Distribution of the T2-MITE Family Transposons in the Xenopus (Silurana) tropicalis Genome

2015 ◽  
Vol 145 (3-4) ◽  
pp. 230-242 ◽  
Author(s):  
Akira Hikosaka ◽  
Yoshinobu Uno ◽  
Yoichi Matsuda
Keyword(s):  
Evolutionary Dynamics ◽  
Expression Patterns ◽  
Mutual Relationship ◽  
Chromosomal Distribution ◽  
Transposition Activity ◽  
Tropicalis Genome ◽  
Unique Distribution ◽  
Distribution Uniformity ◽  
Silurana Tropicalis ◽  
Mite Family

The T2 family of miniature inverted-repeat transposable elements (T2-MITE) is a prevalent MITE family found in both Xenopus(Silurana) tropicalis and X. laevis. Some subfamilies, particularly T2-A1 and T2-C, may have originated prior to the diversification of the 2 Xenopus lineages and currently include active members in X. tropicalis, whereas another subfamily, T2-E, may have lost its transposition activity even earlier. The distribution of each T2-MITE subfamily in X. tropicalis was investigated and compared to evaluate the evolutionary dynamics of the T2-MITE subfamilies. The subfamilies showed differences in chromosomal distribution, uniformity of insertion density on scaffolds, ratios of upstream to downstream insertions with respect to genes, and their distance from genes. Among these, the T2-C subfamily was interesting because it was frequently inserted upstream and close to genes and because genes with close insertions of this subfamily showed high correlations in spatial expression patterns. This unique distribution and long-lived transposition activity may reflect a mutual relationship evolved between this subfamily and the host.

scholarly journals The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hui Liu ◽  
Wei Qu ◽  
Kaikai Zhu ◽  
Zong-Ming Cheng
Keyword(s):  
Protein Kinases ◽  
Evolutionary Dynamics ◽  
Expression Patterns ◽  
Gene Families ◽  
Gray Mold ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Go Enrichment ◽  
Potential Link ◽  
Wild Strawberry

Abstract Background Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.

scholarly journals Genome-wide investigation of the AP2/ERF gene family in  ginger: evolution and expression profiles during rhizome and inflorescence development

2021 ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
Yun Ren ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Chromosomal Distribution ◽  
Inflorescence Development ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Erf Transcription Factors

Abstract Background:AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis (Arabidopsis thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of ginger (Zingiber officinale), which is an important edible and medicinal horticultural plant. The recently published whole genome sequence of ginger allowed us to study the tissue and expression profiles of AP2/ERF genes in ginger on a genome-wide basis.Results:In this study, 163 AP2/ERF genes of ginger (ZoAP2/ERF) were identified and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic analysis, namely, AP2 (35 members), ERF (125 members) and RAV (3 members). A total of 10 motifs were detected in ginger AP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes.Conclusion:A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and rhizome development stages by transcriptom sequence and quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of ZoAP2/ERF genes and improvement of ginger.

scholarly journals Genome-Wide Identification and Analysis of the NPR1-Like Gene Family in Bread Wheat and Its Relatives

2019 ◽  
Vol 20 (23) ◽  
pp. 5974 ◽  
Author(s):  
Xian Liu ◽  
Zhiguo Liu ◽  
Xinhui Niu ◽  
Qian Xu ◽  
Long Yang
Keyword(s):  
Gene Family ◽  
Bread Wheat ◽  
Plant Immunity ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Aegilops Tauschii ◽  
Regulatory Elements ◽  
Protein Domain ◽  
Chromosomal Distribution ◽  
Specific Expression

NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1), and its paralogues NPR3 and NPR4, are bona fide salicylic acid (SA) receptors and play critical regulatory roles in plant immunity. However, comprehensive identification and analysis of the NPR1-like gene family had not been conducted so far in bread wheat and its relatives. Here, a total of 17 NPR genes in Triticum aestivum, five NPR genes in Triticum urartu, 12 NPR genes in Triticum dicoccoides, and six NPR genes in Aegilops tauschii were identified using bioinformatics approaches. Protein properties of these putative NPR1-like genes were also described. Phylogenetic analysis showed that the 40 NPR1-like proteins, together with 40 NPR1-related proteins from other plant species, were clustered into three major clades. The TaNPR1-like genes belonging to the same Arabidopsis subfamilies shared similar exon-intron patterns and protein domain compositions, as well as conserved motifs and amino acid residues. The cis-regulatory elements related to SA were identified in the promoter regions of TaNPR1-like genes. The TaNPR1-like genes were intensively mapped on the chromosomes of homoeologous groups 3, 4, and 5, except TaNPR2-D. Chromosomal distribution and collinearity analysis of NPR1-like genes among bread wheat and its relatives revealed that the evolution of this gene family was more conservative following formation of hexaploid wheat. Transcriptome data analysis indicated that TaNPR1-like genes exhibited tissue/organ-specific expression patterns and some members were induced under biotic stress. These findings lay the foundation for further functional characterization of NPR1-like proteins in bread wheat and its relatives.

scholarly journals Genome-wide survey and characterization of transcription factors in the silk gland of the silkworm, Bombyx mori

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259870
Author(s):  
Yan Ma ◽  
Qiwei Sun ◽  
Lihua Huang ◽  
Qin Luo ◽  
Wenhui Zeng ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Bombyx Mori ◽  
Large Scale ◽  
Expression Patterns ◽  
Silk Gland ◽  
Cellular Functions ◽  
Chromosomal Distribution ◽  
Genome Data ◽  
Silkworm Genome ◽  
Full Length Transcript

Transcription factors (TFs) are key proteins that modulate gene transcription and thereby lead to changes in the gene expression profile and the subsequent alteration of cellular functions. In the silk gland (SG) of silkworm Bombyx mori, an important silk-producing insect, TFs are of vital importance in the regulation of silk protein synthesis in this organ. However, which TFs exist and express in the SG remains largely unknown. Here, we report the large-scale identification of TFs in the SG based on available full-length transcript sequences and the most recent version of silkworm genome data. In total, 348 candidate TFs were identified by strict filtration and were classified into 56 TF families. Chromosomal distribution, motif composition, and phylogenetic relationship analyses revealed the typical characteristics of these TFs. In addition, the expression patterns of 348 TFs in various tissues of B. mori, especially the SG of fourth-molt (4LM) and day-3 and day-4 fifth-instar (5L3D and 5L4D) larvae, were investigated based on public RNA-seq data and gene microarray data, followed by spatiotemporal verification of TF expression levels by quantitative real-time PCR (qRT-PCR). This report describes the first comprehensive analysis of TFs in the B. mori SG. The results can serve as a baseline for further studies of the roles of TFs in the B. mori SG.

scholarly journals Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1855
Author(s):  
Dan Luo ◽  
Ziqi Jia ◽  
Yong Cheng ◽  
Xiling Zou ◽  
Yan Lv
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chromosomal Distribution ◽  
Brassica Napus L ◽  
Oil Crops ◽  
Genome Wide ◽  
Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

scholarly journals Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ting Zhu ◽  
Yue Liu ◽  
Liting Ma ◽  
Xiaoying Wang ◽  
Dazhong Zhang ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Gene Family ◽  
Gene Structure ◽  
Expression Patterns ◽  
Wheat Yield ◽  
Chromosomal Distribution ◽  
Positive Role ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Duplication Events

Abstract Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

scholarly journals Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11938
Author(s):  
Shilin Sun ◽  
Bo Wang ◽  
Qi Jiang ◽  
Zhuoran Li ◽  
Site Jia ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gene Family ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Gene Gain ◽  
Betula Platyphylla ◽  
Ros Scavenging ◽  
Promoter Regions ◽  
Chromosomal Distribution ◽  
Qrt Pcr

Background DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear. Methods The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results. Results A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17­ were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17­-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.

scholarly journals Dietary Breadth is Positively Correlated with Venom Complexity in Cone Snails

2015 ◽  
Author(s):  
Mark A Phuong ◽  
Gusti N Mahardika ◽  
Michael E Alfaro
Keyword(s):  
Evolutionary Dynamics ◽  
Gene Diversity ◽  
Expression Patterns ◽  
Snail Species ◽  
Ecological Data ◽  
Dietary Breadth ◽  
Venom Composition ◽  
Taxonomic Class ◽  
Venom Evolution ◽  
Cone Snails

Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist. We discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90% of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. Our results suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity. These results indicate that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.

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