Genome-wide identification, evolution, and expression analysis of the KT/HAK/KUP family in pear

Genome ◽  
2018 ◽  
Vol 61 (10) ◽  
pp. 755-765 ◽  
Author(s):  
Yingzhen Wang ◽  
Jiahong Lü ◽  
Dan Chen ◽  
Jun Zhang ◽  
Kaijie Qi ◽  
...  
Keyword(s):  
Higher Plants ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Duplicated Genes ◽  
Salt Stress Tolerance ◽  
Chromosomal Distribution ◽  
Qrt Pcr ◽  
Physiological Processes ◽  
Genome Wide ◽  
Duplication Events

The K+ transporter/high-affinity K+/K+ uptake (KT/HAK/KUP) family, as one of the largest K+ transporter families in higher plants, plays an essential role in plant growth, mineral element absorption, salt stress tolerance, and other physiological processes. However, little is known about this family in pear (Pyrus). Here, we identified 20 K+ transporter genes in pear (P. bretschneideri) using genome-wide analysis. Their gene structure, chromosomal distribution, conserved motifs, phylogenetics, duplication events, and expression patterns were also examined. The results of phylogenetic analysis showed that PbrKT/HAK/KUP genes were clustered into three major groups (Groups I–III). Among the 20 PbrKT/HAK/KUP genes, 18 were mapped to nine chromosomes and two to scaffolds. Four WGD/segmental gene pairs were identified, indicating that WGD/segmental duplication may have contributed to the expansion of the KT/HAK/KUP family in pear. Among the four pairs of WGD/segmentally duplicated genes, both members of three pairs had been subjected to purifying selection, whereas the fourth pair had been subjected to positive selection. Furthermore, phenotypic experiments showed that the growth of pear seedlings was affected by potassium deficiency treatment. Expression patterns of 20 PbrKT/HAK/KUP genes in roots were further assayed with qRT-PCR. PbrHAK1 and PbrHAK12/16 were significantly expressed in response to K+ deficiency, suggesting that these genes are crucial for K+ uptake in pear, especially under the condition of K+ starvation. Our results provide a foundation for further study on the function of KT/HAK/KUP genes in pear.

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 Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress

2019 ◽  
Vol 20 (6) ◽  
pp. 1425 ◽  
Author(s):  
Dongli Wang ◽  
Sen Meng ◽  
Wanlong Su ◽  
Yu Bao ◽  
Yingying Lu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Editing ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Structural Features ◽  
Specific Expression ◽  
Poplar Genome ◽  
Physiological Processes ◽  
Genome Wide

Poplar (Populus) is one of the most important woody plants worldwide. Drought, a primary abiotic stress, seriously affects poplar growth and development. Multiple organellar RNA editing factor (MORF) genes—pivotal factors in the RNA editosome in Arabidopsis thaliana—are indispensable for the regulation of various physiological processes, including organelle C-to-U RNA editing and plasmid development, as well as in the response to stresses. Although the poplar genome sequence has been released, little is known about MORF genes in poplar, especially those involved in the response to drought stress at the genome-wide level. In this study, we identified nine MORF genes in the Populus genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the P. trichocarpa (Ptr) MORF family members were classified into six groups (Groups I–VI). A microsynteny analysis indicated that two (22.2%) PtrMORF genes were tandemly duplicated and seven genes (77.8%) were segmentally duplicated. Based on the dN/dS ratios, purifying selection likely played a major role in the evolution of this family and contributed to functional divergence among PtrMORF genes. Moreover, analysis of qRT-PCR data revealed that PtrMORFs exhibited tissue- and treatment-specific expression patterns. PtrMORF genes in all group were involved in the stress response. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes in poplar, and, in particular, for improving the drought resistance of poplar by genetics manipulation.

scholarly journals Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jing Wen ◽  
Peng-Feng Li ◽  
Feng Ran ◽  
Peng-Cheng Guo ◽  
Jia-Tian Zhu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Small Scale ◽  
Preferential Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Duplication Events ◽  
Small Scale Duplication

Abstract Background NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we report the global characterization of NPF in the important oil crop Brassica napus, including that for phylogeny, gene/protein structures, duplications, and expression patterns. Results A total of 199 B. napus (BnaNPFs) NPF-coding genes were identified. Phylogenetic analyses categorized these genes into 11 subfamilies, including three new ones. Sequence feature analysis revealed that members of each subfamily contain conserved gene and protein structures. Many hormone−/abiotic stress-responsive cis-acting elements and transcription factor binding sites were identified in BnaNPF promoter regions. Chromosome distribution analysis indicated that BnaNPFs within a subfamily tend to cluster on one chromosome. Syntenic relationship analysis showed that allotetraploid creation by its ancestors (Brassica rapa and Brassica oleracea) (57.89%) and small-scale duplication events (39.85%) contributed to rapid BnaNPF expansion in B. napus. A genome-wide spatiotemporal expression survey showed that NPF genes of each Arabidopsis and B. napus subfamily have preferential expression patterns across developmental stages, most of them are expressed in a few organs. RNA-seq analysis showed that many BnaNPFs (32.66%) have wide exogenous hormone-inductive profiles, suggesting important hormone-mediated patterns in diverse bioprocesses. Homologs in a clade or branch within a given subfamily have conserved organ/spatiotemporal and hormone-inductive profiles, indicating functional conservation during evolution. qRT-PCR-based comparative expression analysis of the 12 BnaNPFs in the NPF2–1 subfamily between high- and low-glucosinolate (GLS) content B. napus varieties revealed that homologs of AtNPF2.9 (BnaNPF2.12, BnaNPF2.13, and BnaNPF2.14), AtNPF2.10 (BnaNPF2.19 and BnaNPF2.20), and AtNPF2.11 (BnaNPF2.26 and BnaNPF2.28) might be involved in GLS transport. qRT-PCR further confirmed the hormone-responsive expression profiles of these putative GLS transporter genes. Conclusion We identified 199 B. napus BnaNPFs; these were divided into 11 subfamilies. Allopolyploidy and small-scale duplication events contributed to the immense expansion of BnaNPFs in B. napus. The BnaNPFs had preferential expression patterns in different tissues/organs and wide hormone-induced expression profiles. Four BnaNPFs in the NPF2–1 subfamily may be involved in GLS transport. Our results provide an abundant gene resource for further functional analysis of BnaNPFs.

scholarly journals Genome-wide identification and analysis of class III peroxidases in Betula pendula

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kewei Cai ◽  
Huixin Liu ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Plant Life ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
And Function

Abstract Background Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula. Results We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

scholarly journals Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

2022 ◽  
Vol 23 (2) ◽  
pp. 614
Author(s):  
Weiqi Sun ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Stress Protein ◽  
Purifying Selection ◽  
Cis Acting ◽  
Genome Wide ◽  
Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

scholarly journals Genome-wide identification and expression profiling of glutathione transferase gene family under multiple stresses and hormone treatments in wheat (Triticum aestivum L.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ruibin Wang ◽  
Jingfei Ma ◽  
Qian Zhang ◽  
Chunlai Wu ◽  
Hongyan Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Glutathione Transferase ◽  
Purifying Selection ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Qrt Pcr ◽  
Duplication Events

Abstract Background Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one of the most important crops, but the functions of GST genes in wheat were less studied. Results A total of 330 TaGST genes were identified from the wheat genome and named according to the nomenclature of rice and Arabidopsis GST genes. They were classified into eight classes based on the phylogenetic relationship among wheat, rice, and Arabidopsis, and their gene structure and conserved motif were similar in the same phylogenetic class. The 43 and 171 gene pairs were identified as tandem and segmental duplication genes respectively, and the Ka/Ks ratios of tandem and segmental duplication TaGST genes were less than 1 except segmental duplication gene pair TaGSTU24/TaGSTU154. The 59 TaGST genes were identified to have syntenic relationships with 28 OsGST genes. The expression profiling involved in 15 tissues and biotic and abiotic stresses suggested the different expression and response patterns of the TaGST genes. Furthermore, the qRT-PCR data showed that GST could response to abiotic stresses and hormones extensively in wheat. Conclusions In this study, a large GST family with 330 members was identified from the wheat genome. Duplication events containing tandem and segmental duplication contributed to the expansion of TaGST family, and duplication genes might undergo extensive purifying selection. The expression profiling and cis-elements in promoter region of 330 TaGST genes implied their roles in growth and development as well as adaption to stressful environments. The qRT-PCR data of 14 TaGST genes revealed that they could respond to different abiotic stresses and hormones, especially salt stress and abscisic acid. In conclusion, this study contributed to the further functional analysis of GST genes family in wheat.

scholarly journals Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 981
Author(s):  
Jichun Xia ◽  
Dong Wang ◽  
Yuzhou Peng ◽  
Wenning Wang ◽  
Qianqian Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Brassica Species ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Functional Identification ◽  
Brassica Napus L ◽  
Intron Structure ◽  
Duplication Events

The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

2016 ◽  
Author(s):  
Kousuke Hanada ◽  
Ayumi Tezuka ◽  
Masafumi Nozawa ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Synonymous Substitution ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Highly Qualified ◽  
Duplication Events ◽  
Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

scholarly journals Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium)

2019 ◽  
Author(s):  
Lanjie Zhao ◽  
Youjun Lu ◽  
Wei Chen ◽  
Jinbo Yao ◽  
Yan Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Potential Functions ◽  
Pcr Analysis ◽  
Type I ◽  
Clade B ◽  
Genome Wide

Abstract Background: Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED ( AHL ) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton. Results: To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL 20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp . The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules. Conclusion: In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three type based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.

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