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- 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
-
http://dx.doi.org/10.1007/s10142-018-0606-z
- 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
-
http://dx.doi.org/10.1007/s10142-018-0605-0
- 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
-
http://dx.doi.org/10.1007/s10142-018-0600-5
- 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
-
http://dx.doi.org/10.1007/s10142-018-0596-x
- 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
-
http://dx.doi.org/10.1007/s10142-018-0602-3
- 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
-
http://dx.doi.org/10.1007/s10142-018-0601-4
- 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
-
http://dx.doi.org/10.1007/s10142-018-0597-9
- 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
-
http://dx.doi.org/10.1007/s10142-018-0598-8
- 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
-
http://dx.doi.org/10.1007/s10142-018-0599-7