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Plant gene family

Roshan Kumar Singh, Shweta Shweta, Mehanathan Muthamilarasan, Rekha Rani, Manoj Prasad
Aquaporins are versatile proteins involved in several biological as well as molecular functions, and they have been extensively studied in various plant systems. Increasing evidences indicate their role in biotic and abiotic stresses, and therefore, studying these proteins in a naturally stress-tolerant crop would provide further insights into the roles of this important protein family. Given this, the present study was performed in foxtail millet (Setaria italica), a model plant for studying biofuel, stress tolerance, and C4 photosynthetic traits...
February 13, 2019: Functional & Integrative Genomics
Haibo Wang, Hu Xin, Junyun Guo, Yong Gao, Chao Liu, Dongqin Dai, Lizhou Tang
Hexokinase, the key rate-limiting enzyme of plant respiration and glycolysis metabolism, has been found to play a vital role in plant sugar sensing and sugar signal transduction. Using Jatropha curcas genome database and bioinformatics method, J. curcas HXK gene family (JcHXK) was identified and its phylogenetic evolution, functional domain, signal peptide at the N-terminal, and expression analysis were conducted. The results showed that a total of 4 HXK genes (JcHXK1, JcHXK2, JcHXK3, and JcHKL1) with 9 exons were systematically identified from J...
February 12, 2019: Molecular Biology Reports
Hong Yue, Xi Chang, Yongqiang Zhi, Lan Wang, Guangwei Xing, Weining Song, Xiaojun Nie
The WRKY gene family plays a unique role in plant stress tolerance. Quinoa is a cultivated crop worldwide that is known for its high stress tolerance. The WRKY gene family in quinoa has not yet been studied. Using a genome-wide search method, we identified 1226 WRKY genes in 15 plant species, seven animal species, and seven fungi species. WRKY proteins were not found in animal species and five fungi species, but were, however, widespread in land plants. A total of 92 CqWRKY genes were identified in quinoa. Based on the phylogenetic analysis, these CqWRKY genes were classified into three groups...
February 11, 2019: Genes
Ganyu Gu, Andrea Ottesen, Samantha Bolten, Lan Wang, Yaguang Luo, Steve Rideout, Shuxia Lyu, Xiangwu Nou
Indigenous bacterial populations in fresh-cut produce processing facilities can have a profound effect on the survival and proliferation of inadvertently contaminating foodborne pathogens. In this study, environmental samples were collected from a variety of Zone 3 sites in a processing plant before and after daily routine sanitation. Viable mesophilic aerobic bacteria population was evaluated using both culturing method and quantitative real-time PCR (qPCR) after propidium monoazide treatment. Zone 3 surface microbiota were analyzed using 16S rRNA gene amplicon sequencing with the Qiime2 bioinformatic pipeline...
February 2, 2019: International Journal of Food Microbiology
Pierre Gautrat, Virginie Mortier, Carole Laffont, Annick De Keyser, Justine Fromentin, Florian Frugier, Sofie Goormachtig
The number of legume root nodules resulting from a symbiosis with rhizobia is tightly controlled by the plant. Certain members of the CLAVATA3/Embryo Surrounding Region (CLE) peptide family, specifically MtCLE12 and MtCLE13 in Medicago truncatula, act in the systemic autoregulation of nodulation (AON) pathway that negatively regulates the number of nodules. Little is known about the molecular pathways that operate downstream of the AON-related CLE peptides. Here, by means of a transcriptome analysis, we show that roots ectopically expressing MtCLE13 deregulate only a limited number of genes, including three down-regulated genes encoding lysin motif receptor-like kinases (LysM-RLKs), among which are the nodulation factor (NF) receptor NF Perception gene (NFP) and two up-regulated genes, MtTML1 and MtTML2, encoding Too Much Love (TML)-related Kelch-repeat containing F-box proteins...
February 8, 2019: Journal of Experimental Botany
Xi Cheng, Guohui Li, Chenhui Ma, Muhammad Abdullah, Jinyun Zhang, Hai Zhao, Qing Jin, Yongping Cai, Yi Lin
The content and size of stone cell clusters affects the quality of pear fruit, and monolignol polymerization and deposition in the cell walls constitute a required step for stone cell formation. Laccase (LAC) is the key enzyme responsible for the polymerization of monolignols. However, there are no reports on the LAC family in pear (Pyrus bretschneideri), and the identity of the members responsible for lignin synthesis has not been clarified. Here, 41 LACs were identified in the whole genome of pear. All Pyrus bretschneideri LACs (PbLACs) were distributed on 13 chromosomes and divided into four phylogenetic groups (I-IV)...
2019: PloS One
Mao Hua-Ying, Wang Wen-Ju, Su Wei-Hua, Su Ya-Chun, Liu Feng, Li Cong-Na, Wang Ling, Zhang Xu, Xu Li-Ping, Que You-Xiong
Six Sec14-like PITP genes from sugarcane were identified, two of them were cloned, and their biological functions were characterized indicating their involvement in plant defense against biotic and abiotic stresses. Sec14, a phosphatidylinositol transfer protein (PITP) is widely present in eukaryotes. In this study, the structure and expression patterns of six Sec14-like PITP genes (ScSEC14-1, ScSEC14p, ScSFH1, ScSFH2, ScPATL1, and ScPATL2) from sugarcane were analyzed, and two of them (ScSEC14-1 and ScSEC14p) were cloned and functionally verified...
February 12, 2019: Plant Cell Reports
Yujuan Zhang, Donghua Li, Rong Zhou, Xiao Wang, Komivi Dossa, Linhai Wang, Yanxin Zhang, Jingyin Yu, Huihui Gong, Xiurong Zhang, Jun You
BACKGROUND: Soil salinity is one of the major serious factors that affect agricultural productivity of almost all crops worldwide, including the important oilseed crop sesame. In order to improve salinity resistance in sesame, it is crucial to understand the molecular mechanisms underlying the adaptive response to salinity stress. RESULTS: In the present study, two contrasting sesame genotypes differing in salt tolerance were used to decipher the adaptive responses to salt stress based on morphological, transcriptome and metabolome characterizations...
February 11, 2019: BMC Plant Biology
Manoj Kumar Gupta, Ramakrishna Vadde, Gayatri Gouda, Ravindra Donde, Jitendra Kumar, Lambodar Behera
In silico approach was utilised to identify differentially expressed key hub genes during BPH infestation on Bt rice plant, under laboratory conditions. Re-analysis of GSE74745 data with in-house R scripts and STRING database reveals that only 5 key hub genes, namely Os05g0176100, Os06g0683200, Os07g0208500, Os07g0252400 and Os07g0424400, belonging to cellulose synthase family, are differentially expressed and have confidence score ≥0.9 among themselves. Conserve domain analysis of all proteins encoded via these 5 key hub genes reveals that they have a common cellulose synthase domain, in which "Plant-Conserved Region" (PCR) is highly conserved...
February 1, 2019: Journal of Molecular Graphics & Modelling
Shuangwei Song, Liaoyang Hao, Pan Zhao, Ya Xu, Naiqin Zhong, Hongji Zhang, Ning Liu
Auxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants. Despite their physiological importance, systematic analysis of ARF genes in potato have not been investigated yet. Our genome-wide analysis identified 20 StARF (Solanum tuberosum ARF) genes from potato and found that they are unevenly distributed in all the potato chromosomes except chromosome X. Sequence alignment and conserved motif analysis suggested the presence of all typical domains in all but StARF18c that lacks B3 DNA-binding domain...
February 11, 2019: Scientific Reports
Christine G Stöhr, Sandra Steffens, Iris Polifka, Rudolf Jung, Andreas Kahlmeyer, Philipp Ivanyi, Florian Weber, Arndt Hartmann, Bernd Wullich, Sven Wach, Helge Taubert
The Piwi-like genes belong to the Argonaute gene family and are conserved in plants, animals and humans. In addition to their essential role in the germ line and as stem cell-associated genes, Piwi-like proteins play a role in different cancer types but have yet to be studied in renal cell carcinoma (RCC). We investigated tissue micro arrays (TMAs) with tumor samples of two independent cohorts of RCC patients (N = 265 and N = 345); we used immunohistochemistry to assess the protein expression of Piwi-like 1...
February 11, 2019: Scientific Reports
Liuqing Ma, Pengfei Ma, Dezhu Li
Burmanniaceae is one major group within the monocot order Dioscoreales that has not had its plastome sequenced. Members of Burmanniaceae are mostly achlorophyllous, although the genus Burmannia also includes autotrophs. Here, we report sequencing and analysis of the first Burmanniaceae plastid genome from Burmannia disticha L.. This plastome is 157,480 bp and was assembled as a circular sequence with the typical quadripartite structure of plant plastid genomes. This plastome has a regular number of potentially functional genes with a total of 111, including 78 protein coding genes, 4 ribosomal RNA (rRNA) genes, and 29 tRNA genes...
October 2018: Plant Diversity
Zhi Zou, Xicai Zhang
DNA-binding with one finger (Dof) proteins comprise a plant-specific transcription factor family involved in plant growth, development and stress responses. This study presents a genome-wide comparison of Dof family genes in physic nut ( Jatropha curcas ) and castor bean ( Ricinus communis ), two Euphorbiaceae plants that have not experienced any recent whole-genome duplication. A total of 25 or 24 Dof genes were identified from physic nut and castor genomes, respectively, where JcDof genes are distributed across nine out of 11 chromosomes...
2019: PeerJ
Haoshuang Zhan, Xiaojun Nie, Ting Zhang, Shuang Li, Xiaoyu Wang, Xianghong Du, Wei Tong, Weining Song
Salt stress is one of the most serious limiting factors in worldwide agricultural production, resulting in huge annual yield loss. Since 1995, melatonin ( N -acetyl-5-methoxytryptamine)-an ancient multi-functional molecule in eukaryotes and prokaryotes-has been extensively validated as a regulator of plant growth and development, as well as various stress responses, especially its crucial role in plant salt tolerance. Salt stress and exogenous melatonin lead to an increase in endogenous melatonin levels, partly via the phyto-melatonin receptor CAND2/PMTR1...
February 7, 2019: International Journal of Molecular Sciences
Elham R S Soliman, Peter Meyer
The REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 (RRTF1) gene encodes a member of the ERF/AP2 transcription factor family involved in redox homeostasis. The RRTF1 gene shows tissue-specific responsiveness to various abiotic stress treatments including a response to salt stress in roots. An interesting feature of this response is an adaptation phase that follows its activation, when promoter levels revert to a base line level, even if salt stress is maintained. It is unclear if adaption is controlled by a switch in promoter activity or by changes in transcript levels...
February 7, 2019: Molecular Biotechnology
A P Vasav, V T Barvkar
BACKGROUND: Cytochrome P450 (P450) is a functionally diverse and multifamily class of enzymes which catalyses vast variety of biochemical reactions. P450 genes play regulatory role in growth, development and secondary metabolite biosynthesis. Solanum lycopersicum L. (Tomato) is an economically important crop plant and model system for various studies with massive genomic data. The comprehensive identification and characterization of P450 genes was lacking. Probing tomato genome for P450 identification would provide valuable information about the functions and evolution of the P450 gene family...
February 7, 2019: BMC Genomics
Jun Wang, Qiang Zhang, Yi Wang, Jing Huang, Nengjie Luo, Shengbo Wei, Jian Jin
BACKGROUND: TRIANGULAR HULL1 (TH1), a member of the rice ALOG gene family, has been characterized as a rice lemma/palea-related gene. To understand the gene regulatory network that controlled by TH1, we analyzed the transcriptome from a TH1 knock out (KO) line, which was generated by CRISPR/Cas9. Our study may shed some light on the molecular mechanism of lemma/palea development. RESULTS: We obtained 20 T0 th1-C transgenic plants by CRISPR/Cas9. Among the 20 plants, there were eight bi-allelic mutations, five homozygous mutations, three heterozygous mutations, and four Non-KO plants...
February 6, 2019: Rice
Juan Alonso-Serra, Omid Safronov, Kean-Jin Lim, Sara J Fraser-Miller, Olga B Blokhina, Ana Campilho, Sun-Li Chong, Kurt Fagerstedt, Raisa Haavikko, Ykä Helariutta, Juha Immanen, Jaakko Kangasjärvi, Tiina J Kauppila, Mari Lehtonen, Laura Ragni, Sitaram Rajaraman, Riikka-Marjaana Räsänen, Pezhman Safdari, Maija Tenkanen, Jari T Yli-Kauhaluoma, Teemu H Teeri, Clare J Strachan, Kaisa Nieminen, Jarkko Salojärvi
•Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem-environment barrier called periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied in higher resolution. •We dissected the stem of silver birch (Betula pendula) into eight major tissue types, and characterized them by a combined transcriptomics and metabolomics approach...
February 6, 2019: New Phytologist
Xueyang Min, Xiaoyu Jin, Wenxian Liu, Xingyi Wei, Zhengshe Zhang, Boniface Ndayambaza, Yanrong Wang
Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance and play major determinants of aluminum (Al) tolerance in plants. Alfalfa ( Medicago sativa L.) is the most extensively cultivated forage crop in the world, yet most alfalfa cultivars are not Al tolerant. The basic knowledge of the MATE transcripts family and the characterisation of specific MATE members involved in alfalfa Al stress remain unclear. In this study, 88 alfalfa MATE (MsMATE) transporters were identified at the whole transcriptome level...
2019: PeerJ
Muhammad Shoaib, Wenlong Yang, Qiangqiang Shan, Muhammad Sajjad, Aimin Zhang
Cytokinins (CKs) are involved in determining the final grain yield in wheat. Multiple gene families are responsible for the controlled production of CKs in plants, including isopentenyl transferases for de novo synthesis, zeatin O-glucosyltransferases for reversible inactivation, β-glucosidases for reactivation, and CK oxidases/dehydrogenases for permanent degradation. Identifying and characterizing the genes of these families is an important step in furthering our understanding of CK metabolism. Using bioinformatics tools, we identified four new TaIPT , four new TaZOG , and 25 new TaGLU genes in common wheat...
2019: PeerJ
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