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You searched for: Journal Functional & integrative genomics Remove constraint Journal: Functional & integrative genomics Publication Year 2018 Remove constraint Publication Year: 2018 Source 2018 v.18 no.4 Remove constraint Source: 2018 v.18 no.4
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1. Exploration of miRNAs and target genes of cytoplasmic male sterility line in cotton during flower bud development

Author:
Nie, Hushuai; Wang, Yumei; Su, Ying; Hua, Jinping
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 457-476
ISSN:
1438-793X
Subject:
Gossypium hirsutum; RNA libraries; buds; cell death; cotton; crops; cytoplasmic male sterility; developmental stages; gene expression regulation; heterosis; hybrids; microRNA; pollen germination; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sexual reproduction; transcriptomics; vegetative growth
Abstract:
... 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 ...
DOI:
10.1007/s10142-018-0606-z

2. GA3 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

Author:
Upadhyay, Anuradha; Maske, Smita; Jogaiah, Satisha; Kadoo, NarendraY.; Gupta, VidyaS.
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 439-455
ISSN:
1438-793X
Subject:
RNA; Vitis vinifera; breeding; chromosome mapping; flowering; gene expression regulation; genes; genetic markers; gibberellic acid; metabolism; quantitative polymerase chain reaction; sucrose; table grapes; transcription factors; transcriptome; transcriptomics
Abstract:
... 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 clust ...
DOI:
10.1007/s10142-018-0605-0

3. Genome sequence and comparative analysis of Bacillus cereus BC04, reveals genetic diversity and alterations for antimicrobial resistance

Author:
Srinivasan, VijayaBharathi; Angrasan, Mahavinod; Chandel, Neha; Rajamohan, Govindan
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 477-487
ISSN:
1438-793X
Subject:
Bacillus cereus; antibiotic resistance; digestive system; drugs; enzymes; feces; foodborne illness; genes; genetic variation; genomic islands; hemolysins; nucleotide sequences; stress response; virulence; India
Abstract:
... 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, modifyin ...
DOI:
10.1007/s10142-018-0600-5

4. Genomic and physiological analyses of an indigenous strain, Enterococcus faecium 17OM39

Author:
Ghattargi, VikasC.; Nimonkar, YogeshS.; Burse, ShaunakA.; Davray, Dimple; Kumbhare, ShreyasV.; Shetty, SudarshanA.; Gaikwad, MeghanaA.; Suryavanshi, MangeshV.; Doijad, SwapnilP.; Utage, Bhimashankar; Sharma, OmPrakash; Shouche, YogeshS.; Meti, BharatiS.; Pawar, ShrikantP.
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 385-399
ISSN:
1438-793X
Subject:
Enterococcus faecium; adults; anti-infective agents; antimicrobial properties; bacteria; bile salts; blood serum; cell lines; essential amino acids; exopolysaccharides; feces; genes; genomics; hemolysis; human health; humans; hydrophobicity; intestinal microorganisms; pH; plasmids; probiotics; proteinases; ribosomal RNA; sequence analysis; stress response; virulence; vitamins
Abstract:
... 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 17O ...
DOI:
10.1007/s10142-018-0596-x

5. Integrated analysis of mRNA-seq and miRNA-seq for host susceptibilities to influenza A (H7N9) infection in inbred mouse lines

Author:
Bao, Suying; Jia, Lilong; Zhou, Xueya; Zhang, Zhi-Gang; Wu, HazelWai Lan; Yu, Zhe; Ng, Gordon; Fan, Yanhui; Wong, DanaS. M.; Huang, Shishu; Wang To, KelvinKai; Yuen, Kwok-Yung; Yeung, ManLung; Song, You-Qiang
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 411-424
ISSN:
1438-793X
Subject:
Orthomyxoviridae; disease severity; genes; genetic background; genetic factors; histopathology; host-pathogen relationships; immunohistochemistry; influenza; mice; microRNA; pandemic; pathogenicity; staining; temporal variation; therapeutics; time series analysis; transcription (genetics); transcriptome; virus replication
Abstract:
... 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 miR ...
DOI:
10.1007/s10142-018-0602-3

6. Landscape of long non-coding RNAs in Trichophyton mentagrophytes-induced rabbit dermatophytosis lesional skin and normal skin

Author:
Xiao, Wudian; Hu, Yongsong; Tong, Yan; Cai, Mingcheng; He, Hongbing; Liu, Buwei; Shi, Yu; Wang, Jie; Qin, Yinghe; Lai, Songjia
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 401-410
ISSN:
1438-793X
Subject:
Trichophyton mentagrophytes; Y chromosome; biopsy; dermatomycoses; exons; females; gene expression regulation; microRNA; non-coding RNA; pathogenesis; rabbits; sequence analysis; transcriptome
Abstract:
... 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 R ...
DOI:
10.1007/s10142-018-0601-4

7. Selection of growth-related genes and dominant genotypes in transgenic Yellow River carp Cyprinus carpio L.

Author:
Luo, Lifei; Huang, Rong; Zhang, Aidi; Yang, Cheng; Chen, Liangming; Zhu, Denghui; Li, Yongming; He, Libo; Liao, Lanjie; Zhu, Zuoyan; Wang, Yaping
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 425-437
ISSN:
1438-793X
Subject:
Cyprinus carpio; body weight; carp; feed conversion; genes; genome-wide association study; genotype; growth traits; marker-assisted selection; phenotype; progeny; single nucleotide polymorphism; transgenic animals; Yellow River
Abstract:
... 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 con ...
DOI:
10.1007/s10142-018-0597-9
PubMed:
29623522
PubMed Central:
PMC6004361

8. Sequence and functional characterization of MIRNA164 promoters from Brassica shows copy number dependent regulatory diversification among homeologs

Author:
Jain, Aditi; Anand, Saurabh; Singh, NeerK; Das, Sandip
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 369-383
ISSN:
1438-793X
Subject:
Arabidopsis lyrata; Brassica carinata; Brassica juncea; Brassica napus; Brassica nigra; Brassica oleracea; Capsella; binding sites; diploidy; genes; genomics; karyotyping; leaves; microRNA; phylogeny; polyploidy; promoter regions; sequence homology; topology; transcription factors; trichomes
Abstract:
... 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 MI ...
DOI:
10.1007/s10142-018-0598-8

9. The SbcC and SbcD homologs of the cyanobacterium Anabaena sp. strain PCC7120 (Alr3988 and All4463) contribute independently to DNA repair

Author:
Pandey, Sarita; Kirti, Anurag; Kumar, Arvind; Rajaram, Hema
Source:
Functional & integrative genomics 2018 v.18 no.4 pp. 357-367
ISSN:
1438-793X
Subject:
Anabaena; DNA adducts; DNA repair; bacteria; cell physiology; chromosomes; eukaryotic cells; gamma radiation; mitomycin; mutants; operon; prokaryotic cells; proteins
Abstract:
... 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 hypoth ...
DOI:
10.1007/s10142-018-0599-7