Genome-Wide Analysis of HAK/KUP/KT Potassium Transporter Genes in Banana (Musa Acuminata L.) and Their Tissue-Specific Expression Profiles Under Potassium Stress

Abstract Potassium is one of the most essential inorganic cations for plant growth and development. The high affinity K+ (HAK)/K+ uptake (KUP)/K+ transporter (KT) family plays essential roles in the regulation of cellular K+ levels and the maintenance of osmotic balance. However, the roles of these genes in the responses of bananas to low-potassium stress are unclear. In this study, 24 HAK/KUP/KT (MaHAK) genes were identified from banana genomic data. These genes were further classified into four groups based on phylogenetic analysis, gene structure and conserved domain analysis. Segmental duplication events played an important role in the expansion of the MaHAK gene family. Transcriptome analysis revealed the expression patterns of MaHAKs in various tissues under different K+ conditions. MaHAK14b was upregulated under both short- and long-term K+-deficient conditions, suggesting that it plays crucial roles in K+ uptake at low K+ concentrations. Furthermore, MaHAK14b mediated K+ uptake when it was heterologously expressed in the yeast mutant R5421 on low K+ medium. Collectively, these findings provide a foundation for further functional analysis of MaHAK genes, which may be used to improve stress resistance in bananas.

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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 ◽

10.1139/gen-2017-0163 ◽

2018 ◽

Vol 61 (2) ◽

pp. 121-130 ◽

Cited By ~ 4

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.

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Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

International Journal of Molecular Sciences ◽

10.3390/ijms21197180 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7180

Author(s):

Hongfeng Wang ◽

Hongjiao Jiang ◽

Yiteng Xu ◽

Yan Wang ◽

Lin Zhu ◽

...

Keyword(s):

Medicago Truncatula ◽

Expression Profiles ◽

Expression Patterns ◽

Ectopic Expression ◽

Feedback Regulation ◽

Specific Expression ◽

Systematic Analysis ◽

Model Legume ◽

Genome Wide ◽

A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

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Genome-wide and expression analysis of B-box gene family in pepper

BMC Genomics ◽

10.1186/s12864-021-08186-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jing Ma ◽

Jia-xi Dai ◽

Xiao-wei Liu ◽

Duo Lin

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Transient Expression Assay ◽

Specific Expression ◽

Tissue Specific ◽

Duplication Events ◽

Onion Inner Epidermis

Abstract Background BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family has been identified in Arabidopsis, rice, tomato and some other model plant genomes. Results Here, 24 CaBBX genes were identified in pepper (Capsicum annuum L.), and the phylogenic analysis, structures, chromosomal location, gene expression patterns and subcellular localizations were also carried out to understand the evolution and function of CaBBX genes. All these CaBBXs were divided into five classes, and 20 of them distributed in 11 of 12 pepper chromosomes unevenly. Most duplication events occurred in subgroup I. Quantitative RT-PCR indicated that several CaBBX genes were induced by abiotic stress and hormones, some had tissue-specific expression profiles or differentially expressed at developmental stages. Most of CaBBX members were predicated to be nucleus-localized in consistent with the transient expression assay by onion inner epidermis of the three tested CaBBX members (CaBBX5, 6 and 20). Conclusion Several CaBBX genes were induced by abiotic stress and exogenous phytohormones, some expressed tissue-specific and variously at different developmental stage. The detected CaBBXs act as nucleus-localized transcription factors. Our data might be a foundation in the identification of CaBBX genes, and a further understanding of their biological function in future studies.

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Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

International Journal of Molecular Sciences ◽

10.3390/ijms19103246 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3246 ◽

Cited By ~ 9

Author(s):

Jianbo Li ◽

Jin Zhang ◽

Huixia Jia ◽

Zhiqiang Yue ◽

Mengzhu Lu ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Purifying Selection ◽

Molecular Characteristics ◽

Specific Expression ◽

Cis Acting ◽

Shsp Gene ◽

Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

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

BMC Genomics ◽

10.1186/s12864-020-07274-7 ◽

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.

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Genome-wide analysis of gibberellin-dioxygenases genes in rice

10.21203/rs.2.14733/v1 ◽

2019 ◽

Author(s):

Wei Liu ◽

Jishuai Huang ◽

Yanghong Xu ◽

Qiannan Zhang ◽

Jun Hu

Keyword(s):

Plant Architecture ◽

Plant Hormone ◽

Special Functions ◽

Expression Profiles ◽

Expression Patterns ◽

Specific Expression ◽

Conserved Motifs ◽

Genome Wide Analysis ◽

Genome Wide ◽

Available Information

Abstract Background Gibberellins (GAs), a pivotal plant hormone, play fundamental roles in plant development and growth. In rice, gibberellin-dioxygenases (GAoxes), OsGA20ox, OsGA3ox and OsGA2ox, are involved in the biosynthesis and deactivation of gibberellins. However, a comprehensive genome-wide analysis of gibberellin-dioxygenases genes is still uncovered.Results In this study, a total of 95 candidate OsGAox genes were found and 19 OsGAox genes were further analyzed. Results of phylogenetic tree showed that the OsGAox genes in Arabidopsis and rice were divided into four subgroups and shared some common features. Furthermore, analysis of gene structure and conserved motifs revealed that splicing phase and motifs were well conserved during the evolution of GAox genes in Arabidopsis and rice, and some specific motifs still need to be further studied. Exploration of expression profiles indicated that most of OsGAox genes exhibited tissue-specific expression patterns, implied their complicated functions. Moreover, the expression patterns of these genes under GA 3 and PAC treatment were investigated, and result showed that some genes, OsGA2ox3, OsGA2ox5, OsGA2ox7, OsGA2ox9, OsGA20ox2, and OsGA20ox4, may play a major role in GA homeostasis to cope with exogenous GA.Conclusions Our study provided a comprehensive analysis of the OsGAox gene family. Splicing characteristics and conserved motifs indicated the evolutionary conserved function in plants. Expression profiles indicated that each OsGAox gene has complicated and special functions. Although plenty of GAoxes were involved in the endogenous GA metabolism, only some of them acted in response to the exogenous GA treatment, which provided available information for researchers to manipulate the chemical GAs to improve the plant architecture and production.

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Genome Wide Analysis of Amino Acid Transporter Superfamily in Solanum lycopersicum

Plants ◽

10.3390/plants10020289 ◽

2021 ◽

Vol 10 (2) ◽

pp. 289

Author(s):

Fatima Omari Alzahrani

Keyword(s):

Amino Acid ◽

Solanum Lycopersicum ◽

Expression Profiles ◽

Expression Patterns ◽

Functional Characterization ◽

Fleshy Fruit ◽

Amino Acid Transporters ◽

Sequencing Data ◽

Specific Expression ◽

Duplication Events

Amino acid transporters (AATs) are integral membrane proteins and have several functions, including transporting amino acids across cellular membranes. They are critical for plant growth and development. This study comprehensively identified AAT-encoding genes in tomato (Solanum lycopersicum), which is an important vegetable crop and serves as a model for fleshy fruit development. In this study, 88 genes were identified in the S. lycopersicum genome and grouped into 12 subfamilies, based on previously identified AATs in Arabidopsis, rice (Oryza sativa), and potato (Solanum tuberosum) plants. Chromosomal localization revealed that S. lycopersicum AAT (SlAAT) genes are distributed on the 12 S. lycopersicum chromosomes. Segmental duplication events contribute mainly to the expansion of SlAAT genes and about 32% (29 genes) of SlAAT genes were found to originate from this type of event. Expression profiles of SlAAT genes in various tissues of S. lycopersicum using RNA sequencing data from the Tomato Functional Genomics Database showed that SlAAT genes exhibited tissue-specific expression patterns. Comprehensive data generated in this study will provide a platform for further studies on the SlAAT gene family and will facilitate the functional characterization of SlAAT genes.

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

BMC Ecology and Evolution ◽

10.1186/s12862-021-01873-y ◽

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.

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

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04567-18 ◽

2019 ◽

Vol 144 (2) ◽

pp. 79-91 ◽

Cited By ~ 1

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.

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

International Journal of Genomics ◽

10.1155/2015/823427 ◽

2015 ◽

Vol 2015 ◽

pp. 1-17 ◽

Cited By ~ 2

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.

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