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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.
July 7, 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
Mehdi Mansouri, Mohammad Reza Naghavi, Hoshang Alizadeh, Ghasem Mohammadi-Nejad, Seyed Ahmad Mousavi, Ghasem Hosseini Salekdeh, Yuichi Tada
Aegilops tauschii is the diploid progenitor of the bread wheat D-genome. It originated from Iran and is a source of abiotic stress tolerance genes. However, little is known about the molecular events of salinity tolerance in Ae. tauschii. This study investigates the leaf transcriptional changes associated with long-term salt stress. Total RNA extracted from leaf tissues of control and salt-treated samples was sequenced using the Illumina technology, and more than 98 million high-quality reads were assembled into 255,446 unigenes with an average length of 1398 bp and an N50 of 2269 bp...
June 21, 2018: Functional & Integrative Genomics
Chengmao Xie, Xiaohui Cai, Xiaoju Wang, Li Lin, Yan Long, Xin Cui
ABCA1 is expressed in placental trophoblasts, such that when the expression level of ABCA1 changes, the function of trophoblasts dramatically changes. However, the mechanism by which ABCA1 affects the function of trophoblast cells remains unclear. Here, we used biochemical and transcriptomic to uncover the potential mechanism of the effect of ABCA1 on trophoblast function. HTR8/SVneo cells were either treated with the agonist T0901317 or transfected with siRNA to regulate ABCA1 expression levels. A human gene expression microarray was used to analyze the expression spectrum of ABCA1...
June 21, 2018: Functional & Integrative Genomics
Xiaojian Zhou, Xiaozhu Wu, Tongjian Li, Mingliang Jia, Xinshen Liu, Yulan Zou, Zixia Liu, Feng Wen
Auxin response factors (ARFs) are one type of essential family of transcription factors that bind with auxin response elements (AuxRE), and play vital roles in variety of plant development and physiological processes. Brachypodium distachyon, related to the major cereal grain species, were recently developed to be a good model organism for functional genomics research. So far, genome-wide overview of the ARF gene family in B. distachyon was not available. Here, a systemic analysis of ARF gene family members in B...
June 20, 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...
June 18, 2018: Functional & Integrative Genomics
Feng Que, Guang-Long Wang, Tong Li, Ya-Hui Wang, Zhi-Sheng Xu, Ai-Sheng Xiong
The homeobox gene family, a large family represented by transcription factors, has been implicated in secondary growth, early embryo patterning, and hormone response pathways in plants. However, reports about the information and evolutionary history of the homeobox gene family in carrot are limited. In the present study, a total of 130 homeobox family genes were identified in the carrot genome. Specific codomain and phylogenetic analyses revealed that the genes were classified into 14 subgroups. Whole genome and proximal duplication participated in the homeobox gene family expansion in carrot...
June 16, 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...
June 13, 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...
June 12, 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...
June 8, 2018: Functional & Integrative Genomics
Matteo Buti, Marianna Pasquariello, Domenico Ronga, Justyna Anna Milc, Nicola Pecchioni, Viet The Ho, Chiara Pucciariello, Pierdomenico Perata, Enrico Francia
Low temperature is a major factor limiting rice growth and yield, and seedling is one of the developmental stages at which sensitivity to chilling stress is higher. Tolerance to chilling is a complex quantitative trait, so one of the most effective approaches to identify genes and pathways involved is to compare the stress-induced expression changes between tolerant and sensitive genotypes. Phenotypic responses to chilling of 13 Japonica cultivars were evaluated, and Thaibonnet and Volano were selected as sensitive and tolerant genotypes, respectively...
June 6, 2018: Functional & Integrative Genomics
Songtao Yang, Xiaojing Liu, Shuai Qiao, Wenfang Tan, Ming Li, Junyan Feng, Cong Zhang, Xiang Kang, Tianbao Huang, Youlin Zhu, Lan Yang, Dong Wang
Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important root crops in the world. Initial formation and development of storage roots (SRs) are key factors affecting its yields. In order to study the molecular mechanism and regulatory networks of the SRs development process, we have analyzed root transcriptomes between the high and low starch content sweet potato accessions at three different developmental stages. In this study, we assembled 46,840 unigenes using Illumina paired-end sequencing reads and identified differentially expressed genes (DEGs) between two accessions...
May 12, 2018: Functional & Integrative Genomics
André S Santos, Rommel T Ramos, Artur Silva, Raphael Hirata, Ana L Mattos-Guaraldi, Roberto Meyer, Vasco Azevedo, Liza Felicori, Luis G C Pacheco
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis...
May 11, 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...
May 11, 2018: Functional & Integrative Genomics
Israr Ahmed, Deepanker Yadav, Pawan Shukla, P B Kirti
Annexins are multifunctional proteins with roles in plant development and alleviation of stress tolerance. In the present communication, we report on the effect of heterologous expression of Brassica juncea annexin, AnnBj2 in tobacco. Transgenic tobacco plants expressing AnnBj2 exhibited salt-tolerant and abscisic acid (ABA)-insensitive phenotype at the seedling stage. Biochemical analysis showed that AnnBj2 transgenic plants retained higher chlorophyll and proline content, and lower malondialdehyde (MDA) levels compared to the null line under salt stress...
May 10, 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...
May 8, 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)...
May 5, 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...
May 5, 2018: Functional & Integrative Genomics
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