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Functional & Integrative Genomics

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https://www.readbyqxmd.com/read/29754269/starch-content-differences-between-two-sweet-potato-accessions-are-associated-with-specific-changes-in-gene-expression
#1
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
https://www.readbyqxmd.com/read/29752561/searching-whole-genome-sequences-for-biochemical-identification-features-of-emerging-and-reemerging-pathogenic-corynebacterium-species
#2
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
https://www.readbyqxmd.com/read/29748923/proteomics-analysis-reveals-marker-proteins-for-minor-vein-initiation-in-rice-leaf
#3
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
https://www.readbyqxmd.com/read/29744759/heterologous-expression-of-brassica-juncea-annexin-annbj2-confers-salt-tolerance-and-aba-insensitivity-in-transgenic-tobacco-seedlings
#4
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
https://www.readbyqxmd.com/read/29737453/integrating-cnvs-into-meta-qtl-identified-gbp4-as-positional-candidate-for-adult-cattle-stature
#5
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
https://www.readbyqxmd.com/read/29730773/comparison-of-gene-co-networks-reveals-the-molecular-mechanisms-of-the-rice-oryza-sativa-l-response-to-rhizoctonia-solani-ag1-ia-infection
#6
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
https://www.readbyqxmd.com/read/29730772/genome-annotation-and-comparative-genomic-analysis-of-bacillus-subtilis-mj01-a-new-bio-degradation-strain-isolated-from-oil-contaminated-soil
#7
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
https://www.readbyqxmd.com/read/29675811/systematic-analysis-and-comparison-of-the-phd-finger-gene-family-in-chinese-pear-pyrus-bretschneideri-and-its-role-in-fruit-development
#8
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...
April 20, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29666977/candidate-genes-of-flavonoid-biosynthesis-in-selaginella-bryopteris-l-baker-identified-by-rna-seq
#9
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...
April 18, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29651641/transcriptome-wide-identification-and-expression-profile-analysis-of-the-bhlh-family-genes-in-camellia-sinensis
#10
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...
April 12, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29626311/exploration-of-mirnas-and-target-genes-of-cytoplasmic-male-sterility-line-in-cotton-during-flower-bud-development
#11
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...
April 7, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29626310/ga-3-application-in-grapes-vitis-vinifera-l-modulates-different-sets-of-genes-at-cluster-emergence-full-bloom-and-berry-stage-as-revealed-by-rna-sequence-based-transcriptome-analysis
#12
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...
April 6, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29623522/selection-of-growth-related-genes-and-dominant-genotypes-in-transgenic-yellow-river-carp-cyprinus-carpio-l
#13
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...
April 5, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29619642/genome-sequence-and-comparative-analysis-of-bacillus-cereus-bc04-reveals-genetic-diversity-and-alterations-for-antimicrobial-resistance
#14
Vijaya Bharathi Srinivasan, Mahavinod Angrasan, Neha Chandel, Govindan Rajamohan
In this study, we delineated the genome sequence of a Bacillus cereus strain BC04 isolated from a stool sample in India. The draft genome is 5.1 Mb in size and consists of total 109 scaffolds, GC content is 35.2% with 5182 coding genes. The comparative analysis with other completely sequenced genomes highlights the unique presence of genomic islands, hemolysin, capsular synthetic protein, modifying enzymes accC7 and catA15, regulators of antibiotic resistance MarR and LysR with annotated functions related to virulence, stress response, and antimicrobial resistance...
April 4, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29564648/transcriptome-analysis-of-brassica-juncea-var-tumida-tsen-responses-to-plasmodiophora-brassicae-primed-by-the-biocontrol-strain-zhihengliuella-aestuarii
#15
Yuanli Luo, Daiwen Dong, Yu Su, Xuyi Wang, Yumei Peng, Jiang Peng, Changyong Zhou
Mustard clubroot, caused by Plasmodiophora brassicae, is a serious disease that affects Brassica juncea var. tumida Tsen, a mustard plant that is the raw material for a traditional fermented food manufactured in Chongqing, China. In our laboratory, we screened the antagonistic bacteria Zhihengliuella aestuarii against P. brassicae. To better understand the biocontrol mechanism, three transcriptome analyses of B. juncea var. tumida Tsen were conducted using Illumina HiSeq 4000, one from B. juncea only inoculated with P...
March 22, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29564647/integrated-analysis-of-mrna-seq-and-mirna-seq-for-host-susceptibilities-to-influenza-a-h7n9-infection-in-inbred-mouse-lines
#16
Suying Bao, Lilong Jia, Xueya Zhou, Zhi-Gang Zhang, Hazel Wai Lan Wu, Zhe Yu, Gordon Ng, Yanhui Fan, Dana S M Wong, Shishu Huang, Kelvin Kai Wang To, Kwok-Yung Yuen, Man Lung Yeung, You-Qiang Song
Host genetic factors play an important role in diverse host outcomes after influenza A (H7N9) infection. Studying differential responses of inbred mouse lines with distinct genetic backgrounds to influenza virus infection could substantially increase our understanding of the contributory roles of host genetic factors to disease severity. Here, we utilized an integrated approach of mRNA-seq and miRNA-seq to investigate the transcriptome expression and regulation of host genes in C57BL/6J and DBA/2J mouse strains during influenza virus infection...
March 21, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29560532/landscape-of-long-non-coding-rnas-in-trichophyton-mentagrophytes-induced-rabbit-dermatophytosis-lesional-skin-and-normal-skin
#17
Wudian Xiao, Yongsong Hu, Yan Tong, Mingcheng Cai, Hongbing He, Buwei Liu, Yu Shi, Jie Wang, Yinghe Qin, Songjia Lai
Emerging evidences suggest that long non-coding RNAs (lncRNAs) play important role in disease development. However, the role of rabbit lncRNAs in the pathogenesis of dermatophytosis remains elusive. The present study aimed to study and characterize lncRNA transcriptome in 8 T. mentagrophytes-induced female rabbit dermatophytosis lesional (TM) and 4 normal saline-infected (NS) skin biopsies using RNAseq. We identified 5883 lncRNAs in 12 strand-specific RNA-seq libraries and found 64 differentially expressed lncRNAs (q < 0...
March 20, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29556852/genomic-and-physiological-analyses-of-an-indigenous-strain-enterococcus-faecium-17om39
#18
Vikas C Ghattargi, Yogesh S Nimonkar, Shaunak A Burse, Dimple Davray, Shreyas V Kumbhare, Sudarshan A Shetty, Meghana A Gaikwad, Mangesh V Suryavanshi, Swapnil P Doijad, Bhimashankar Utage, Om Prakash Sharma, Yogesh S Shouche, Bharati S Meti, Shrikant P Pawar
The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity...
March 19, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29532337/sequence-and-functional-characterization-of-mirna164-promoters-from-brassica-shows-copy-number-dependent-regulatory-diversification-among-homeologs
#19
Aditi Jain, Saurabh Anand, Neer K Singh, Sandip Das
The impact of polyploidy on functional diversification of cis-regulatory elements is poorly understood. This is primarily on account of lack of well-defined structure of cis-elements and a universal regulatory code. To the best of our knowledge, this is the first report on characterization of sequence and functional diversification of paralogous and homeologous promoter elements associated with MIR164 from Brassica. The availability of whole genome sequence allowed us to identify and isolate a total of 42 homologous copies of MIR164 from diploid species-Brassica rapa (A-genome), Brassica nigra (B-genome), Brassica oleracea (C-genome), and allopolyploids-Brassica juncea (AB-genome), Brassica carinata (BC-genome) and Brassica napus (AC-genome)...
March 12, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29524012/the-sbcc-and-sbcd-homologs-of-the-cyanobacterium-anabaena-sp-strain-pcc7120-alr3988-and-all4463-contribute-independently-to-dna-repair
#20
Sarita Pandey, Anurag Kirti, Arvind Kumar, Hema Rajaram
The ubiquitous SbcCD exonuclease complex has been shown to perform an important role in DNA repair across prokaryotes and eukaryotes. However, they have remained uncharacterized in the ancient and stress-tolerant cyanobacteria. In the cyanobacterium Anabaena sp. strain PCC7120, SbcC and SbcD homologs, defined on the basis of the presence of corresponding functional domains, are annotated as hypothetical proteins, namely Alr3988 and All4463 respectively. Unlike the presence of sbcC and sbcD genes in a bicistronic operon in most organisms, these genes were distantly placed on the chromosome in Anabaena, and found to be negatively regulated by LexA...
March 9, 2018: Functional & Integrative Genomics
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