scholarly journals Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds

Chromosoma ◽  
2021 ◽  
Vol 130 (1) ◽  
pp. 15-25
Author(s):  
Phuong T. N. Hoang ◽  
Jean-Marie Rouillard ◽  
Jiří Macas ◽  
Ivona Kubalová ◽  
Veit Schubert ◽  
...  
Keyword(s):  
Growth Rate ◽  
Chromosome Number ◽  
Chromosome Evolution ◽  
Sequence Similarity ◽  
Flowering Plants ◽  
The Other ◽  
Probe Design ◽  
Congeneric Species ◽  
Specific Design ◽  
Spirodela Polyrhiza

AbstractDuckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera.

scholarly journals Animal chromosome counts reveal similar range of chromosome numbers but with less polyploidy in animals compared to flowering plants

2020 ◽  
Author(s):  
Cristian Román-Palacios ◽  
Cesar A. Medina ◽  
Shing H. Zhan ◽  
Michael S. Barker
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Chromosome Evolution ◽  
Chromosome Count ◽  
Flowering Plants ◽  
Similar Distribution ◽  
Chromosome Counts ◽  
Remarkable Similarity ◽  
Similar Range

AbstractUnderstanding the mechanisms that underlie chromosome evolution may provide insights into the processes underpinning the origin, persistence, and evolutionary tempo of lineages. Here we present the first database of chromosome counts for animals (the Animal Chromosome Count database, ACC) summarizing chromosome numbers for ∼18,000 species. We found remarkable similarity in the distribution of chromosome counts between animals and flowering plants. At larger timescales, selection towards a specific range might explain the similar distribution of chromosome counts between these two groups. Nevertheless, changes in chromosome number are still potential drivers of divergence among species at shorter timescales. We also found that while animals and plants exhibit similar frequencies of speciation-related changes in chromosome number, plant speciation is more often related to changes in ploidy. Based on the ACC, our analyses suggest that changes in chromosome number alone could help explain patterns of diversity within animal clades.

scholarly journals The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome

2021 ◽  
Author(s):  
Alexander Mackintosh ◽  
Dominik Laetsch ◽  
Tobias Baril ◽  
Robert Foster ◽  
Vlad Dincă ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Genome Assembly ◽  
Chromosome Evolution ◽  
Population Genomics ◽  
The Other ◽  
Z Chromosome ◽  
Valuable Resource ◽  
Male Individual ◽  
Show Evidence ◽  
Chromosome Level

The lesser marbled fritillary, Brenthis ino (Rottemburg, 1775), is a species of Palearctic butterfly. Male B. ino individuals have been reported to have between 12 and 14 pairs of chromosomes, a much reduced chromosome number than is typical in butterflies. Here we present a chromosome-level genome assembly for B. ino, as well as gene and transposable element annotations. The assembly is 411.8 Mb in span with contig and scaffold N50s of 9.6 and 29.5 Mb respectively. We also show evidence that the male individual from which we generated HiC data was heterozygous for a neo-Z chromosome, consistent with inheriting 14 chromosomes from one parent and 13 from the other. This genome assembly will be a valuable resource for studying chromosome evolution in Lepidoptera, as well as for comparative and population genomics more generally.

Growth and Performance of Agriculture Sector in India

2015 ◽  
Vol 3 (2) ◽  
Author(s):  
Naresh Singla ◽  
Mamandeep Kaur
Keyword(s):  
Growth Rate ◽  
Capital Formation ◽  
The Other ◽  
Agricultural Credit ◽  
Agricultural Growth ◽  
Indian Economy ◽  
Agriculture Sector ◽  
Food Grain ◽  
And Performance ◽  
Agricultural Labourers

The growth of agriculture and allied sectors is critical for the Indian economy as about 49 percent of the population is directly or indirectly dependent on agriculture. During the last decade and so, the agriculture sector has undergone profound changes resulting in sharp deceleration in its growth. The study has attempted to analyze growth and performance of the agriculture sector in India since 1980-81 and tries to comprehend some of the factors responsible for the deceleration in growth. The study has shown that agriculture sector has been able to show tremendous improvement in expansion of area and production of food grain and non-food grain crops. However, there are so many underlying factors responsible for slowdown of the agricultural growth. Some of the factors identified include: Increase in area under non-agriculture uses, excessive dependence on rain fed farming, increase in number of agricultural labourers, reducing size of the operation holdings, over use of agri-inputs, inequity in the distribution of agriculture credit along with sharp deceleration in public gross capital formation in agriculture etc. The study pointed in order to achieve higher growth rate, there is a need to enhance the gross capital formation in agriculture sector particularly on irrigation so that more area can be brought under assured irrigation. Bringing equity in distribution of agricultural credit coupled with judicious and need-based agricultural inputs are some of the other recommendations drawn based upon the study.

A polycentric growth model of gallium arsenide epitaxial layers from the gas phase with simultaneous diffusion, adsorption and chemical reaction

1988 ◽  
Vol 53 (12) ◽  
pp. 2995-3013
Author(s):  
Emerich Erdös ◽  
Jindřich Leitner ◽  
Petr Voňka ◽  
Josef Stejskal ◽  
Přemysl Klíma
Keyword(s):  
Growth Rate ◽  
Gallium Arsenide ◽  
Epitaxial Growth ◽  
Gas Phase ◽  
Surface Reaction ◽  
Quantitative Description ◽  
The Other ◽  
Rate Equations ◽  
Impact Interaction ◽  
Partial Pressures

For a quantitative description of the epitaxial growth rate of gallium arsenide, two models are proposed including two rate controlling steps, namely the diffusion of components in the gas phase and the surface reaction. In the models considered, the surface reaction involves a reaction triple - or quadruple centre. In both models three mechanisms are considered which differ one from the other by different adsorption - and impact interaction of reacting particles. In every of the six cases, the pertinent rate equations were derived, and the models have been confronted with the experimentally found dependences of the growth rate on partial pressures of components in the feed. The results are discussed with regard to the plausibility of individual mechanisms and of both models, and also with respect to their applicability and the direction of further investigations.

scholarly journals Independent pseudogenizations and losses of sox15 during amniote diversification following asymmetric ohnolog evolution

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yusaku Ogita ◽  
Kei Tamura ◽  
Shuuji Mawaribuchi ◽  
Nobuhiko Takamatsu ◽  
Michihiko Ito
Keyword(s):  
Sequence Similarity ◽  
The Other ◽  
Vertebrate Evolution ◽  
Skeletal Muscle Regeneration ◽  
Cns Development ◽  
Placental Development ◽  
Relaxed Selection ◽  
Significant Sequence Similarity ◽  
Anuran Amphibians ◽  
Divergent Gene

Abstract Background Four ohnologous genes (sox1, sox2, sox3, and sox15) were generated by two rounds of whole-genome duplication in a vertebrate ancestor. In eutherian mammals, Sox1, Sox2, and Sox3 participate in central nervous system (CNS) development. Sox15 has a function in skeletal muscle regeneration and has little functional overlap with the other three ohnologs. In contrast, the frog Xenopus laevis and zebrafish orthologs of sox15 as well as sox1-3 function in CNS development. We previously reported that Sox15 is involved in mouse placental development as neofunctionalization, but is pseudogenized in the marsupial opossum. These findings suggest that sox15 might have evolved with divergent gene fates during vertebrate evolution. However, knowledge concerning sox15 in other vertebrate lineages than therian mammals, anuran amphibians, and teleost fish is scarce. Our purpose in this study was to clarify the fate and molecular evolution of sox15 during vertebrate evolution. Results We searched for sox15 orthologs in all vertebrate classes from agnathans to mammals by significant sequence similarity and synteny analyses using vertebrate genome databases. Interestingly, sox15 was independently pseudogenized at least twice during diversification of the marsupial mammals. Moreover, we observed independent gene loss of sox15 at least twice during reptile evolution in squamates and crocodile-bird diversification. Codon-based phylogenetic tree and selective analyses revealed an increased dN/dS ratio for sox15 compared to the other three ohnologs during jawed vertebrate evolution. Conclusions The findings revealed an asymmetric evolution of sox15 among the four ohnologs during vertebrate evolution, which was supported by the increased dN/dS values in cartilaginous fishes, anuran amphibians, and amniotes. The increased dN/dS value of sox15 may have been caused mainly by relaxed selection. Notably, independent pseudogenizations and losses of sox15 were observed during marsupial and reptile evolution, respectively. Both might have been caused by strong relaxed selection. The drastic gene fates of sox15, including neofunctionalization and pseudogenizations/losses during amniote diversification, might be caused by a release from evolutionary constraints.

scholarly journals The Consequences of Budding versus Binary Fission on Adaptation and Aging in Primitive Multicellularity

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 661
Author(s):  
Hanna Isaksson ◽  
Peter L. Conlin ◽  
Ben Kerr ◽  
William C. Ratcliff ◽  
Eric Libby
Keyword(s):  
Cell Cycle ◽  
Growth Rate ◽  
Cellular Senescence ◽  
Carrying Capacity ◽  
The Other ◽  
Binary Fission ◽  
Fundamental Aspect ◽  
Accumulated Damage ◽  
Cell Age ◽  
Multicellular Organisms

Early multicellular organisms must gain adaptations to outcompete their unicellular ancestors, as well as other multicellular lineages. The tempo and mode of multicellular adaptation is influenced by many factors including the traits of individual cells. We consider how a fundamental aspect of cells, whether they reproduce via binary fission or budding, can affect the rate of adaptation in primitive multicellularity. We use mathematical models to study the spread of beneficial, growth rate mutations in unicellular populations and populations of multicellular filaments reproducing via binary fission or budding. Comparing populations once they reach carrying capacity, we find that the spread of mutations in multicellular budding populations is qualitatively distinct from the other populations and in general slower. Since budding and binary fission distribute age-accumulated damage differently, we consider the effects of cellular senescence. When growth rate decreases with cell age, we find that beneficial mutations can spread significantly faster in a multicellular budding population than its corresponding unicellular population or a population reproducing via binary fission. Our results demonstrate that basic aspects of the cell cycle can give rise to different rates of adaptation in multicellular organisms.

Aspidistra revoluta, a new species from limestone areas in Chongqing, China

Phytotaxa ◽  
2016 ◽  
Vol 257 (3) ◽  
pp. 280 ◽  
Author(s):  
Hao Zhou ◽  
Si-rong Yi ◽  
Qi Gao ◽  
Jie Huang ◽  
Yu-jing Wei
Keyword(s):  
New Species ◽  
Chromosome Number ◽  
Average Length ◽  
Chromosome Complement ◽  
Pollen Grains ◽  
The Other ◽  
Morphological Comparison ◽  
Chongqing Municipality ◽  
Karyotype Asymmetry ◽  
A New Species

Aspidistra revoluta (Asparagaceae) is described and illustrated as a new species from limestone areas in southern Chongqing Municipality, China. The new species can be distinguished from the other Aspidistra species by its unique umbrella-like pistil with large revolute stigma lobes that bent downwards and touch the base of the perigone. A detailed morphological comparison among A. revoluta, A. nanchuanensis and A. carnosa is provided. The pollen grains of A. revoluta are subspherical and inaperturate, with verrucous exine. The chromosome number is 2n = 38, and the karyotype is formulated as 2n = 22m + 6sm + 10st. The average length of chromosome complement is 4.50 μm, and the karyotype asymmetry indexes A1 and A2 are respectively 0.37±0.03 and 0.49±0.01.

Direct Nucleation of Crystalline SiGe on Substrates by Reactive Thermal CVD with Si2H6 and GeF4

1997 ◽  
Vol 467 ◽  
Author(s):  
Fumio Yoshizawa ◽  
Kunihiro Shiota ◽  
Daisuke Inoue ◽  
Jun-ichi Hanna
Keyword(s):  
Growth Rate ◽  
Gas Phase ◽  
Heterogeneous Nucleation ◽  
Homogeneous Nucleation ◽  
Film Growth ◽  
Early Stage ◽  
Gaseous Mixture ◽  
The Other ◽  
Thermal Cvd ◽  
Initial Deposition

ABSTRACTPolycrystalline SiGe (poly-SiGe) film growth by reactive thermal CVD with a gaseous mixture of Si2H6 and GeF4 was investigated on various substrates such as Al,Cr, Pt, Si, ITO, ZnO and thermally grown SiO2.In Ge-rich film growth, SEM observation in the early stage of the film growth revealed that direct nucleation of crystallites took place on the substrates. The nucleation was governed by two different mechanisms: one was a heterogeneous nucleation on the surface and the other was a homogeneous nucleation in the gas phase. In the former case, the selective nucleation was observed at temperatures lower than 400°C on metal substrates and Si, where the activation of adsorbed GeF4 on the surface played a major role for the nuclei formation, leading to the selective film growth.On the other hand, the direct nucleation did not always take place in Si-rich film growth irrespective of the substrates and depended on the growth rate. In a growth rate of 3.6nm/min, the high crystallinity of poly-Si0.95Ge0.05in a 220nm-thick film was achieved at 450°C due to the no initial deposition of amorphous tissue on SiO2 substrates.

Speciation of cestoda. Evidence for two sibling species in the complex Bothrimonus nylandicus (Schneider 1902) (Cestoda: Cyathocephalidea)

Parasitology ◽  
1988 ◽  
Vol 97 (1) ◽  
pp. 139-147 ◽  
Author(s):  
F. Renaud ◽  
C. Gabrion
Keyword(s):  
Sibling Species ◽  
Definitive Host ◽  
Parasite Species ◽  
Adult Stage ◽  
Life Cycles ◽  
The Other ◽  
Congeneric Species ◽  
Biochemical Genetic ◽  
Autumn And Winter ◽  
Biological Differences

SUMMARYUsing biochemical genetic methods, we have distinguished 2 sibling species in the complex Bothrimonus nylandicus (Schneider, 1902), which infest 2 congeneric species of sole (Solea lascaris and Solea impar) on European coasts (Atlantic and Mediterranean). Neither of the parasite species is specific for either of the sole species, but one of them is present all year round, whereas the other is absent in the autumn and winter and only appears in the spring, subsequently disappearing at the end of the summer. Only S. impar lives in the Mediterranean, and is equally infested by both cestodes, whereas both species occur in the Atlantic and each of them is preferentially infested by 1 species of cestode. The shortness of the adult stage of the parasite in the definitive host and the presence of 2 life-cycles associated with competition between the 2 hosts in the Atlantic could be responsible for the biological differences observed and for maintaining the sibling species in sympatry.

scholarly journals The ameliorative effect of selenium on Azolla caroliniana grown under UV-B stress

2015 ◽  
Vol 95 (1) ◽  
pp. 20-26 ◽  
Author(s):  
E.M. Mostafa ◽  
A.M.A. Hassan
Keyword(s):  
Growth Rate ◽  
Protein Content ◽  
Doubling Time ◽  
The Other ◽  
Total Glutathione ◽  
Nutrient Media ◽  
Relative Growth ◽  
Other Hand ◽  
Ameliorative Effect ◽  
Glutathione Redox

Exposure ofAzollaplants to UV-B radiation for 6 h resulted in a decrease in biomass and relative growth rate (RGR), which coincided with an increase in doubling time (DT) as compared with the control. Also, the protein content decreased. On the other hand, hydrogen peroxyde (H2O2) and malondialdehyde (MDA) accumulated significantly in UV-treatedAzollaplants. Conversely, the addition of selenium (Se) at 1 ppm resulted in a significant increase in biomass and protein content of untreated and UV-treatedAzollaplants, and a significant reduction in both H2O2and MDA. Moreover, the addition of Se to UV-treated and untreatedAzollaplants resulted in a significant increase in total ascorbate and total glutathione (GSH) contents compared with the control and UV-stressedAzollaplants. Also, glutathione redox potential (GSH/TG) increased significantly in UV-treatedAzollaplants in the presence of Se. There also was a significant increase (38%) in ascorbate peroxidase (APX) activity in UV-treated plants compared with the control. APX activity in the presence of Se did not change significantly compared with the control. Glutathione reductase (GR) activity increased significantly in UV-treatedAzolla, while glutathione peroxidase (GSH-PX) activity did not. On the other hand, both GSH-PX and GR activity in untreated and UV-treatedAzollaplants were significantly enhanced by the application of Se to the nutrient media at a concentration of 1 ppm. Therefore, we can conclude that Se protectsAzollaplants from UV-B stress.

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