Bioinformatics and Expression Analysis of IDA-Like Genes Reveal Their Potential Functions in Flower Abscission and Stress Response in Tobacco (Nicotiana tabacum L.)

The inflorescence deficient in abscission-like (IDL) genes have been shown to play critical roles in floral organ abscission, lateral root formation and various stress responses in Arabidopsis. The IDL gene family has been characterized in a number of plant species, while limited information is available about IDL genes of tobacco. In the current study, 15 NtIDL members were identified in the tobacco genome, and were classified into six groups together with IDL members from other species. Evolution analysis suggested that the NtIDL members form group VI might have originated from duplication events. Notably, NtIDL06 shared high similarities with AtIDA in the EPIP sequence, and its encoding gene was highly expressed in the abscission zone of flowers at late developmental stages, implying that NtIDL06 might regulate tobacco flower abscission. In addition, the results from cis-elements analysis of promoters and expression after stress treatments suggested that NtIDL members might be involved in various stress responses of tobacco. The results from this study provide information for further functional analysis related to flower abscission and stress responses of NtIDL genes.

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Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple

International Journal of Genomics ◽

10.1155/2020/3165958 ◽

2020 ◽

Vol 2020 ◽

pp. 1-14 ◽

Cited By ~ 1

Author(s):

Yanhui Liu ◽

Mengnan Chai ◽

Man Zhang ◽

Qing He ◽

Zhenxia Su ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Stress Responses ◽

Leucine Zipper ◽

Developmental Stages ◽

Functional Characterization ◽

Sequencing Data ◽

Basic Leucine Zipper ◽

Expression Levels ◽

Duplication Events

This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.

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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 the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

International Journal of Molecular Sciences ◽

10.3390/ijms23020614 ◽

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.

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The Construction of Plant Expression Vector harbouring Carica Papaya L. WRKY Gene in Escherichia coli

Pertanika Journal of Science and Technology ◽

10.47836/pjst.28.s2.04 ◽

2020 ◽

Vol 28 (S2) ◽

Author(s):

Fauziah Abu Bakar ◽

Pavitra Paramalingam ◽

Kamariah Hasan

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Expression Vector ◽

Carica Papaya ◽

Sequencing Analysis ◽

Wrky Gene ◽

Limited Information ◽

Abiotic Stress Response ◽

Plant Expression ◽

Plant Expression Vector

Carica papaya is a well-liked and economically important fruit with outstanding nutritional and medicinal values. Its susceptibility to abiotic stress which affects the growth and harvest, causes significant yield loss to farmers. In recent years, significant progress has been made to understand the genes that play critical roles in abiotic stress response, especially some transcription factor (TF) encoding genes. Among all TFs, WRKY TF gene family is one of the best-studied TFs involved in various stress responses. To date, only limited information on functionally characterised WRKY TFs is available for C. papaya. The aim of this study was to produce a recombinant construct harbouring WRKY gene in pGEM®-T Easy cloning vector. The presence of a DNA band of the expected size of 465 bp on agarose gel electrophoresis indicated that WRKY gene was successfully amplified from all treated samples. DNA sequencing analysis revealed that the amplified sequence isolated from the treated samples were closely related to Carica papaya species with 97% similarity. Following transformation, 4 out of 5 colonies that were randomly selected showed the WRKY gene had been successfully inserted into pGEM®-T Easy vector and transformed into E. coli. In future, the WRKY gene from pGEMT-WRKY recombinant construct will be cloned into the plant expression vector pCAMBIA 1304 prior to transformation in the plant. The success of demonstrating the WRKY gene towards the response in abiotic stress will enable us to produce stress tolerant transgenic crops under unfavourable conditions via genetic engineering for sustained growth.

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Distinct gene expression patterns in vector-residing Leishmania infantum identify parasite stage-enriched markers

10.1101/679712 ◽

2019 ◽

Cited By ~ 1

Author(s):

Iliano V. Coutinho-Abreu ◽

Tiago D. Serafim ◽

Claudio Meneses ◽

Shaden Kamhawi ◽

Fabiano Oliveira ◽

...

Keyword(s):

Leishmania Infantum ◽

Developmental Stages ◽

Expression Patterns ◽

Principal Component ◽

Sand Fly ◽

Parasite Development ◽

Lutzomyia Longipalpis ◽

Specific Marker ◽

Limited Information ◽

Natural Sand

AbstractPromastigotes of Leishmania infantum undergo a series of extracellular developmental stages inside the natural sand fly vector Lutzomyia longipalpis to reach the infectious stage, the metacyclic promastigote. There is limited information regarding the expression profile of L. infantum developmental stages inside the sand fly vector, and molecular markers that can distinguish the different parasite stages are lacking. We performed RNAseq on unaltered midguts of the sand fly Lutzomyia longipalpis after infection with L. infantum parasites. RNAseq was carried out at various time points throughout parasite development. Principal component analysis mapped the sequences corresponding to the procyclic, nectomonad, leptomonad or metacyclic promastigote stage into distinct positions, with the procyclic stage being the most divergent population. Transcriptional levels across genes varied on average between 10- to 100-fold. Comparison between procyclic and nectomonad promastigotes resulted in 836 differentially expressed (DE) genes; between nectomonad and leptomonad promastigotes in 113 DE genes; and between leptomonad and metacyclic promastigotes in 302 DE genes. Most of the DE genes do not overlap across stages, highlighting the uniqueness of each stage. Furthermore, the different stages of Leishmania parasites exhibited specific transcriptional enrichment across chromosomes. Using the transcriptional signatures exhibited by distinct Leishmania stages during their development in the sand fly midgut, we determined the genes predominantly enriched in each stage, identifying multiple stage-specific markers for L. Infantum. Leading stage-specific marker candidates include genes encoding a zinc transporter in procyclics, a beta-fructofuranidase in nectomonads, a surface antigen-like protein in leptomonads, and an amastin-like surface protein in metacyclics. Overall, these findings demonstrate the transcriptional plasticity of the Leishmania parasite inside the sand fly vector and provide a repertoire of stage-specific markers for further development as molecular tools for epidemiological studies.

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Identification and Expression Analysis of the NAC Gene Family in Coffea canephora

Agronomy ◽

10.3390/agronomy9110670 ◽

2019 ◽

Vol 9 (11) ◽

pp. 670 ◽

Cited By ~ 4

Author(s):

Dong ◽

Jiang ◽

Yang ◽

Xiao ◽

Bai ◽

...

Keyword(s):

Cold Stress ◽

Gene Family ◽

Stress Responses ◽

Developmental Stages ◽

Expression Patterns ◽

Coffea Canephora ◽

Coffee Bean ◽

Systematic Analysis ◽

Nac Gene Family ◽

Basic Features

The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.

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Characterization and expression analysis of GPAT gene family in maize

Canadian Journal of Plant Science ◽

10.1139/cjps-2018-0188 ◽

2019 ◽

Vol 99 (5) ◽

pp. 577-588

Author(s):

Xiaoxuan Xu ◽

Bowei Yan ◽

Ying Zhao ◽

Feng Wang ◽

Xunchao Zhao ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Developmental Stages ◽

Expression Profiles ◽

Cold Treatment ◽

Oil Production ◽

Initial Step ◽

Field Crops ◽

Lysophospholipid Acyltransferases ◽

Elevated Expression

Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the initial step of glycerolipids biosynthesis and contributes to oil production, membrane stabilization, and stress responses in plants. In major field crops, little information on the GPAT gene family and their potential stress-related functions were available. In this study, 15 GPAT gene family members were identified from the maize genome and designated as ZmGPAT1–ZmGPAT14 and ZMS1. The ZmGPAT proteins contained 371–557 amino acids and had a molecular weight between 42.7 and 61.2 kDa. Phylogenetic analysis revealed that ZmGPATs fell into four clusters. All 15 ZmGPAT proteins possessed conserved PlsC/LPLAT (phosphate acyltransferases/lysophospholipid acyltransferases) domains and featured multiple acyltransferase motifs. The expression profiles of ZmGPAT genes were different in various tissues of maize and the elevated expression of several ZmGPAT genes occurred at early seed developmental stages. In response to environmental stresses, differential expression of ZmGPATs had been observed, highlighted by the significant induction of transcripts accumulation of some ZmGPATs under cold treatment. This study will help to better understand the potential roles of GPAT in oil production and development and abiotic stress responses in field crops.

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

BMC Genomics ◽

10.1186/s12864-019-6374-x ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 3

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.

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Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing

Scientific Reports ◽

10.1038/s41598-019-51443-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Waqas Ahmed ◽

Yanshi Xia ◽

Hua Zhang ◽

Ronghua Li ◽

Guihua Bai ◽

...

Keyword(s):

Heat Stress ◽

Abiotic Stress ◽

High Throughput ◽

Chinese Cabbage ◽

Stress Responses ◽

High Throughput Sequencing ◽

Differential Expression Analysis ◽

Plant Responses ◽

Limited Information ◽

Flowering Chinese Cabbage

Abstract Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.

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Morphology, developmental stages and quality parameters of in vitro-produced equine embryos

Reproduction Fertility and Development ◽

10.1071/rd19257 ◽

2019 ◽

Vol 31 (12) ◽

pp. 1758 ◽

Cited By ~ 1

Author(s):

Elaine M. Carnevale ◽

Elizabeth S. Metcalf

Keyword(s):

Embryo Development ◽

Developmental Stages ◽

Inner Cell Mass ◽

Early Stage ◽

Cell Mass ◽

Quality Parameters ◽

Early Embryo ◽

Developmental Competence ◽

Limited Information

Intracytoplasmic sperm injection (ICSI) is used to produce equine embryos invitro. The speed of embryo development invitro is roughly equivalent to what has been described for embryos produced invivo. Morphological evaluations of ICSI-produced embryos are complicated by the presence of debris and the dark nature of equine embryo cytoplasm. Morulas and early blastocysts produced invitro appear similar to those produced invivo. However, with expansion of the blastocyst, distinct differences are observed compared with uterine embryos. In culture, embryos do not undergo full expansion and thinning of the zona pellucida (ZP) or capsule formation. Cells of the inner cell mass (ICM) are dispersed, in contrast with the differentiated trophoblast and ICM observed in embryos collected from uteri. As blastocysts expand invitro, embryo cells often escape the ZP as organised or disorganised extrusions of cells, probably through the hole incurred during ICSI. Quality assessment of invitro-produced early stage equine embryos is in its infancy, because limited information is available regarding the relationship between morphology and developmental competence. Early embryo development invivo is reviewed in this paper, with comparisons made to embryo development invitro and clinical assessments from a laboratory performing commercial ICSI for >15 years.

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