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Functional & Integrative Genomics

Vishnu Sukumari Nath, Sayuj Koyyappurath, Teena Elizabeth Alex, Kiran Ayyanperumal Geetha, Lesly Augustine, Alka Nasser, George Thomas
Transcription factors (TFs) fine-tune the host defense transcriptome in response to pathogen invasions. No information is available on Zingiber zerumbet (Zz) TFs involved in defense response against Pythium myriotylum. Here, we provide a global identification, characterization, and temporal expression profiling of Zz TFs following an incompatible interaction with P. myriotylum using a transcriptome sequencing approach. We identified a total of 903 TFs belonging to 96 families based on their conserved domains...
November 11, 2018: Functional & Integrative Genomics
Prakash G Koringa, Jalpa R Thakkar, Ramesh J Pandit, Ankit T Hinsu, Mithil J Parekh, Ravi K Shah, Subhash J Jakhesara, Chaitanya G Joshi
Microbial colonisation in the forestomach of a ruminant is one of the most crucial factors in determining many of its physiological developments and digestive capabilities. The present study attempts to identify establishment pattern of microbes in relation to food, age and rumen development in the buffalo calves at every fortnight interval from birth to 6 months of age, followed by every month till animals became 1 year of age. Diversity study based on 16S rRNA gene sequencing identified rapidly changing bacterial population during initial 60 days of life, which got assemblage as rumen became physiologically mature with increasing age of animals...
October 24, 2018: Functional & Integrative Genomics
Xiao-Nv Xie, Jing Yu, Li-Hua Zhang, Zhi-Ying Luo, Dong-Sheng Ouyang, Ling-Jie Zheng, Chun-Yang Wang, Li Yang, Ling Chen, Zhi-Rong Tan
This study aimed to investigate the relationship between polymorphisms in the lipid metabolism-related gene PLA2G16 encoding Group XVI phospholipase A2 and the risk of colorectal cancer (CRC) in the Chinese population. A total of 185 patients with CRC and 313 healthy controls were enrolled. Thirteen single nucleotide polymorphisms (SNPs) of PLA2G16 were genotyped with SNPscan™. Linkage disequilibrium and haplotypes were analysed using Haploview software. Multivariate logistic regression was used to determine the association between the various genotypes and CRC risk...
October 20, 2018: Functional & Integrative Genomics
Supriya Saini, Praveen Vats, Susovon Bayen, Priya Gaur, Koushik Ray, Krishna Kishore, Meerim Sartmyrzaeva, Almaz Akunov, Abdirashit Maripov, Akpay Sarybaev, Bhuvnesh Kumar, Shashi Bala Singh
High altitude (HA) is associated with number of stresses. Response of these stresses may vary in different populations depending upon altitude, duration of residency, ancestry, geographical variation, lifestyle, and ethnicities. For understanding population variability in transcriptome, array-based global gene expression profiling was performed on extracted RNA of male volunteers of two different lowland population groups, i.e., Indians and Kyrgyz, at baseline and day 7 of HA exposure (3200 m). A total of 97 genes were differentially expressed at basal in Kyrgyz as compared to Indians (82 downregulated and 15 upregulated), and 196 were differentially expressed on day 7 of HA (118 downregulated and 78 upregulated)...
October 19, 2018: Functional & Integrative Genomics
Xing-Bo Mo, Long-Fei Wu, Xin Lu, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Yong-Hong Zhang, Fei-Yan Deng, Shu-Feng Lei
One major function of lncRNA is to regulate the expression of mRNA, but the patterns of their interactions were largely unknown. We attempted to construct lncRNA-mRNA interaction modules at a genome-wide scale. We performed a genome-wide lncRNA-mRNA eQTL analysis in peripheral blood mononuclear cells of 43 individuals, followed by weighted gene co-expression network analysis and functional enrichment analysis which sought to detect functional modules. There were 4627 significant cis lnc-eQTL pairs (P < 1...
October 2, 2018: Functional & Integrative Genomics
Yi Lu, Guanglei Liu, Hong Jiang, Zhenming Chi, Zhe Chi
Aureobasidium melanogenum HN6.2 is a unique yeast strain who can produce the siderophore of fusigen under iron starvation to guarantee its survival. However, a comprehensive understanding of mechanisms involved in iron acquisition and homeostasis for it is still vacant. In this study, genome sequencing and mining revealed that A. melanogenum HN6.2 strain was the first yeast species that exclusively possessed all the four known mechanisms for the iron acquisition: (i) the siderophore-mediated iron uptake; (ii) reductive iron assimilation; (iii) low-affinity ferrous uptake; and (iv) heme utilization, which suggested its stronger adaptability than Aspergillus fumigatus and Saccharomyces cerevisiae...
September 24, 2018: Functional & Integrative Genomics
Jinsheng Liang, Ying Cui, Yuhuan Meng, Xingsong Li, Xueping Wang, Wanli Liu, Lizhen Huang, Hongli Du
Transcription factors are recognized as the key regulators of gene expression. However, the changes in the correlation of transcription factors and their target genes between normal and tumor tissues are usually ignored. In this research, we used mRNA expression profile data from The Cancer Genome Atlas which included 5726 samples across 11 major human cancers to perform co-expression analysis by the Pearson correlation coefficients. Then, integrating 81,357 pairs of transcription factors and target genes from transcription factors databases to find out the changes in the co-expression correlation of these gene pairs from normal to tumor tissues...
September 24, 2018: Functional & Integrative Genomics
Thangasamy Saminathan, Alejandra Alvarado, Carlos Lopez, Suhas Shinde, Bandara Gajanayake, Venkata L Abburi, Venkata G Vajja, Guru Jagadeeswaran, K Raja Reddy, Padma Nimmakayala, Umesh K Reddy
Elevated CO2 along with drought is a serious global threat to crop productivity. Therefore, understanding the molecular mechanisms plants use to protect these stresses is the key for plant growth and development. In this study, we mimicked natural stress conditions under a controlled Soil-Plant-Atmosphere-Research (SPAR) system and provided the evidence for how miRNAs regulate target genes under elevated CO2 and drought conditions. Significant physiological and biomass data supported the effective utilization of source-sink (leaf to root) under elevated CO2 ...
September 22, 2018: 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
Yunpeng Cao, Yahui Han, Dandan Meng, Muhammad Abdullah, Jiangliu Yu, Dahui Li, Qing Jin, Yi Lin, Yongping Cai
GDSL-type esterase/lipase (GELP) is mainly characterized by a conserved GDSL domain at N terminus, and is widely found in all living species, both prokaryotes and eukaryotes. GELP gene family consists of a wide range of members playing important roles in plant physiological processes, such as development, stress responses, and functional divergences. In our study, 597 GELP genes were identified from six Rosaceae genomes (i.e., Fragaria vesca, Prunus persica, Prunus avium, Prunus mume, Pyrus bretschneideri, and Malus domestica) by a comprehensive analysis...
November 2018: Functional & Integrative Genomics
Xinlei Li, Zhengqi Fan, Haobo Guo, Ning Ye, Tao Lyu, Wen Yang, Jie Wang, Jia-Tong Wang, Bin Wu, Jiyuan Li, Hengfu Yin
Yellow-flowering species are unique in the genus Camellia not only for their bright yellow pigments but also the health-improving substances in petals. However, little is known regarding the biosynthesis pathways of pigments and secondary metabolites. Here, we performed comparative genomics studies in two yellow-flowered species of the genus Camellia with distinctive flowering periods. We obtained 112,190 and 89,609 unigenes from Camellia nitidissima and Camellia chuongtsoensis, respectively, and identified 9547 gene family clusters shared with various plant species and 3414 single-copy gene families...
November 2018: Functional & Integrative Genomics
Diana L Zuluaga, Vittoria Liuzzi, Pasquale Luca Curci, Gabriella Sonnante
Nitrogen is an essential macronutrient for plant growth and reproduction. In durum wheat, an appropriate nitrogen soil availability is essential for an optimal seed development. miRNAs contribute to the environmental change adaptation of plants through the regulation of important genes involved in stress processes. In this work, nitrogen stress response was evaluated in durum wheat seedlings of Ciccio and Svevo cultivars. Eight small RNA libraries from leaves and roots of chronically stressed plants were sequenced to detect conserved and novel miRNAs...
November 2018: Functional & Integrative Genomics
Tao Ma, Jianping Li, Qian Jiang, Sufang Wu, Huaizhi Jiang, Qiaoling Zhang
In order to improve the production and quality of Chinese cashmere, the research of hair follicle development has aroused more and more attention; the regulation mechanism of miRNA in hair follicle development has become a hot spot. A survey of transcriptome profiling screened 10 hair follicle-related miRNAs that were differentially expressed, including miR-let7a. In this study, the expression of miR-let7a was lower in anagen of hair follicle of cashmere goats than that in catagen of hair follicle of cashmere goats (p < 0...
November 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
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