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MiRNA-seq analysis of spleen and head kidney tissue from aquacultured largemouth bass ( Micropterus salmoides ) in response to Aeromonas hydrophila infection Funct. Integr. Genomics (IF 3.058) Pub Date : 2021-01-13 Jian Zhou, Han Zhao, Lu Zhang, Qiang Li, Zhipeng Huang, Zhongmeng Zhao, Hongyu Ke, Yu Xiao, Xutao Su, Qiao Liu, Song Yang, Liulan Zhao
Recently, the same fish diseases, which have been found in pond farming, have been found in the newly tested largemouth bass (Micropterus salmoides) system. Bacterial septicemia caused by Aeromonas hydrophila occurs frequently in largemouth bass culture leading to significant economic losses. To investigate the role miRNA in the largemouth bass disease resistance, twelve (2 tissues (spleen and head
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Integrative analysis of differential circular RNA and long non-coding RNA profiles and associated competing endogenous RNA networks in esophageal squamous cell carcinoma Funct. Integr. Genomics (IF 3.058) Pub Date : 2021-01-07 Jiang-Feng Shen, Jin-Feng Ge, Shi-Ying Zheng, Dong Jiang
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play vital roles in the tumorigenesis of esophageal squamous cell carcinoma (ESCC). Nevertheless, the mechanism and regulatory network associated with this process remain largely unknown. In this study, we performed a comprehensive analysis of the expression of mRNAs, lncRNAs, and circRNAs by RNA-seq. A total of 3265 mRNAs, 1084 lncRNAs, and
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Long-distance chromatin interaction of IGF1 during embryonic and postnatal development in the liver of Sus scrofa Funct. Integr. Genomics (IF 3.058) Pub Date : 2021-01-06 Jinbi Zhang, Wang Yao, Zengxiang Pan, Honglin Liu
The dynamics of chromatin have been the focus of studies aimed at characterizing gene regulation. Among various chromosome conformation capture methods, 4C-seq is a powerful technique to identify genome-wide interactions with a single locus of interest. Insulin-like growth factor 1 (IGF1) is a member of the somatotropin axis that plays a significant role in cell proliferation and growth. Determining
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Transcriptome landscapes of differentially expressed genes related to fat deposits in Nandan-Yao chicken Funct. Integr. Genomics (IF 3.058) Pub Date : 2021-01-06 Cong Xiao, Tiantian Sun, Zhuliang Yang, Wenwen Xu, Juan Wang, Linghu Zeng, Jixian Deng, Xiurong Yang
Nandan-Yao chicken is a Chinese native chicken with lower fat deposition and better meat quality. Fat deposition is a quite complex and important economic trait. However, its molecular mechanism is still unknown in chickens. In the current study, Nandan-Yao chicken was divided into two groups based on the rate of abdominal fat at 120 days old, namely the high-fat group and low-fat group. The total
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Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane Funct. Integr. Genomics (IF 3.058) Pub Date : 2021-01-06 Douglas Jardim-Messeder, Thais Felix-Cordeiro, Lucia Barzilai, Ygor de Souza-Vieira, Vanessa Galhego, Gabriel Afonso Bastos, Gabriela Valente-Almeida, Yuri Ricardo Andrade Aiube, Allana Faria-Reis, Régis Lopes Corrêa, Gilberto Sachetto-Martins
Lignin is the main component of secondary cell walls and is essential for plant development and defense. However, lignin is recognized as a major recalcitrant factor for efficiency of industrial biomass processing. Genes involved in general phenylpropanoid and monolignol-specific metabolism in sugarcane have been previously analyzed at the transcriptomic level. Nevertheless, the number of genes identified
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Comparative analysis of mitochondrial genomes of soybean cytoplasmic male-sterile lines and their maintainer lines Funct. Integr. Genomics (IF 3.058) Pub Date : 2021-01-06 Tingting He, Xianlong Ding, Hao Zhang, Yanwei Li, Linfeng Chen, Tanliu Wang, Longshu Yang, Zhixing Nie, Qijian Song, Junyi Gai, Shouping Yang
In soybean, only one mitochondrial genome of cultispecies has been completely obtained. To explore the effect of mitochondrial genome on soybean cytoplasmic male sterility (CMS), two CMS lines and three maintainer lines were used for sequencing. Comparative analysis showed that mitochondrial genome of the CMS line was more compact than that of its maintainer line, but genes were highly conserved. Conserved
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Transcriptome skimming of lentil ( Lens culinaris Medikus) cultivars with contrast reaction to salt stress Funct. Integr. Genomics (IF 3.058) Pub Date : 2021-01-03 Dharmendra Singh, Chandan Kumar Singh, Jyoti Taunk, Shristi Sharma, Kishor Gaikwad, Vijayata Singh, Satish Kumar Sanwal, Deepti Singh, PC Sharma, Madan Pal
Extensive transcriptomic skimming was conducted to decipher molecular, morphological, physiological, and biochemical responses in salt-tolerant (PDL-1) and salt-sensitive (L-4076) cultivars under control (0 mM NaCl) and salinity stress (120 mM NaCl) conditions at seedling stage. Morphological, physiological, and biochemical studies revealed that PDL-1 exhibited no salt injury and had higher K+/Na+
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Genome-wide diversity analysis of TCP transcription factors revealed cases of selection from wild to cultivated barley Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-11-09 Guangqi Gao, Jinhong Kan, Congcong Jiang, Sunny Ahmar, Jing Zhang, Ping Yang
Plant-specific TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1/2 (TCP) transcription factors have known roles in inflorescence architecture. In barley, there are two family members INTERMEDIUM-C (INT-c/HvTB1-1) and COMPOSITUM 1 (COM1/HvTCP24) which are involved in the manipulation of spike architecture, whereas the participation of TCP family genes in selection from wild (Hordeum vulgare
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Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-10-31 Jingjing Wang, Qi Chen, Wenyi Wu, Yujie Chen, Yincong Zhou, Guoji Guo, Ming Chen
Nutrient stress is the most important environmental stress that limits plant growth and development. Although recent evidence highlights the vital functions of long non-coding RNAs (lncRNA) in response to single nutrient stress in some model plants, a comprehensive investigation of the effect of lncRNAs in response to nutrient stress has not been performed in Arabidopsis thaliana. Here, we presented
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Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-10-27 Handan Emisoglu-Kulahli, Seref Gul, Hande Morgil, Onur Ozcan, Fatih Aygenli, Saba Selvi, Ibrahim Halil Kavakli, Nuri Ozturk
We have previously reported that the deletion of BMAL1 gene has opposite effects in respect to its contribution to the pathways that are effective in the multistage carcinogenesis process. BMAL1 deletion sensitized nearly normal breast epithelial (MCF10A) and invasive breast cancer cells (MDA-MB-231) to cisplatin- and doxorubicin-induced apoptosis, while this deletion also aggravated the invasive potential
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Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-10-21 Gaurav Agarwal, Himabindu Kudapa, Abirami Ramalingam, Divya Choudhary, Pallavi Sinha, Vanika Garg, Vikas K Singh, Gunvant B Patil, Manish K Pandey, Henry T Nguyen, Baozhu Guo, Ramanjulu Sunkar, Chad E Niederhuth, Rajeev K Varshney
Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the
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An overview of the transcriptional responses of two tolerant and susceptible sugarcane cultivars to borer ( Diatraea saccharalis ) infestation Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-10-17 Uilian Stefanello de Mello, Pedro Marcus Pereira Vidigal, Camilo Elber Vital, Adriano Cirino Tomaz, Milene de Figueiredo, Luiz Alexandre Peternelli, Márcio Henrique Pereira Barbosa
Diatraea saccharalis constitutes a threat to the sugarcane productivity, and obtaining borer tolerant cultivars is an alternative method of control. Although there are studies about the relationship between the interaction of D. saccharalis with sugarcane, little is known about the molecular and genomic basis of defense mechanisms that confer tolerance to sugarcane cultivars. Here, we analyzed the
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Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-10-02 Xiaoqian Liu, Shanshan Chu, Chongyuan Sun, Huanqing Xu, Jinyu Zhang, Yongqing Jiao, Dan Zhang
MicroRNAs (miRNAs) have been reported to be correlated with various stress responses in soybean, but only a few miRNAs have been demonstrated to respond to low phosphorus (LP) stress. To unravel the response mechanisms of miRNAs to low-P stress, the roots of two representative soybean genotypes with different P efficiency, Nannong94-156 (a LP-tolerant genotype) and Bogao (a LP-sensitive genotype),
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Occurrence of differing metabolic dysregulations, a glucose driven and another fatty acid centric in gastric cancer subtypes. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-09-19 Karthik Balakrishnan,Kumaresan Ganesan
Gastric cancer is one of the most common cancers and ranks third in cancer-related deaths across globe. Cancer cells are known to take advantage of the altered metabolic processes to sustain their survival, proliferation, and cancer progression. In this investigation, we explored the available genome-wide expression profiles of few hundreds of gastric tumors and non-cancerous gastric tissues and analyzed
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Comparative de novo transcriptome analysis of barley varieties with different malting qualities. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-09-18 Leona Leišová-Svobodová,Vratislav Psota,Štěpán Stočes,Petr Vácha,Ladislav Kučera
Barley is one of the most important crops in the world. Barley is used as both food and feed and is important for malt production. Demands for malting quality differ among countries and customs. Malting quality is a complex characteristic involving barley genetics, the environmental conditions during barley growth, and the technological parameters of the malting process. In this study, the hypothesis
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Correction to: Genome-wide characterization of the cellulose synthase gene superfamily in Pyrus bretschneideri and reveal its potential role in stone cell formation. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-09-11 Guohui Li,Xin Liu,Yuxuan Liang,Yang Zhang,Xi Cheng,Yongping Cai
The above article was published online with the same Figures 7 and 8.
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Comparative transcriptomic analysis reveals the mechanistic basis of Pib-mediated broad spectrum resistance against Magnaporthe oryzae. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-09-07 Jiehua Qiu,Feifei Lu,Meng Xiong,Shuai Meng,Xianglin Shen,Yanjun Kou
Rice blast, caused by the fungus Magnaporthe oryzae, is a highly damaging disease. Introducing genes, which confer a broad spectrum resistance to the disease, such as Pib, makes an important contribution to protecting rice production. However, little is known regarding the mechanistic basis of the products of such genes. In this study, transcriptome of the cultivar Lijiangxintuanheigu (LTH) and its
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Genome-wide association study for phosphate deficiency responsive root hair elongation in chickpea. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-09-05 Pawandeep Singh Kohli,Pankaj Kumar Verma,Rita Verma,Swarup K Parida,Jitendra K Thakur,Jitender Giri
Root hairs (RHs) are single-celled elongated epidermal cells and play a vital role in nutrient absorption, particularly for immobile minerals like phosphorus (P). As an adaptive response to P deficiency, an increase in RH length enhances root-soil contact and absorptive area for P absorption. Genetic variations have been reported for RH length and its response to P deficiency in plants. However, only
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A high-density SNP-based linkage map using genotyping-by-sequencing and its utilization for improved genome assembly of chickpea (Cicer arietinum L.). Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-08-27 Rashmi Gaur,Subodh Verma,Seema Pradhan,Heena Ambreen,Sabhyata Bhatia
Genotyping-by-sequencing (GBS) allows rapid identification of markers for use in development of linkage maps, which expedite efficient breeding programs. In the present study, we have utilized GBS approach to identify and genotype single-nucleotide polymorphism (SNP) markers in an inter-specific RIL population of Cicer arietinum L. X C. reticulatum. A total of 141,639 raw SNPs were identified using
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Genome-wide characterization of the cellulose synthase gene superfamily in Pyrus bretschneideri and reveal its potential role in stone cell formation. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-08-08 Guohui Li,Xin Liu,Yuxuan Liang,Yang Zhang,Xi Cheng,Yongping Cai
Members of the cellulose synthase (CesA) and cellulose synthase–like (Csl) families from the cellulose synthase gene superfamily participate in cellulose and hemicellulose synthesis in the plasma membrane. The members of this superfamily are vital for cell wall construction during plant growth and development. However, little is known about their function in pear fruit, a model for Rosaceae species
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Identification and characterization of Dicer-like genes in leaf rust pathogen (Puccinia triticina) of wheat. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-07-23 Himanshu Dubey,Kanti Kiran,Rajdeep Jaswal,Subhash C Bhardwaj,Tapan Kumar Mondal,Neha Jain,N K Singh,Arvind M Kayastha,Tilak Raj Sharma
Puccinia triticina (P. triticina) is one of the most devastating fungal pathogens of wheat which causes significant annual yield loss to the crop. Understanding the gene regulatory mechanism of the biotrophic pathogen is one of the important aspects of host-pathogen interaction studies. Dicer-like genes are considered as important mediators of RNAi-based gene regulation. In this study, we report the
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Proteomic profiling of developing wheat heads under water-stress. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-07-17 Shahidul Islam,Penghao Wang,Delphine Vincent,Javed M Khan,Angela Juhasz,Dean Diepeveen,Richard J Lipscombe,Wujun Ma,Rudi Appels
A replicated iTRAQ (isobaric tags for relative and absolute quantification) study on developing wheat heads from two doubled haploid (DH) lines identified from a cross between cv Westonia x cv Kauz characterized the proteome changes influenced by reproductive stage water-stress. All lines were exposed to 10 days of water-stress from early booting (Zadok 40), with sample sets taken from five head developmental
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Transcriptome analysis of different rice cultivars provides novel insights into the rice response to bacterial leaf streak infection. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-06-21 Ling Lu,Dewei Yang,Dingzhong Tang,Shengping Li,Zhiwei Chen
Bacterial leaf streak (BLS) is now the fourth-most devastating disease in rice. Dular and H359 are two indica rice varieties with contrasting responses to BLS. Dular displays high resistance, while H359 is susceptible. In this study, RNA-seq was used to examine the early molecular processes deployed during the resistance response of Dular and H359 at different times after inoculation. Differentially
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Identification of lncRNAs involved in wheat tillering development in two pairs of near-isogenic lines. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-06-01 Wanlin Zhou,Haoran Shi,Zhiqiang Wang,Yueting Zhao,Xiangjian Gou,Caixia Li,Guangdeng Chen,Shihang Liu,Mei Deng,Jian Ma,Youliang Zheng,Yuming Wei,Yaxi Liu
Emerging evidence demonstrates that lncRNAs participate in various developmental processes in plants via post-transcription regulation. However, few lncRNAs have been identified as regulators of tiller development in wheat (Triticum aestivum L.). In this study, high-throughput ribosomal depleted RNA sequencing was performed on the tillering nodes of two pairs of near-isogenic lines that differed only
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CRISPR/Cas9 genome editing shows the important role of AZC_2928 gene in nitrogen-fixing bacteria of plants. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-06-01 Xiaojing Wang,Sang Lv,Tao Liu,Jiale Wei,Shiyuan Qu,Yi Lu,Junbiao Zhang,Sanda Oo,Baohong Zhang,Xiaoping Pan,Huawei Liu
AZC_2928 gene (GenBank accession no. BAF88926.1) of Azorhizobium caulinodans ORS571 has sequence homology to 2,3-aminomutases. However, its function is unknown. In this study, we are for the first time to knock out the gene completely in A. caulinodans ORS571 using the current advanced genome editing tool, CRISPR/Cas9. Our results show that the editing efficiency is 34% and AZC_2928 plays an extremely
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One-to-one relationships between milk miRNA content and protein abundance in neonate duodenum support the potential for milk miRNAs regulating neonate development. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-05-27 Katelyn Huff,Aridany Suárez-Trujillo,Shihuan Kuang,Karen Plaut,Theresa Casey
Breast milk plays an essential role for offspring development; however, there lacks evidence of how specific milk components like nucleic acids mechanistically function to regulate neonate development. Previously, we found that maternal high-fat diet (HFD) not only significantly affected mRNA and miRNA content of the secreted milk transcriptome in mice but also affected the duodenal proteome of suckling
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Systematic analyses reveal RNA editing events involved in skeletal muscle development of goat (Capra hircus). Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-05-24 Liu Yang,Li Li,Bismark Kyei,Jiazhong Guo,Siyuan Zhan,Wei Zhao,Yumo Song,Tao Zhong,Linjie Wang,Lingyang Xu,Hongping Zhang
RNA editing is a posttranscriptional molecular process involved with specific nucleic modification, which can enhance the diversity of gene products. Adenosine-to-inosine (A-to-I, I is read as guanosine by both splicing and translation machinery) is the main type of RNA editing in mammals, which manifested as AG (adenosine-to-guanosine) in sequence data. Here, we aimed to explore patterns of RNA editing
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Chaperone client proteins evolve slower than non-client proteins. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-05-06 Manish Prakash Victor,Debarun Acharya,Sandip Chakraborty,Tapash Chandra Ghosh
Chaperones are important molecular machinery that assists proteins to attain their native three-dimensional structure crucial for function. Earlier studies using experimental evolution showed that chaperones impose a relaxation of sequence constraints on their “client” proteins, which may lead to the fixation of slightly deleterious mutations on the latter. However, we hypothesized that such a phenomenon
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Correction to: Analysis of the quinoa genome reveals conservation and divergence of the flowering pathways. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-11-18 Agnieszka A Golicz,Ursula Steinfort,Hina Arya,Mohan B Singh,Prem L Bhalla
The above article was published online with incorrect Fig. 5 legend. The legend for Fig. 4 was repeated in Fig. 5.
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Use of gene expression profile to identify potentially relevant transcripts to myofibrillar fragmentation index trait. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-04-14 Maria Malane Magalhães Muniz,Larissa Fernanda Simielli Fonseca,Ana Fabrícia Braga Magalhães,Danielly Beraldo Dos Santos Silva,Angela Canovas,Stephanie Lam,Jesus Aparecido Ferro,Fernando Baldi,Artur Loyola Chardulo,Lucia Galvão de Albuquerque
The myofibrillar fragmentation index (MFI) is an indicative trait for meat tenderness. Longissimus thoracis muscle samples from the 20 most extreme bulls (out of 80 bulls set) for MFI (high (n = 10) and low (n = 10) groups) trait were used to perform transcriptomic analysis, using RNA Sequencing (RNA-Seq). An average of 24.616 genes was expressed in the Nellore muscle transcriptome analysis. A total
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Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-03-25 Tongqiang Fan,Qixiang Zhang,Yuanyuan Hu,Zhengjia Wang,Youjun Huang
Non-coding RNAs with lengths greater than 200 bp are known as long non-coding RNAs (lncRNAs), and these RNAs play important role in gene regulation and plant development. However, to date, little is known regarding the role played by lncRNAs during flowering in hickory (Carya cathayensis). Here, we performed whole transcriptome RNA-sequencing of samples from hickory female and male floral buds, in
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Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-03-20 Nicolás D Franco-Sierra,Luisa F Posada,Germán Santa-María,Magally Romero-Tabarez,Valeska Villegas-Escobar,Javier C Álvarez
Bacillus subtilis is a remarkably diverse bacterial species that displays many ecological functions. Given its genomic diversity, the strain Bacillus subtilis EA-CB0575, isolated from the rhizosphere of a banana plant, was sequenced and assembled to determine the genomic potential associated with its plant growth promotion potential. The genome was sequenced by Illumina technology and assembled using
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Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-02-29 Xiaoyue Li,Cunyuan Li,Yueren Xu,Rui Yao,Huixiang Li,Wei Ni,Renzhe Quan,Mengdan Zhang,Li Liu,Shuting Yu,Yaseen Ullah,Ruirui Hu,Yaxin Li,Tao Guo,Xiaokui Wang,Shengwei Hu
Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes such as growth, development, and reproduction of animals. Here, we used RNA-seq technology
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Deep RNA-seq analysis reveals key responding aspects of wild banana relative resistance to Fusarium oxysporum f. sp. cubense tropical race 4. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-02-17 Wei-Ming Li,Miguel Dita,Mathieu Rouard,Wei Wu,Nicolas Roux,Jiang-Hui Xie,Xue-Jun Ge
Tropical race 4 of Fusarium oxysporum f. sp. cubense (FocTR4) is seriously threatening the banana industry worldwide. Resistant genotypes are present in wild relatives of banana, but little is known about the genetic and molecular mechanisms driving resistance responses. In this work, through in-depth expression analysis, we compared the responses of the resistant wild relative Musa acuminata ssp.
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Genome-wide analysis of the TCP transcription factor genes in five legume genomes and their response to salt and drought stresses. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-02-07 Lei Ling,Wenrui Zhang,Yimin An,Binghao Du,Dan Wang,Changhong Guo
The teosinte branched1, cycloidea, and proliferating cell factor family (TCP) proteins, plant-specific transcription factors, are involved in the regulation of plant development; however, the TCP gene family of legumes has been based primarily on a single crop. Here, a total of 55, 22, 26, 21, and 25 genes containing the VQ motif were identified from the genomes of Glycine max, Cicer arietinum, Phaseolus
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UNAGI: an automated pipeline for nanopore full-length cDNA sequencing uncovers novel transcripts and isoforms in yeast. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-01-18 Mohamad Al Kadi,Nicolas Jung,Shingo Ito,Shoichiro Kameoka,Takashi Hishida,Daisuke Motooka,Shota Nakamura,Tetsuya Iida,Daisuke Okuzaki
Sequencing the entire RNA molecule leads to a better understanding of the transcriptome architecture. SMARTer (Switching Mechanism at 5′-End of RNA Template) is a technology aimed at generating full-length cDNA from low amounts of mRNA for sequencing by short-read sequencers such as those from Illumina. However, short read sequencing such as Illumina technology includes fragmentation that results in
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Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-01-10 Sonia Balyan,Shaji V Joseph,Rashmi Jain,Roseeta Devi Mutum,Saurabh Raghuvanshi
MicroRNAs lie at the core of biological regulatory networks in plants. The recent discovery of isomiRs that are length variants of the annotated mature miRNAs has further unveiled the complexity of miRNome. Delineation of their functional relevance is critical to understand the complete functional spectrum of the miRNome. To apprehend the role of 5′ isomiRs in rice, we performed a comprehensive analysis
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Genome-wide identification and expression analysis of the CLC superfamily genes in tea plants (Camellia sinensis). Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-01-03 Anqi Xing,Yuanchun Ma,Zichen Wu,Shouhua Nong,Jiaojiao Zhu,Hua Sun,Jing Tao,Bo Wen,Xujun Zhu,Wanping Fang,Xiaocheng Li,Yuhua Wang
The voltage-gated chloride channel (CLC) superfamily is one of the most important anion channels that is widely distributed in bacteria and plants. CLC is involved in transporting various anions such as chloride (Cl-) and fluoride (F-) in and out of cells. Although Camellia sinensis is a hyper-accumulated F plant, there is no studies on the CLC gene superfamily in the tea plant. Here, 8 CLC genes were
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Bacterial diversity and functional metagenomics expounding the diversity of xenobiotics, stress, defense and CRISPR gene ontology providing eco-efficiency to Himalayan Hot Springs. Funct. Integr. Genomics (IF 3.058) Pub Date : 2020-01-02 Ishfaq Nabi Najar,Mingma Thundu Sherpa,Sayak Das,Nagendra Thakur
Sikkim is one of the bio-diverse states of India, which harbors diverse alkaline and sulfur rich hot springs in its vicinity. However, there is a dearth of data present in terms of microbial and its functional diversity as only a few hot springs have been studied in this area. Thus, in this regard, microbial and functional diversity of two hot springs by NGS, PLFA, and culture-independent approaches
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An RNAi suppressor activates in planta virus-mediated gene editing. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-12-18 Xian Zhang,Lihua Kang,Qi Zhang,Qiqi Meng,Yafei Pan,Zhiming Yu,Nongnong Shi,Stephen Jackson,Xinlian Zhang,Huizhong Wang,Mahmut Tor,Yiguo Hong
RNA-guided CRISPR/Cas9 technology has been developed for gene/genome editing (GE) in organisms across kingdoms. However, in planta delivery of the two core GE components, Cas9 and small guide RNA (sgRNA), often involves time-consuming and labor-intensive production of transgenic plants. Here we show that Foxtail mosaic virus, a monocot- and dicot-infecting potexvirus, can simultaneously express Cas9
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A transcriptomic analysis of Nsmce1 overexpression in mouse hippocampal neuronal cell by RNA sequencing. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-12-02 Mengting Gong,Zhen Wang,Yanjun Liu,Wenxing Li,Shoudong Ye,Jie Zhu,Hui Zhang,Jing Wang,Kan He
Mouse Nsmce1 gene is the homolog of non-structural maintenance of chromosomes element 1 (NSE1) that is mainly involved in maintenance of genome integrity, DNA damage response, and DNA repair. Defective DNA repair may cause neurological disorders such as Alzheimer’s disease (AD). So far, there is no direct evidence for the correlation between Nsmce1 and AD. In order to explore the function of Nsmce1
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Endoplasmic reticulum retention signaling and transmembrane channel proteins predicted for oilseed ω3 fatty acid desaturase 3 (FAD3) genes. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-11-28 Mohammad Fazel Soltani Gishini,Alireza Zebarjadi,Maryam Abdoli-Nasab,Mokhtar Jalali Javaran,Danial Kahrizi,David Hildebrand
Oilseed crop oils contain a variety of unsaturated fatty acids that are synthesized and regulated by fatty acid desaturases (FADs). In this study, 14 FAD3 (ω3 desaturase) protein sequences from oilseeds are analyzed and presented through the application of several computational tools. The results indicated a close relationship between Brassica napus and Camelina sativa, as well as between Salvia hispanica
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Genome-wide identification and characterization of long non-coding RNAs during differentiation of visceral preadipocytes in rabbit. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-11-19 Kun Du,Guo-Ze Wang,An-Yong Ren,Ming-Cheng Cai,Gang Luo,Xian-Bo Jia,Shen-Qiang Hu,Jie Wang,Shi-Yi Chen,Song-Jia Lai
Emerging evidence suggests that long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes, including adipogenesis. Despite being considered an ideal animal model for studying adipogenesis, little is known about the roles of lncRNAs in the regulation of rabbit preadipocyte differentiation. In the present study, visceral preadipocytes isolated from newborn rabbits were cultured
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Dynamic response of RNA editing to temperature in grape by RNA deep sequencing. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-11-19 Aidi Zhang,Xiaohan Jiang,Fuping Zhang,Tengfei Wang,Xiujun Zhang
RNA editing is a post-transcriptional process of modifying genetic information on RNA molecules, which provides cells an additional level of gene expression regulation. Unlike mammals, in land plants, RNA editing converts C-to-U residues in organelles. However, its potential roles in response to different stressors (heat, salt, and so on) remains unclear. Grape is one of the most popular and economically
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Comprehensive analysis of the expression profile of circRNAs and their predicted protein-coding ability in the muscle of mdx mice. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-11-18 Zubiao Song,Yanmei Liu,Xiaobo Fang,Mengshu Xie,Zhenyu Ma,Zhigang Zhong,Xuelin Feng,Weixi Zhang
Duchenne muscular dystrophy (DMD) is an X-linked genetic neuromuscular disease that is characterized by progressive muscle wasting and by defects in the regenerative capacity and inflammatory infiltration of muscle. Many noncoding RNAs (ncRNAs) participate in the pathophysiological mechanisms of this disease. To explore the role of circular RNAs (circRNAs), a type of ncRNAs, in DMD, microarray analysis
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Blocked synthesis of sporopollenin and jasmonic acid leads to pollen wall defects and anther indehiscence in genic male sterile wheat line 4110S at high temperatures. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-11-15 Xuetong Yang,Jiali Ye,Lingli Zhang,Xiyue Song
Environment-sensitive genic male sterility is a valid tool for hybrid production and hybrid breeding, but there are no previous reports of the molecular mechanism of fertility conversion. In this study, RNA-seq, phenotypic and cytological observations, and physiological indexes were applied to analyze thermo-sensitive genic male sterility line 4110S under different temperature conditions to explore
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RNA-Seq revealed that infection with white tip nematodes could downregulate rice photosynthetic genes. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-11-12 Hong-Le Wang,Si-Hua Yang,Mei Lv,Shan-Wen Ding,Jun-Yi Li,Chun-Ling Xu,Hui Xie
White-tip nematode, Aphelenchoides besseyi is a kind of widely distributed migratory parasitic nematode that can infect plant shoots. Transcriptome sequencing of plant parasitic nematodes and their host plants is helpful for understanding their interaction relationship. This study first reported expression patterns of defense-related genes in rice, and rice transcriptomes at different periods after
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Hippocampus-specific regulation of long non-coding RNA and mRNA expression in germ-free mice. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-11-01 Chanjuan Zhou,Xuechen Rao,Haiyang Wang,Benhua Zeng,Yue Yu,Jianjun Chen,Jiaju Zhong,Xunzhong Qi,Li Zeng,Peng Zheng,Wei Hong,Peng Xie
Gut microbiota can affect multiple brain functions and cause behavioral alterations through the microbiota-gut-brain axis. In our previous study, we found that the absence of gut microbiota can influence the expression of microRNAs and mRNAs in the hippocampal region of the germ-free (GF) mice. Long non-coding RNAs (lncRNAs) are increasingly being recognized as an important functional transcriptional
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Correction to: A large-scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice. Funct. Integr. Genomics (IF 3.058) Pub Date : 2018-07-10 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.
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Correction to: The heterologous expression of Arabidopsis PAP2 induces anthocyanin accumulation and inhibits plant growth in tomato. Funct. Integr. Genomics (IF 3.058) Pub Date : 2018-05-01 Nan Li,Han Wu,Qiangqiang Ding,Huihui Li,Zhifei Li,Jing Ding,Yi Li
In the original version of this article the "Acknowledgements" and the "Competing interests" were inadvertently omitted. The information missing in the original article is now given below.
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Addition to Special Issue "miRNA in Model and Complex Organisms". Funct. Integr. Genomics (IF 3.058) Pub Date : 2017-04-08
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Erratum to: Transcriptomics analysis of hulless barley during grain development with a focus on starch biosynthesis. Funct. Integr. Genomics (IF 3.058) Pub Date : 2017-01-07 Yawei Tang,Xingquan Zeng,Yulin Wang,Lijun Bai,Qijun Xu,Zexiu Wei,Hongjun Yuan,Tashi Nyima
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Erratum to: Genomic and functional features of the biosurfactant producing Bacillus sp. AM13. Funct. Integr. Genomics (IF 3.058) Pub Date : 2016-11-26 Shraddha Shaligram,Shreyas V Kumbhare,Dhiraj P Dhotre,Manohar G Muddeshwar,Atya Kapley,Neetha Joseph,Hemant J Purohit,Yogesh S Shouche,Shrikant P Pawar
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Erratum to: Control of flowering time and spike development in cereals: the earliness per se Eps-1 region in wheat, rice, and Brachypodium. Funct. Integr. Genomics (IF 3.058) Pub Date : 2016-08-24 Maria E Faricelli,Miroslav Valárik,Jorge Dubcovsky
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A transcriptomic study of selenium against liver injury induced by beta-cypermethrin in mice by RNA-seq. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-10-28 Kan He,Qingyang Tang,Mengting Gong,Silin Yang,Xianping Chen,Huiqiu Zhu,Dahai Liu,Bei Huang
Evidence from biochemical liver function index and histopathology analysis suggested that selenium could effectively repair the liver injury caused by beta-cypermethrin (β-CYP). However, the molecular mechanism of selenium against liver injury induced by β-CYP remains unclear. In the present study, dynamic changes in gene expression profiles before and after the treatment of Na2SeO3 in liver injury
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Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-10-26 Jamie A O'Rourke,Chantal E McCabe,Michelle A Graham
Preserving crop yield is critical for US soybean production and the global economy. Crop species have been selected for increased yield for thousands of years with individual lines selected for improved performance in unique environments, constraints not experienced by model species such as Arabidopsis. This selection likely resulted in novel stress adaptations, unique to crop species. Given that iron
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Evaluation of circulating leukocyte transcriptome and its relationship with immune function and blood markers in dairy cows during the transition period. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-10-25 Andrea Minuti,Nusrat Jahan,Vincenzo Lopreiato,Fiorenzo Piccioli-Cappelli,Lorenzo Bomba,Stefano Capomaccio,Juan J Loor,Paolo Ajmone-Marsan,Erminio Trevisi
Dairy cows during the transition period are faced with important physiological changes which include a dysfunctional immune system and an increased inflammatory state. New data are necessary to understand the key factors involved in the immune system regulation. Six dairy cows were sampled during transition period to investigate the leukocyte transcriptome changes and its relationship with blood biomarkers
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Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-10-25 Dekang Zhu,Zhishuang Yang,Jinge Xu,Mingshu Wang,Renyong Jia,Shun Chen,Mafeng Liu,Xinxin Zhao,Qiao Yang,Ying Wu,Shaqiu Zhang,Yunya Liu,Ling Zhang,Yanling Yu,Xiaoyue Chen,Anchun Cheng
Riemerella anatipestifer is a gram-negative bacterium that leads to severe contagious septicemia in ducks, turkeys, chickens, and wild waterfowl. Here, a pan-genome with 32 R. anatipestifer genomes is re-established, and the mathematical model is calculated to evaluate the expansion of R. anatipestifer genomes, which were determined to be open. Average nucleotide identity (ANI) and phylogenetic analysis
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Membrane proteomic analysis reveals the intestinal development is deteriorated by intrauterine growth restriction in piglets. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-10-04 Shimeng Huang,Cong Liu,Na Li,Zhenhua Wu,Tiantian Li,Dandan Han,Zhen Li,Jiangchao Zhao,Junjun Wang
The alterations of the intestinal proteome were observed in intrauterine growth restriction (IUGR) piglets during early life by gel-based approaches. Nevertheless, how IUGR affects the intestinal membrane proteome during neonatal development remains unclear. Here, we applied the iTRAQ-based proteomics technology and biochemical analysis to investigate the impact of IUGR on the membrane proteome of
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Characterization of natural genetic variation identifies multiple genes involved in salt tolerance in maize. Funct. Integr. Genomics (IF 3.058) Pub Date : 2019-09-14 Devinder Sandhu,Manju V Pudussery,Rohit Kumar,Andrew Pallete,Paul Markley,William C Bridges,Rajandeep S Sekhon
Progressive decline in irrigation water is forcing farmers to use brackish water which increases soil salinity and exposes the crop plants to salinity. Maize, one of the most important crops, is sensitive to salinity. Salt tolerance is a complex trait controlled by a number of physiological and biochemical processes. Scant information is available on the genetic architecture of salt tolerance in maize
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