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Functional & Integrative Genomics

Tiago Benedito Dos Santos, João D M Soares, Joni E Lima, Juliana C Silva, Suzana T Ivamoto, Viviane Y Baba, Silvia G H Souza, Alan P R Lorenzetti, Alexandre R Paschoal, Anderson R Meda, Milton Y Nishiyama Júnior, Úrsula C de Oliveira, João B Mokochinski, Romain Guyot, Inácio L M Junqueira-de-Azevedo, Antônio V O Figueira, Paulo Mazzafera, Osvaldo R Júnior, Luiz G E Vieira, Luiz F P Pereira, Douglas S Domingues
Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots...
September 8, 2018: Functional & Integrative Genomics
Claudia E Osorio, Nuan Wen, Jaime H Mejias, Bao Liu, Stephen Reinbothe, Diter von Wettstein, Sachin Rustgi
Ubiquitous nature of prolamin proteins dubbed gluten from wheat and allied cereals imposes a major challenge in the treatment of celiac disease, an autoimmune disorder with no known treatment other than abstinence diet. Administration of hydrolytic glutenases as food supplement is an alternative to deliver the therapeutic agents directly to the small intestine, where sensitization of immune system and downstream reactions take place. The aim of the present research was to evaluate the capacity of wheat grain to express and store hydrolytic enzymes capable of gluten detoxification...
August 29, 2018: Functional & Integrative Genomics
Savannah Beyer, Sintayehu Daba, Priyanka Tyagi, Harold Bockelman, Gina Brown-Guedira, Mohsen Mohammadi
Two hundred one hexaploid wheat accessions, representing 200 years of selection and breeding history, were sampled from the National Small Grains Collection in Aberdeen, ID, and evaluated for five root traits at the seedling stage. A paper roll-supported hydroponic system was used for seedling growth. Replicated roots samples were analyzed by WinRHIZO. We observed accessions with nearly no branching and accessions with up to 132 cm of branching. Total seminal root length ranged from 70 to 248 cm, a 3.5-fold difference...
August 27, 2018: Functional & Integrative Genomics
Rui Zhao, Feng-Qing Li, Lin-Li Tian, De-Si Shang, Yan Guo, Jia-Rui Zhang, Ming Liu
Recently, accumulating evidence has demonstrated that non-coding RNAs (ncRNAs) play a vital role in oncogenicity. Nevertheless, the regulatory mechanisms and functions remain poorly understood, especially for lncRNAs and circRNAs. In this study, we simultaneously detected, for the first time, the expression profiles of the whole transcriptome, including miRNA, circRNA and lncRNA + mRNA, in five pairs of laryngeal squamous cell carcinoma (LSCC) and matched non-carcinoma tissues by microarrays. Five miRNAs, four circRNAs, three lncRNAs and five mRNAs that were dysregulated were selected to confirm the verification of the microarray data by quantitative real-time PCR (qRT-PCR) in 20 pairs of LSCC samples...
August 21, 2018: Functional & Integrative Genomics
Anil Kumar, Gazaldeep Kaur, Parul Goel, Kaushal Kumar Bhati, Mandeep Kaur, Vishnu Shukla, Ajay Kumar Pandey
Oligopeptide transporters (OPT) are integral cell membrane proteins that play a critical role in the transport of small peptides, secondary amino acids, glutathione conjugates, and mineral uptake. In the present study, 67 putative wheat yellow stripe-like transporter (YSL) proteins belonging to the subfamily of OPT transporters were identified. Phylogeny analysis resulted in the distribution of wheat YSLs into four discrete clades. The highest number of YSLs was present on the A genome and the chromosome 2 of hexaploid wheat...
August 17, 2018: Functional & Integrative Genomics
Priyanka Das, Arun Lahiri Majumder
The negative effects of soil salinity towards grape yield depend upon salt concentration, cultivar type, developmental stage, and rootstock. Thompson Seedless variety of grape plant is considered moderately sensitive to salinity when grown upon its own root stock. In recent epoch, identification of key genes responsive to salinity offers hope to generate salinity-tolerant crop plants by their overexpression through genetic manipulation. In the present report, salt responsive transcriptome analysis of Thompson Seedless grape variety was done to identify vital genes involved in salinity tolerance which could be used further to generate salt liberal grape plant or other crop plants...
July 19, 2018: Functional & Integrative Genomics
Kanwardeep Singh, Johar Singh, Suruchi Jindal, Gaganjot Sidhu, Amandeep Dhaliwal, Kulvinder Gill
Particularly PIN1, PIN protein-mediated rate-limiting auxin distribution plays a critical role in plant differentiation. Although well-characterized in Arabidopsis, little is known about the structural and functional relationship of the PIN1 gene among other plants. Here, we report that the gene structure remained conserved among bryophytes and angiosperms while the gene size varied by ~ 17%. Although the positions were conserved, highly variable intron phase suggests preference for specific regions in the gene sequence for independent events of intron insertion...
July 2, 2018: Functional & Integrative Genomics
Shikha Tyagi, Tanu Sri, Anupama Singh, Pratiksha Mayee, S M Shivaraj, Prateek Sharma, Anandita Singh
SOC1, a MADS-box type II transcription factor, integrates environmental and endogenous cues to promote flowering in angiosperms. Recent reports implicating SOC1 in roles beyond floral transition prompted functional characterization of SOC1 in polyploid rapeseed mustard genomes. Gene characterization in Brassicas necessitates analysis of composite homeolog function. While insertional mutagenesis is untenable in Brassicas owing to gene redundancy, gain-of-function approach entails serial characterization of individual homeologs...
June 25, 2018: Functional & Integrative Genomics
Christina Theoharaki, Evangelia Chronopoulou, Dimitrios Vlachakis, Farid S Ataya, Panagiotis Giannopoulos, Sofia Maurikou, Katholiki Skopelitou, Anastassios C Papageorgiou, Nikolaos E Labrou
Erwinia carotovora, a widespread plant pathogen that causes soft rot disease in many plants, is considered a major threat in agriculture. Bacterial glutathione transferases (GSTs) play important roles in a variety of metabolic pathways and processes, such as the biodegradation of xenobiotics, protection against abiotic stress, and resistance against antimicrobial drugs. The GST family of canonical soluble enzymes from Erwinia carotovora subsp. atroseptica strain SCRI1043 (EcaGSTs) was investigated. Genome analysis showed the presence of six putative canonical cytoplasmic EcaGSTs, which were revealed by phylogenetic analysis to belong to the well-characterized GST classes beta, nu, phi, and zeta...
June 25, 2018: Functional & Integrative Genomics
Sezgi Biyiklioglu, Burcu Alptekin, B Ani Akpinar, Andrea C Varella, Megan L Hofland, David K Weaver, Brian Bothner, Hikmet Budak
The original version of this article contained a mistake. The word "RefSeq v.1" was incorrectly inserted on page 7. The correct sentence should be: To identify the differentially regulated transcripts, clean RNA-Seq reads were mapped onto the T. aestivum Chinese Spring chromosome 3B pseudomolecule.
September 2018: Functional & Integrative Genomics
Dan Feng, Yanwei Wang, Tiegang Lu, Zhiguo Zhang, Xiao Han
Leaf veins play a critical role in resource supplication and photosynthate translocation; thus, it is considered as an important agricultural trait for crop breeding. The rice minor veins are parallelly grown along all the parts of the leaf from base to tip. To understand the process of minor vein development, anatomy analysis was performed to reveal the initiation and development of minor veins in rice leaf. The frequency of minor vein initiation follows a decreased tendency from leaf base to tip. An iTRAQ-based proteomics analysis was performed in rice leaf sections...
September 2018: Functional & Integrative Genomics
Xiu-Kai Cao, Yong-Zhen Huang, Yi-Lei Ma, Jie Cheng, Zhen-Xian Qu, Yun Ma, Yue-Yu Bai, Feng Tian, Feng-Peng Lin, Yu-Lin Ma, Hong Chen
Copy number variation (CNV) of DNA sequences, functionally significant but yet fully ascertained, is believed to confer considerable increments in unexplained heritability of quantitative traits. Identification of phenotype-associated CNVs (paCNVs) therefore is a pressing need in CNV studies to speed up their exploitation in cattle breeding programs. Here, we provided a new avenue to achieve this goal that is to project the published CNV data onto meta-quantitative trait loci (meta-QTL) map which connects causal genes with phenotypes...
September 2018: Functional & Integrative Genomics
Jinfeng Zhang, Wenjuan Zhao, Rong Fu, Chenglin Fu, Lingxia Wang, Huainian Liu, Shuangcheng Li, Qiming Deng, Shiquan Wang, Jun Zhu, Yueyang Liang, Ping Li, Aiping Zheng
Rhizoctonia solani causes rice sheath blight, an important disease affecting the growth of rice (Oryza sativa L.). Attempts to control the disease have met with little success. Based on transcriptional profiling, we previously identified more than 11,947 common differentially expressed genes (TPM > 10) between the rice genotypes TeQing and Lemont. In the current study, we extended these findings by focusing on an analysis of gene co-expression in response to R. solani AG1 IA and identified gene modules within the networks through weighted gene co-expression network analysis (WGCNA)...
September 2018: Functional & Integrative Genomics
Touraj Rahimi, Ali Niazi, Tahereh Deihimi, Seyed Mohsen Taghavi, Shahab Ayatollahi, Esmaeil Ebrahimie
One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled...
September 2018: Functional & Integrative Genomics
Yunpeng Cao, Yahui Han, Dandan Meng, Muhammad Abdullah, Dahui Li, Qing Jin, Yi Lin, Yongping Cai
PHD-finger proteins, which belongs to the type of zinc finger family, and that play an important role in the regulation of both transcription and the chromatin state in eukaryotes. Currently, PHD-finger proteins have been well studied in animals, while few studies have been carried out on their function in plants. In the present study, 129 non-redundant PHD-finger genes were identified from 5 Rosaceae species (pear, apple, strawberry, mei, and peach); among them, 31 genes were identified in pear. Subsequently, we carried out a bioinformatics analysis of the PHD-finger genes...
September 2018: Functional & Integrative Genomics
Ravi S Singh, Ravi Kesari, Ujjwal Kumar, Vikash Kumar Jha, Anjani Kumar, Tribhuwan Kumar, Awadhesh K Pal, Prabhash K Singh
In the present study, de novo transcriptome analysis of Selaginella bryopteris in frond and root was performed to understand the regulation of flavonoid (FL) biosynthesis. High-quality data of 5.84 and 5.86 Gb was generated for frond and root, respectively, that assembled into 94,713 and 81,567 transcripts. A total of 87,471 and 73,395 unigenes were obtained from frond and root, respectively. A total of 41,267 and 31,048 CDS of frond and root, respectively, were annotated by BLASTX, which showed maximum hits against S...
September 2018: Functional & Integrative Genomics
Xin Cui, Yong-Xin Wang, Zhi-Wei Liu, Wen-Li Wang, Hui Li, Jing Zhuang
The tea plant is an important commercial horticulture crop cultivated worldwide. Yield and quality of this plant are influenced by abiotic stress. The bHLH family transcription factors play a pivotal role in the growth and development, including abiotic stress response, of plants. A growing number of bHLH proteins have been functionally characterized in plants. However, few studies have focused on the bHLH proteins in tea plants. In this study, 120 CsbHLH TFs were identified from tea plants using computational prediction method...
September 2018: Functional & Integrative Genomics
Hushuai Nie, Yumei Wang, Ying Su, Jinping Hua
Cytoplasmic male sterility (CMS) lines provide crucial material to harness heterosis for crop plants, which serves as an important strategy for hybrid seed production. However, the molecular mechanism remains obscure. Although microRNAs (miRNAs) play important roles in vegetative growth and reproductive growth, there are few reports on miRNAs regulating the development of male sterility in Upland cotton. In present study, 12 small RNA libraries were constructed and sequenced for two development stages of flower buds from a CMS line and its maintainer line...
July 2018: Functional & Integrative Genomics
Anuradha Upadhyay, Smita Maske, Satisha Jogaiah, Narendra Y Kadoo, Vidya S Gupta
In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3 ) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA3 , whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3-4 mm berry stages...
July 2018: Functional & Integrative Genomics
Lifei Luo, Rong Huang, Aidi Zhang, Cheng Yang, Liangming Chen, Denghui Zhu, Yongming Li, Libo He, Lanjie Liao, Zuoyan Zhu, Yaping Wang
Transgenic Yellow River carp is characterized by rapid growth rate and high feed-conversion efficiency and exhibits a great application prospect. However, there is still a significant separation of growth traits in the transgenic Yellow River carp family; as such, growth-related genotypes must be screened for molecular marker-assisted selection. In this study, 23 growth-related candidate genes containing 48 SNP markers were screened through bulked segregant analysis (BSA) among transgenic Yellow River carp family members showing significant separation of growth traits...
July 2018: Functional & Integrative Genomics
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