inactivation of different regions of the X. We here propose an alternative hypothesis, in which inactivation of the marsupial X is a chromosome-wide event, but is differentially regulated in different tissues. This hypothesis was suggested by the relationship between the positions and activity of genes on the kangaroo paternal X. In the absence of an HPRT polymorphism, we have used somatic cell hybridization to assess the activity of the paternal HPRT allele in lymphocytes and fibroblasts. The absence of the paternal X, and of the paternal forms of G6PD or PGK, from 33 cell hybrids made by fusing HPRT-deficient rodent cells with lymphocytes or fibroblasts of heterozygous females, suggests that the HPRT gene on the paternal X is inactive in both tissues and therefore not selectable. Since HPRT is located medially on the Xq near GLA, which shares the same characteristics of activity, we suggest that the locus-specific and tissue-specific patterns of activity result from a differential spread of inactivation from a single control locus, located near HPRT and GLA, outwards in both directions to G6PD and PGK. The nucleolus organizer region on the short arm does not seem to be part of the inactivated unit.

scholarly journals Characterization of AtNUC-L1 Reveals a Central Role of Nucleolin in Nucleolus Organization and Silencing of AtNUC-L2 Gene in Arabidopsis

2007 ◽  
Vol 18 (2) ◽  
pp. 369-379 ◽  
Author(s):  
Frederic Pontvianne ◽  
Isabel Matía ◽  
Julien Douet ◽  
Sylvette Tourmente ◽  
Francisco J. Medina ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Normal Growth ◽  
Growth Conditions ◽  
Nucleolus Organizer ◽  
Multifunctional Protein ◽  
Eukaryotic Organism ◽  
Model Plant Arabidopsis Thaliana ◽  
Fibrillar Component

Nucleolin is one of the most abundant protein in the nucleolus and is a multifunctional protein involved in different steps of ribosome biogenesis. In contrast to animals and yeast, the genome of the model plant Arabidopsis thaliana encodes two nucleolin-like proteins, AtNUC-L1 and AtNUC-L2. However, only the AtNUC-L1 gene is ubiquitously expressed in normal growth conditions. Disruption of this AtNUC-L1 gene leads to severe plant growth and development defects. AtNUC-L1 is localized in the nucleolus, mainly in the dense fibrillar component. Absence of this protein in Atnuc-L1 plants induces nucleolar disorganization, nucleolus organizer region decondensation, and affects the accumulation levels of pre-rRNA precursors. Remarkably, in Atnuc-L1 plants the AtNUC-L2 gene is activated, suggesting that AtNUC-L2 might rescue, at least partially, the loss of AtNUC-L1. This work is the first description of a higher eukaryotic organism with a disrupted nucleolin-like gene and defines a new role for nucleolin in nucleolus structure and rDNA chromatin organization.

Meiotic behaviour of the holocentric chromosomes of Nezara viridula (Insecta, Heteroptera) analysed by C-banding and silver impregnation

1985 ◽  
Vol 27 (5) ◽  
pp. 491-497 ◽  
Author(s):  
J. P. M. Camacho ◽  
J. Belda ◽  
J. Cabrero
Keyword(s):  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Nucleolus Organizer ◽  
Silver Impregnation ◽  
Nezara Viridula ◽  
Holocentric Chromosomes ◽  
Cytological Analysis ◽  
C Banding ◽  
I Cells ◽  
Do So

While silver impregnation reveals the presence of kinetochores in monocentric chromosomes, it does not do so in the holocentric system of Nezara viridula. Here, C-banding and silver impregnation techniques reveal that C-heterochromatin is present in the greater part of the Y chromosome and at the nucleolus organizer region (NOR) of the largest autosome (A 1) and in the extra NOR located in the X chromosome of a single exceptional male. Furthermore, one telomere of each autosome appeared lightly C-banded. The largest, A1, bivalent shows chiasmata almost always located at the chromosome ends. This bivalent may orient axially or equatorially in metaphase I cells depending on whether it carries a single chiasma or two chiasmata, respectively. From our cytological analysis we deduce that centromeric activity is preferentially located at the two telomeric ends and that the presence of chiasmata at an end excludes such activity.Key words: diffuse centromere, C-banding, holocentric, insect chromosomes.

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