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You searched for: Journal Genes & genomics Remove constraint Journal: Genes & genomics Publication Year 2018 Remove constraint Publication Year: 2018 Source 2018 v.40 no.2 Remove constraint Source: 2018 v.40 no.2
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1. Association analysis of the SNP (rs345476947) in the FUT2 gene with the production and reproductive traits in pigs

Author:
Wang, Haifei; Wu, Sen; Wu, Jiayun; Sun, Shouyong; Wu, Shenglong; Bao, Wenbin
Source:
Genes & genomics 2018 v.40 no.2 pp. 199-206
ISSN:
1976-9571
Subject:
neonates; duodenum; lymph; eyes; gene expression; spleen; genotype; Large White; introns; selection methods; messenger RNA; muscles; reproductive traits; kidneys; sows; backfat; single nucleotide polymorphism; quantitative polymerase chain reaction; liver; fat thickness; genetic variation; piglets; birth weight
Abstract:
... The FUT2 gene was considered as an important candidate for pathogenic infections, while the potential associations between this gene and the production and reproductive traits of pigs have not been explored. In this study, we detected the genetic variants of porcine FUT2 gene and analyzed the associations of the polymorphisms with FUT2 mRNA expression and production and reproductive traits (age at ...
DOI:
10.1007/s13258-017-0623-7

2. Comparative genomic analysis of Lactobacillus plantarum GB-LP4 and identification of evolutionarily divergent genes in high-osmolarity environment

Author:
Jung, Jaehoon; Kim, Kwondo; Yoo, DongAhn; Lee, Chanho; Kang, Jungsun; Cho, Kyungjin; Kang, Dae-Kyung; Kwak, Woori; Yoon, SookHee; Sohn, Hawsun; Kim, Heebal; Cho, Seoae
Source:
Genes & genomics 2018 v.40 no.2 pp. 217-223
ISSN:
1976-9571
Subject:
Lactobacillus plantarum; fermentation; fermented vegetables; genes; genetic variation; genome assembly; genomics; homeostasis; osmolarity; osmotic pressure; pH; probiotics
Abstract:
... Lactobacillus plantarum is one of the widely-used probiotics and there have been a large number of advanced researches on the effectiveness of this species. However, the difference between previously reported plantarum strains, and the source of genomic variation among the strains were not clearly specified. In order to understand further on the molecular basis of L. plantarum on Korean traditiona ...
DOI:
10.1007/s13258-017-0555-2
PubMed:
29568414
PubMed Central:
PMC5846872

3. De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery

Author:
Han, Chong; Li, Qiang; Li, Xiufeng; Zhang, Zhipeng; Huang, Jianrong
Source:
Genes & genomics 2018 v.40 no.2 pp. 167-176
ISSN:
1976-9571
Subject:
transcriptomics; microsatellite repeats; gene ontology; polymerase chain reaction; data collection; unigenes; transcriptome; genomics; genetic variation; hybridization probes; genetic markers; China
Abstract:
... Sphaeroma terebrans, an economically and ecologically important marine wood-boring isopod, is mainly distributed in tropical and subtropical mangroves. Nevertheless, available genomic and transcriptomic information for this isopod is extremely deficient. Here, we first performed the assembly of S. terebrans transcriptome by Illumina sequencing. A total of 51,092 high-quality unigenes with an avera ...
DOI:
10.1007/s13258-017-0618-4

4. Identification of novel EST-SSR markers by transcriptome sequencing in ridgetail white prawn Exopalaemon carinicauda

Author:
Wang, Jiajia; Ge, Qianqian; Li, Jitao; Gao, Haiyu; Li, Jian; Zhao, Fazhen
Source:
Genes & genomics 2018 v.40 no.2 pp. 207-215
ISSN:
1976-9571
Subject:
transcriptomics; microsatellite repeats; loci; DNA primers; gene ontology; breeding; expressed sequence tags; mariculture; polymerase chain reaction; genomics; shrimp; genetic variation; genetic markers; China
Abstract:
... The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of ...
DOI:
10.1007/s13258-017-0571-2

5. Performance evaluation method for read mapping tool in clinical panel sequencing

Author:
Lee, Hojun; Lee, Ki-Wook; Lee, Taeseob; Park, Donghyun; Chung, Jongsuk; Lee, Chung; Park, Woong-Yang; Son, Dae-Soon
Source:
Genes & genomics 2018 v.40 no.2 pp. 189-197
ISSN:
1976-9571
Subject:
bioinformatics; biopsy; clinical trials; genome; high-throughput nucleotide sequencing; liquids; system optimization
Abstract:
... In addition to the rapid advancement in Next-Generation Sequencing (NGS) technology, clinical panel sequencing is being used increasingly in clinical studies and tests. However, tools that are used in NGS data analysis have not been comparatively evaluated in performance for panel sequencing. This study aimed to evaluate the tools used in the alignment process, the first procedure in bioinformatic ...
DOI:
10.1007/s13258-017-0621-9
PubMed:
29568413
PubMed Central:
PMC5846869

6. Physiological and proteomic analysis of plant growth enhancement by the rhizobacteria Bacillus sp. JS

Author:
Kim, JiSeong; Lee, JeongEun; Nie, Hualin; Lee, YongJae; Kim, SunTae; Kim, Sun-Hyung
Source:
Genes & genomics 2018 v.40 no.2 pp. 129-136
ISSN:
1976-9571
Subject:
Bacillus (bacteria); Lactuca sativa; Nicotiana tabacum; binding proteins; chlorophyll; lettuce; plant growth-promoting rhizobacteria; plant proteins; proteomics; rhizosphere bacteria; shoots; tobacco; two-dimensional gel electrophoresis
Abstract:
... In this study, the effects of the plant growth-promoting rhizobacterium (PGPR), Bacillus sp. JS on the growth of tobacco (Nicotiana tabacum ‘Xanthi’) and lettuce (Lactuca sativa ‘Crispa’), were evaluated by comparing various growth parameters between plants treated with the bacterium and those exposed to water or nutrient broth as control. In both tobacco and lettuce, fresh weight and length of sh ...
DOI:
10.1007/s13258-017-0615-7

7. The complete mitochondrial genomes of Tarsiger cyanurus and Phoenicurus auroreus: a phylogenetic analysis of Passeriformes

Author:
Zhang, Huabin; Bai, Yuze; Shi, Xuejia; Sun, Linxia; Wang, Zhengfei; Wu, Xiaobing
Source:
Genes & genomics 2018 v.40 no.2 pp. 151-165
ISSN:
1976-9571
Subject:
Carduelis; Emberiza; Muscicapidae; Paridae; birds; genes; mitochondrial DNA; mitochondrial genome; monophyly; paraphyly; ribosomal RNA; transfer RNA
Abstract:
... Passeriformes is the largest group within aves and the phylogenetic relationships between Passeriformes have caused major disagreement in ornithology. Particularly, the phylogenetic relationships between muscicapoidea and sylvioidea are complex, and their taxonomic boundaries have not been clearly defined. Our aim was to study the status of two bird species: Tarsiger cyanurus and Phoenicurus auror ...
DOI:
10.1007/s13258-017-0617-5

8. The relationship between genetic polymorphisms in apolipoprotein E (ApoE) gene and osteonecrosis of the femoral head induced by steroid in Chinese Han population

Author:
Yuan, Lin; Li, Wei; Wang, Xianquan; Yang, Guang; Yu, Haiyang; Sun, Shui
Source:
Genes & genomics 2018 v.40 no.2 pp. 225-231
ISSN:
1976-9571
Subject:
Chinese people; alleles; apolipoprotein E; bone diseases; case-control studies; femur; haplotypes; lipid metabolism; patients; polymerase chain reaction; restriction fragment length polymorphism; risk; single nucleotide polymorphism
Abstract:
... Previous studies suggested that apolipoprotein E (ApoE) genetic polymorphisms (SNPs) may result in abnormal lipid metabolism. Therefore, genetic polymorphisms in ApoE may be associated with the occurrence of osteonecrosis of the femoral head (ONFH). A case control study was designed to include 580 patients with steroid-induced ONFH and 560 age- and sex-matched non steroid-induced ONFH control subj ...
DOI:
10.1007/s13258-017-0625-5

9. Transcriptomic analysis of the heat stress response for a commercial baker’s yeast Saccharomyces cerevisiae

Author:
Varol, Duygu; Purutçuoğlu, Vilda; Yılmaz, Remziye
Source:
Genes & genomics 2018 v.40 no.2 pp. 137-150
ISSN:
1976-9571
Subject:
Saccharomyces cerevisiae; environmental factors; gene expression regulation; genes; heat shock proteins; heat shock response; heat stress; industrial applications; microarray technology; nucleic acid hybridization; statistical analysis; temperature; transcription (genetics); transcription factors; transcriptome; transcriptomics
Abstract:
... The aim of this study is to explore the effects of heat stresses on global gene expression profiles and to identify the candidate genes for the heat stress response in commercial baker’s yeast (Saccharomyces cerevisiae) by using microarray technology and comparative statistical data analyses. The data from all hybridizations and array normalization were analyzed using the GeneSpringGX 12.1 (Agilen ...
DOI:
10.1007/s13258-017-0616-6

10. Ty3/Gypsy retrotransposons in the Pacific abalone Haliotis discus hannai: characterization and use for species identification in the genus Haliotis

Author:
Lee, Sung-Il; Gim, Jeong-An; Lim, Min-Ji; Kim, Heui-Soo; Nam, Bo-Hye; Kim, Nam-Soo
Source:
Genes & genomics 2018 v.40 no.2 pp. 177-187
ISSN:
1976-9571
Subject:
Haliotis discus hannai; abalone; genetic markers; genome; phylogeny; polymerase chain reaction; retrotransposons; species identification; terminal repeat sequences; transposons
Abstract:
... Transposable elements are highly abundant elements that are present in all eukaryotic species. Here, we present a molecular description of abalone retrotransposon (Abret) elements. The genome of Haliotis discus hannai contains 130 Abret elements which were all Ty3/Gypsy retrotransposons. The Ty1/Copia elements were absent in the H. discus hannai genome. Most of the elements were not complete due t ...
DOI:
10.1007/s13258-017-0619-3