scholarly journals Genome-Wide Identification and Characterization of theLRR-RLKGene Family in TwoVerniciaSpecies

2015 ◽  
Vol 2015 ◽  
pp. 1-17 ◽  
Author(s):  
Huiping Zhu ◽  
Yangdong Wang ◽  
Hengfu Yin ◽  
Ming Gao ◽  
Qiyan Zhang ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Consensus Sequence ◽  
Expression Patterns ◽  
Functional Studies ◽  
Industrial Oil ◽  
Extensive Evaluation ◽  
Genome Wide ◽  
Pathogen Response ◽  
Lrr Domain

Leucine-rich repeat receptor-like kinases (LRR-RLKs) make up the largest group of RLKs in plants and play important roles in many key biological processes such as pathogen response and signal transduction. To date, most studies on LRR-RLKs have been conducted on model plants. Here, we identified 236 and 230LRR-RLKsin two industrial oil-producing trees:Vernicia fordiiandVernicia montana, respectively. Sequence alignment analyses showed that the homology of the RLK domain (23.81%) was greater than that of the LRR domain (9.51%) among theVf/VmLRR-RLKs. The conserved motif of the LRR domain inVf/VmLRR-RLKsmatched well the known plant LRR consensus sequence but differed at the third last amino acid (W or L). Phylogenetic analysis revealed thatVf/VmLRR-RLKswere grouped into 16 subclades. We characterized the expression profiles ofVf/VmLRR-RLKsin various tissue types including root, leaf, petal, and kernel. Further investigation revealed thatVf/VmLRR-RLKorthologous genes mainly showed similar expression patterns in response to tree wilt disease, except 4 pairs ofVf/VmLRR-RLKsthat showed opposite expression trends. These results represent an extensive evaluation ofLRR-RLKsin two industrial oil trees and will be useful for further functional studies on these proteins.

scholarly journals Genome-Wide Identification and Characterization of Fox Genes in the Honeybee, Apis cerana, and Comparative Analysis with Other Bee Fox Genes

2018 ◽  
Vol 2018 ◽  
pp. 1-12
Author(s):  
Hongyi Nie ◽  
Haiyang Geng ◽  
Yan Lin ◽  
Shupeng Xu ◽  
Zhiguo Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Bombus Terrestris ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Apis Cerana ◽  
Tissue Expression ◽  
Genome Wide ◽  
Fox Genes

The forkhead box (Fox) gene family, one of the most important families of transcription factors, participates in various biological processes. However, Fox genes in Hymenoptera are still poorly known. In this study, 14 Fox genes were identified in the genome of Apis cerana. In addition, 16 (Apis mellifera), 13 (Apis dorsata), 16 (Apis florea), 17 (Bombus terrestris), 16 (Bombus impatiens), and 18 (Megachile rotundata) Fox genes were identified in their genomes, respectively. Phylogenetic analyses suggest that FoxA is absent in the genome of A. dorsata genome. Similarly, FoxG is missing in the genomes A. cerana and A. dorsata. Temporal expression profiles obtained by quantitative real-time PCR revealed that Fox genes have distinct expression patterns in A. cerana, especially for three genes ACSNU03719T0 (AcFoxN4), ACSNU05765T0 (AcFoxB), and ACSNU07465T0 (AcFoxL2), which displayed high expression at the egg stage. Tissue expression patterns showed that FoxJ1 is significantly higher in the antennae of A. cerana and A. mellifera compared to other tissues. These results may facilitate a better understanding of the potential physiological functions of the Fox gene family in A. cerana and provide valuable information for a comprehensive functional analysis of the Fox gene family in Hymenopterans.

scholarly journals Genome-Wide Identification of Banana Csl Gene Family and Their Different Responses to Low Temperature between Chilling-Sensitive and Tolerant Cultivars

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 122
Author(s):  
Weina Yuan ◽  
Jing Liu ◽  
Tomáš Takáč ◽  
Houbin Chen ◽  
Xiaoquan Li ◽  
...  
Keyword(s):  
Low Temperature ◽  
Expression Patterns ◽  
Rna Seq ◽  
Plant Tolerance ◽  
Quantitative Real Time Pcr ◽  
Genomic Features ◽  
Functional Studies ◽  
Genome Wide ◽  
Gene Structures

The cell wall plays an important role in responses to various stresses. The cellulose synthase-like gene (Csl) family has been reported to be involved in the biosynthesis of the hemicellulose backbone. However, little information is available on their involvement in plant tolerance to low-temperature (LT) stress. In this study, a total of 42 Csls were identified in Musa acuminata and clustered into six subfamilies (CslA, CslC, CslD, CslE, CslG, and CslH) according to phylogenetic relationships. The genomic features of MaCsl genes were characterized to identify gene structures, conserved motifs and the distribution among chromosomes. A phylogenetic tree was constructed to show the diversity in these genes. Different changes in hemicellulose content between chilling-tolerant and chilling-sensitive banana cultivars under LT were observed, suggesting that certain types of hemicellulose are involved in LT stress tolerance in banana. Thus, the expression patterns of MaCsl genes in both cultivars after LT treatment were investigated by RNA sequencing (RNA-Seq) technique followed by quantitative real-time PCR (qPCR) validation. The results indicated that MaCslA4/12, MaCslD4 and MaCslE2 are promising candidates determining the chilling tolerance of banana. Our results provide the first genome-wide characterization of the MaCsls in banana, and open the door for further functional studies.

scholarly journals Identifying Transcriptomic Correlates of Histology using Deep Learning

2020 ◽  
Author(s):  
Liviu Badea ◽  
Emil Stănescu
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Genome Wide ◽  
Gene Perturbations ◽  
Whole Slide Images

AbstractLinking phenotypes to specific gene expression profiles is an extremely important problem in biology, which has been approached mainly by correlation methods or, more fundamentally, by studying the effects of gene perturbations. However, genome-wide perturbations involve extensive experimental efforts, which may be prohibitive for certain organisms. On the other hand, the characterization of the various phenotypes frequently requires an expert’s subjective interpretation, such as a histopathologist’s description of tissue slide images in terms of complex visual features (e.g. ‘acinar structures’). In this paper, we use Deep Learning to eliminate the inherent subjective nature of these visual histological features and link them to genomic data, thus establishing a more precisely quantifiable correlation between transcriptomes and phenotypes. Using a dataset of whole slide images with matching gene expression data from 39 normal tissue types, we first developed a Deep Learning tissue classifier with an accuracy of 94%. Then we searched for genes whose expression correlates with features inferred by the classifier and demonstrate that Deep Learning can automatically derive visual (phenotypical) features that are well correlated with the transcriptome and therefore biologically interpretable. As we are particularly concerned with interpretability and explainability of the inferred histological models, we also develop visualizations of the inferred features and compare them with gene expression patterns determined by immunohistochemistry. This can be viewed as a first step toward bridging the gap between the level of genes and the cellular organization of tissues.

scholarly journals Identifying transcriptomic correlates of histology using deep learning

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242858
Author(s):  
Liviu Badea ◽  
Emil Stănescu
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Genome Wide ◽  
Gene Perturbations ◽  
Whole Slide Images

Linking phenotypes to specific gene expression profiles is an extremely important problem in biology, which has been approached mainly by correlation methods or, more fundamentally, by studying the effects of gene perturbations. However, genome-wide perturbations involve extensive experimental efforts, which may be prohibitive for certain organisms. On the other hand, the characterization of the various phenotypes frequently requires an expert’s subjective interpretation, such as a histopathologist’s description of tissue slide images in terms of complex visual features (e.g. ‘acinar structures’). In this paper, we use Deep Learning to eliminate the inherent subjective nature of these visual histological features and link them to genomic data, thus establishing a more precisely quantifiable correlation between transcriptomes and phenotypes. Using a dataset of whole slide images with matching gene expression data from 39 normal tissue types, we first developed a Deep Learning tissue classifier with an accuracy of 94%. Then we searched for genes whose expression correlates with features inferred by the classifier and demonstrate that Deep Learning can automatically derive visual (phenotypical) features that are well correlated with the transcriptome and therefore biologically interpretable. As we are particularly concerned with interpretability and explainability of the inferred histological models, we also develop visualizations of the inferred features and compare them with gene expression patterns determined by immunohistochemistry. This can be viewed as a first step toward bridging the gap between the level of genes and the cellular organization of tissues.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yushan Liu ◽  
Yizhou Wang ◽  
Jiabo Pei ◽  
Yadong Li ◽  
Haiyue Sun
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Lignin Content ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Land Plant ◽  
Phylogenetic Structure ◽  
Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

scholarly journals Genome-wide Identification and Expression Analysis of the YTH Domain-containing RNA-binding Protein Family in Citrus Sinensis

2019 ◽  
Vol 144 (2) ◽  
pp. 79-91 ◽  
Author(s):  
Zhigang Ouyang ◽  
Huihui Duan ◽  
Lanfang Mi ◽  
Wei Hu ◽  
Jianmei Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Messenger Rna ◽  
Citrus Sinensis ◽  
Rna Binding ◽  
Developmental Stages ◽  
Rna Binding Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Wide ◽  
Yth Domain

In eukaryotic systems, messenger RNA regulations, including splicing, 3′-end formation, editing, localization, and translation, are achieved by different RNA-binding proteins and noncoding RNAs. The YTH domain is a newly identified RNA-binding domain that was identified by comparing its sequence with that of splicing factor YT521-B. Previous study showed that the YTH gene plays an important role in plant resistance to abiotic and biotic stress. In this study, 211 YTH genes were identified in 26 species that represent four major plant lineages. Phylogenetic analysis revealed that these genes could be divided into eight subgroups. All of the YTH genes contain a YT521 domain and have different structures. Ten YTH genes were identified in navel orange (Citrus sinensis). The expression profiles of these CitYTH genes were analyzed in different tissues and at different fruit developmental stages, and CitYTH genes displayed distinct expression patterns under heat, cold, salt, and drought stress. Furthermore, expression of the CitYTH genes in response to exogenous hormones was measured. Nuclear localization was also confirmed for five of the proteins encoded by these genes after transient expression in Nicotiana benthamiana cells. This study provides valuable information on the role of CitYTHs in the signaling pathways involved in environmental stress responses in Citrus.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

2020 ◽  
Author(s):  
Yuxin Pan ◽  
Jinpeng Wang ◽  
Zhenyi Wang ◽  
Hengwei Liu ◽  
Lan Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Cotton Species ◽  
Expressional Analysis ◽  
Significant Positive Selection

Abstract Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

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