scholarly journals Long range assembly of sequences helps to unravel the genome structure and small variation of the wheat‐ Haynaldia villosa translocated chromosome 6VS 6AL

2021 ◽  
Author(s):  
Liping Xing ◽  
Lu Yuan ◽  
Zengshuai Lv ◽  
Qiang Wang ◽  
Chunhong Yin ◽  
...  
Keyword(s):  
Long Range ◽  
Genome Structure ◽  
Small Variation ◽  
Haynaldia Villosa

scholarly journals An Empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data

2021 ◽  
Vol 20 (1) ◽  
pp. 1-15
Author(s):  
Qi Zhang ◽  
Zheng Xu ◽  
Yutong Lai
Keyword(s):  
Long Range ◽  
Latent Variables ◽  
Empirical Bayes ◽  
Genome Structure ◽  
Peak Detection ◽  
Data Matrix ◽  
Dispersion Modeling ◽  
Empirical Bayes Approach ◽  
Over Dispersion ◽  
Bayes Approach

Abstract Hi-C experiments have become very popular for studying the 3D genome structure in recent years. Identification of long-range chromosomal interaction, i.e., peak detection, is crucial for Hi-C data analysis. But it remains a challenging task due to the inherent high dimensionality, sparsity and the over-dispersion of the Hi-C count data matrix. We propose EBHiC, an empirical Bayes approach for peak detection from Hi-C data. The proposed framework provides flexible over-dispersion modeling by explicitly including the “true” interaction intensities as latent variables. To implement the proposed peak identification method (via the empirical Bayes test), we estimate the overall distributions of the observed counts semiparametrically using a Smoothed Expectation Maximization algorithm, and the empirical null based on the zero assumption. We conducted extensive simulations to validate and evaluate the performance of our proposed approach and applied it to real datasets. Our results suggest that EBHiC can identify better peaks in terms of accuracy, biological interpretability, and the consistency across biological replicates. The source code is available on Github (https://github.com/QiZhangStat/EBHiC).

scholarly journals Long range genome structure around the human α-globin complex analysed by PFGE

1987 ◽  
Vol 15 (15) ◽  
pp. 6197-6207 ◽  
Author(s):  
N. Fischel-Ghodsian ◽  
R.D. Nicholls ◽  
D.R. Higgs
Keyword(s):  
Long Range ◽  
Genome Structure

scholarly journals An Empirical Bayes Approach for the Identification of Long-range Chromosomal Interaction from Hi-C Data

2018 ◽  
Author(s):  
Qi Zhang ◽  
Zheng Xu ◽  
Yutong Lai
Keyword(s):  
Long Range ◽  
Latent Variables ◽  
Empirical Bayes ◽  
Genome Structure ◽  
Peak Detection ◽  
Data Matrix ◽  
Dispersion Modeling ◽  
Empirical Bayes Approach ◽  
Over Dispersion ◽  
Bayes Approach

Hi-C experiments have become very popular for studying the 3D genome structure in recent years. Identification of long-range chromosomal interaction, i.e., peak detection, is crucial for Hi-C data analysis. But it remains a challenging task due to the inherent high dimensionality, sparsity and the over-dispersion of the Hi-C count data matrix. We propose EBHiC, an empirical Bayes approach for peak detection from Hi-C data. The proposed framework provides flexible over-dispersion modeling by explicitly including the 'true' interaction intensities as latent variables. To implement the proposed peak identification method (via the empirical Bayes test), we estimate the overall distributions of the observed counts semiparametrically using a smoothed EM algorithm, and the empirical null by discrete curve fitting. We conducted extensive simulations to validate and evaluate the performance of our proposed approach and applied it to real datasets. Our results suggest that EBHiC can better identify peaks than Fit-Hi-C in terms of accuracy, biological interpretability, and the consistency across biological replicates.

scholarly journals A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 285 ◽  
Author(s):  
Lisa S Mathew ◽  
Manuel Spannagl ◽  
Ameena Al-Malki ◽  
Binu George ◽  
Maria F Torres ◽  
...  
Keyword(s):  
Long Range ◽  
Genetic Map ◽  
Date Palm ◽  
Genome Structure ◽  
Phoenix Dactylifera ◽  
Structure Conservation

scholarly journals Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qian Xiong ◽  
Yuxin Hu ◽  
Wenqi Lv ◽  
Qinghua Wang ◽  
Guoxiang Liu ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Small Variation ◽  
Molecular Data ◽  
Evolutionary Relationships ◽  
Single Family ◽  
Chloroplast Genomes ◽  
Morphological Criteria ◽  
Cp Genome

Abstract Background The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales. Results The five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats. Conclusions Our results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

scholarly journals Chloroplast Genomes of Five Oedogonium Species: Genome Structure, Phylogenetic Analysis and Adaptive Evolution

2021 ◽  
Author(s):  
xiong qian ◽  
Yuxin Hu ◽  
Wenqi Lv ◽  
Qinghua Wang ◽  
Guoxiang Liu ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Small Variation ◽  
Molecular Data ◽  
Evolutionary Relationships ◽  
Chloroplast Genomes ◽  
Morphological Criteria ◽  
The Difference ◽  
Cp Genome

Abstract BackgroundThe order Oedogoniales can be divided into three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales.ResultsThe five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats.ConclusionsOur results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

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