scholarly journals Genome-Wide Analysis and Expression Profiling of HD-ZIP III Genes in Three Brassica Species

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 684
Author(s):  
Han Wang ◽  
Wenna Shao ◽  
Min Yan ◽  
Ye Xu ◽  
Shaohua Liu ◽  
...  
Keyword(s):  
Leucine Zipper ◽  
Brassica Species ◽  
Class Iii ◽  
Transcription Profiling ◽  
Promoter Regions ◽  
Single Nucleotide ◽  
Response Diversity ◽  
Genome Wide ◽  
Gene Expression Levels

Class III homeodomain-leucine zipper (HD-ZIP III) genes encode plant-specific transcription factors that play pivotal roles in plant growth and development. There is no systematic report on HD-ZIP III members in Brassica plants and their responses to stress are largely unknown. In this study, a total of 10, 9 and 16 HD-ZIP III genes were identified from B. rapa, B. oleracea and B. napus, respectively. The phylogenetic analysis showed that HD-ZIP III proteins were grouped into three clades: PHB/PHV, REV and CNA/HB8. Genes in the same group tended to have similar exon–intron structures. Various phytohormone-responsive elements and stress-responsive elements were detected in the promoter regions of HD-ZIP III genes. Gene expression levels in different tissues, as well as under different stress conditions, were investigated using public transcription profiling data. The HD-ZIP III genes were constitutively expressed among all the tested tissues and were highly accumulated in root and stem. In B. rapa, only one BrREV gene especially responded to heat stress, BrPHB and BrREV members were downregulated upon cold stress and most HD-ZIP III genes exhibited divergent responses to drought stress. In addition, we investigated the genetic variation at known miR165/166 complementary sites of the identified HD-ZIP III genes and found one single nucleotide polymorphism (SNP) in PHB members and two SNPs in REV members, which were further confirmed using Sanger sequencing. Taken together, these results provide information for the genome-wide characterization of HD-ZIP III genes and their stress response diversity in Brassica species.

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

scholarly journals Transcriptome-wide Identification and Characterization of microRNAs and Their Targets in a Highly Adaptable Conifer Platycladus orientalis

2022 ◽  
Vol 147 (1) ◽  
pp. 7-17
Author(s):  
Ying Yang ◽  
Xian-Ge Hu ◽  
Bingsong Zheng ◽  
Yue Li ◽  
Tongli Wang ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Leucine Zipper ◽  
Class Iii ◽  
Conifer Species ◽  
Essential Information ◽  
Sequencing Platform ◽  
Platycladus Orientalis ◽  
Wide Range ◽  
Identification And Characterization

MicroRNAs (miRNAs) are short noncoding RNAs (20–25 nucleotides) that regulate gene expression posttranscriptionally. However, identification and characterization of miRNAs remain limited for conifer species. In this study, we applied transcriptome-wide miRNAs sequencing to a conifer species Platycladus orientalis, which is highly adaptable to a wide range of environmental adversities, including drought, barren soil, and mild salinity. A total of 17,181,542 raw reads were obtained from the Illumina sequencing platform; 31 conserved and 91 novel miRNAs were identified, and their unique characteristics were further analyzed. Ten randomly selected miRNAs were validated by quantificational real-time polymerase chain reaction. Through miRNA target predictions based on psRNATarget, 2331 unique mRNAs were predicted to be targets of P. orientalis miRNAs that involved in 187 metabolic pathways in KEGG database. These targets included not only important transcription factors (e.g., class III homeodomain leucine zipper targeted by por-miR166d) but also indispensable nontranscriptional factor proteins (i.e., por-miR482a-3p regulated nucleotide-binding site leucine-rich repeat protein). Interestingly, six miRNAs (por-miR16, -miR44, -miR60-5p, -miR69–3p, -miR166b-5p, and -miR395c) were found in adaptation-related pathways (e.g., drought), indicating their possible involved in this species’ stress-tolerance characteristics. The present study provided essential information for understanding the regulatory role of miRNAs in P. orientalis and sheds light on their possible use in tree improvement for stress tolerance.

scholarly journals Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Weizhuo Zhu ◽  
Yiyi Guo ◽  
Yeke Chen ◽  
Dezhi Wu ◽  
Lixi Jiang
Keyword(s):  
Brassica Napus ◽  
Stress Condition ◽  
Expression Patterns ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Good Opportunity ◽  
Domain Structures ◽  
Genome Wide ◽  
A Genome

Abstract Background Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. Results In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus. Conclusion The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.

Isolation and characterization of a class III homeodomain-leucine zipper-like gene fromGossypium barbadense

DNA Sequence ◽  
2006 ◽  
Vol 17 (5) ◽  
pp. 334-341 ◽  
Author(s):  
Chengxiang Qiu ◽  
Kaijing Zuo ◽  
Jie Qin ◽  
Jingya Zhao ◽  
Hua Ling ◽  
...  
Keyword(s):  
Leucine Zipper ◽  
Class Iii ◽  
Isolation And Characterization

scholarly journals Chromosome-Wide Characterization of Intragenic Crossover in Shiitake Mushroom, Lentinula edodes

2021 ◽  
Vol 7 (12) ◽  
pp. 1076
Author(s):  
Wenbing Gong ◽  
Nan Shen ◽  
Lin Zhang ◽  
Yinbing Bian ◽  
Yang Xiao
Keyword(s):  
Lentinula Edodes ◽  
Critical Role ◽  
Central Component ◽  
Nucleotide Polymorphisms ◽  
Single Spore ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Cis And Trans ◽  
Qtls Mapping

Meiotic crossover plays a critical role in generating genetic variations and is a central component of breeding. However, our understanding of crossover in mushroom-forming fungi is limited. Here, in Lentinula edodes, we characterized the chromosome-wide intragenic crossovers, by utilizing the single-nucleotide polymorphisms (SNPs) datasets of an F1 haploid progeny. A total of 884 intragenic crossovers were identified in 110 single-spore isolates, the majority of which were closer to transcript start sites. About 71.5% of the intragenic crossovers were clustered into 65 crossover hotspots. A 10 bp motif (GCTCTCGAAA) was significantly enriched in the hotspot regions. Crossover frequencies around mating-type A (MAT-A) loci were enhanced and formed a hotspot in L. edodes. Genome-wide quantitative trait loci (QTLs) mapping identified sixteen crossover-QTLs, contributing 8.5–29.1% of variations. Most of the detected crossover-QTLs were co-located with crossover hotspots. Both cis- and trans-QTLs contributed to the nonuniformity of crossover along chromosomes. On chr2, we identified a QTL hotspot that regulated local, global crossover variation and crossover hotspot in L. edodes. These findings and observations provide a comprehensive view of the crossover landscape in L. edodes, and advance our understandings of conservation and diversity of meiotic recombination in mushroom-forming fungi.

scholarly journals Genome-Wide Characterization of SPL Gene Family in Codonopsis pilosula Reveals the Functions of CpSPL2 and CpSPL10 in Promoting the Accumulation of Secondary Metabolites and Growth of C. pilosula Hairy Root

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1588
Author(s):  
Jing Yang ◽  
Zhonglong Guo ◽  
Wentao Wang ◽  
Xiaoyan Cao ◽  
Xiaozeng Yang
Keyword(s):  
Physcomitrella Patens ◽  
Light Stress ◽  
Promoter Regions ◽  
Cis Acting ◽  
Codonopsis Pilosula ◽  
Genome Data ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors play critical roles in regulating diverse aspects of plant growth and development, including vegetative phase change, plant architecture, anthocyanin accumulation, lateral root growth, etc. In the present study, 15 SPL genes were identified based on the genome data of Codonopsis pilosula, a well-known medicinal plant. Phylogenetic analysis clustered CpSPLs into eight groups (G1-G8) along with SPLs from Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa and Physcomitrella patens. CpSPLs in the same group share similar gene structure and conserved motif composition. Cis-acting elements responding to light, stress and phytohormone widely exist in their promoter regions. Our qRT-PCR results indicated that 15 CpSPLs were differentially expressed in different tissues (root, stem, leaf, flower and calyx), different developmental periods (1, 2 and 3 months after germination) and various conditions (NaCl, MeJA and ABA treatment). Compared with the control, overexpression of CpSPL2 or CpSPL10 significantly promoted not only the growth of hairy roots, but also the accumulation of total saponins and lobetyolin. Our results established a foundation for further investigation of CpSPLs and provided novel insights into their biological functions. As far as we know, this is the first experimental research on gene function in C. pilosula.

scholarly journals Evolutionary adaptability linked to length variation in short genic tandem repeats

2018 ◽  
Author(s):  
William B Reinar ◽  
Jonfinn B Knutsen ◽  
Sissel Jentoft ◽  
Ole K Tørresen ◽  
Melinka A Butenko ◽  
...  
Keyword(s):  
Protein Function ◽  
Tandem Repeats ◽  
Phenotypic Traits ◽  
Length Variation ◽  
Interaction Sites ◽  
Genome Wide ◽  
Mutational Hotspots ◽  
Intergenic Regions ◽  
Gene Expression Levels

AbstractThere is increasing evidence that short tandem repeats (STRs) – mutational hotspots present in genes and in intergenic regions throughout most genomes – may influence gene and protein function and consequently affect the phenotype of an organism. However, the overall importance of STRs and their standing genetic variation within a population, e.g. if and how they facilitate evolutionary change and local adaptation, is still debated. Through genome-wide characterization of STRs in over a thousand wild Arabidopsis thaliana accessions we demonstrate that STRs display significant variation in length across the species’ geographical distribution. We find that length variants are correlated with environmental conditions, key adaptive phenotypic traits as well as gene expression levels. Further, we show that coding STRs are overrepresented in putative protein interaction sites. Taken together, our results suggest that these hypervariable loci play a major role in facilitating adaptation in plants, and due to the ubiquitous presence of STRs throughout the tree of life, similar roles in other organisms are likely.

scholarly journals A robust two-sample Mendelian Randomization method integrating GWAS with multi-tissue eQTL summary statistics

2020 ◽  
Author(s):  
Kevin J. Gleason ◽  
Fan Yang ◽  
Lin S. Chen
Keyword(s):  
Mixed Model ◽  
Mendelian Randomization ◽  
Summary Statistics ◽  
Nucleotide Polymorphisms ◽  
Model Framework ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Causal Genes ◽  
Detect Gene Expression ◽  
Gene Expression Levels

AbstractIn the post-genome-wide association era, two-sample Mendelian Randomization (MR) methods have been applied to detect genetically-regulated risk factors for complex diseases. Two-sample MR considers single nucleotide polymorphisms (SNPs) associated with a putative exposure as instrumental variables (IVs) to assess the effect of the exposure on an outcome by leveraging two sets of summary statistics: IV-to-exposure and IV-to-outcome statistics from existing GWASs. Traditional MR methods impose strong assumptions on the validity of IVs, and recent literature has relaxed the assumptions allowing some IVs to be invalid but generally requiring a large number of nearly independent IVs. When treating expression-quantitative-trait-loci (eQTLs) as IVs to detect gene expression levels affecting diseases, existing methods are limited in applicability since the numbers of independent eQTLs for most genes in the genome are limited. To address those challenges, we propose a robust two-sample MR framework that requires fewer IVs and allows moderate IV correlations and some IVs to be invalid. This is achieved by leveraging existing multi-tissue eQTL summary statistics (multiple sets of IV-to-exposure statistics) and GWAS statistics in a mixed model framework. We conducted simulation studies to evaluate the performance of the proposed method and apply it to detect putative causal genes for schizophrenia.

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