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You searched for: Journal Genomics Remove constraint Journal: Genomics Publication Year 2020 Remove constraint Publication Year: 2020 Source 2020 v.112 no.1 Remove constraint Source: 2020 v.112 no.1
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1. Abiotic stress induced miRNA-TF-gene regulatory network: A structural perspective

Author:
Sharma, Rinku; Upadhyay, Shashankaditya; Bhat, Basharat; Singh, Garima; Bhattacharya, Sudeepto; Singh, Ashutosh
Source:
Genomics 2020 v.112 no.1 pp. 412-422
ISSN:
0888-7543
Subject:
Arabidopsis; cold; cold stress; cultivars; databases; drought; flooded conditions; genes; meta-analysis; microRNA; salt stress; transcription (genetics); transcription factors; transcriptome
Abstract:
... MicroRNAs (miRNAs) and transcription factors (TFs) are the largest families of trans-acting gene regulatory species, which are pivotal players in a complex regulatory network. Recently, extensive research on miRNAs and TFs in agriculture has identified these trans-acting regulatory species, as an effective tool for engineering new crop cultivars to increase yield and quality as well tolerance to e ...
DOI:
10.1016/j.ygeno.2019.03.004

2. Accurate prediction of maize grain yield using its contributing genes for gene-based breeding

Author:
Zhang, Meiping; Cui, Yanru; Liu, Yun-Hua; Xu, Wenwei; Sze, Sing-Hoi; Murray, Seth C.; Xu, Shizhong; Zhang, Hong-Bin
Source:
Genomics 2020 v.112 no.1 pp. 225-236
ISSN:
0888-7543
Subject:
Zea mays; alleles; corn; crops; data collection; genotype; grain yield; humans; livestock; medicine; messenger RNA; phenotype; phenotypic selection; prediction; progeny
Abstract:
... Accurately predicting the phenotypes of complex traits is crucial to enhanced breeding in plants and livestock, and to enhanced medicine in humans. Here we reports the first study accurately predicting complex traits using their contributing genes, especially their number of favorable alleles (NFAs), genotypes and transcript expressions, with the grain yield of maize, Zea mays L. When the NFAs or ...
DOI:
10.1016/j.ygeno.2019.02.001

3. Alternative metabolic routes in channeling xylose to cordycepin production of Cordyceps militaris identified by comparative transcriptome analysis

Author:
Wongsa, Boontariga; Raethong, Nachon; Chumnanpuen, Pramote; Wong-ekkabut, Jirasak; Laoteng, Kobkul; Vongsangnak, Wanwipa
Source:
Genomics 2020 v.112 no.1 pp. 629-636
ISSN:
0888-7543
Subject:
Cordyceps militaris; adenosine monophosphate; biomass; biosynthesis; carbon; cordycepin; gene expression regulation; genes; glutamic acid; growth models; metabolites; pentoses; quantitative polymerase chain reaction; transcription (genetics); transcriptome; transcriptomics; xylose
Abstract:
... The responsive mechanism of C. militaris TBRC7358 on xylose utilization was investigated by comparative analysis of transcriptomes, growth kinetics and cordycepin productions. The result showed that the culture grown on xylose exhibited high production yield of cordycepin on dry biomass. Comparing xylose to other carbon sources, a set of significantly up-regulated genes in xylose were enriched in ...
DOI:
10.1016/j.ygeno.2019.04.015

4. Analysis of synonymous codon usage patterns of HPRT1 gene across twelve mammalian species

Author:
De Mandal, Surajit; Mazumder, Tarikul Huda; Panda, Amrita Kumari; Kumar, Nachimuthu Senthil; Jin, Fengliang
Source:
Genomics 2020 v.112 no.1 pp. 304-311
ISSN:
0888-7543
Subject:
codons; dopamine; evolution; gene expression; guanine; hypoxanthine; mammals; mutation; neurons; neurotransmitters
Abstract:
... Genetic changes in Hypoxanthine guanine phosphoribosyltransferace (HPRT1) gene can alter the expression of the dopamine neurotransmitter leads to abnormal neuron function, a disease called Lesch-Nyhan syndrome (LNS). Although different studies were conducted on LNS, information on codon usage bias (CUB) of HPRT1 gene is limited. The present study examines the genetic determinants of CUB in HPRT1 g ...
DOI:
10.1016/j.ygeno.2019.02.010

5. A proposed core genome scheme for analyses of the Salmonella genus

Author:
Pearce, Madison E.; Chattaway, Marie A.; Grant, Kathie; Maiden, Martin C.J.
Source:
Genomics 2020 v.112 no.1 pp. 371-378
ISSN:
0888-7543
Subject:
Salmonella bongori; Salmonella enterica; foods; genome; hosts; human diseases; humans; loci; secondary infection
Abstract:
... The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed ...
DOI:
10.1016/j.ygeno.2019.02.016
PubMed:
30905613
PubMed Central:
PMC6978875

6. A TRIZ-inspired bat algorithm for gene selection in cancer classification

Author:
Al-Betar, Mohammed Azmi; Alomari, Osama Ahmad; Abu-Romman, Saeid M.
Source:
Genomics 2020 v.112 no.1 pp. 114-126
ISSN:
0888-7543
Subject:
algorithms; comparative study; data collection; gene expression; genes; neoplasms; patients; prognosis; selection methods
Abstract:
... Gene expression data are expected to make a great contribution in the producing of efficient cancer diagnosis and prognosis. Gene expression data are coded by large measured genes, and only of a few number of them carry precious information for different classes of samples. Recently, several researchers proposed gene selection methods based on metaheuristic algorithms for analysing and interpretin ...
DOI:
10.1016/j.ygeno.2019.09.015

7. Characterization and comparison of the mitochondrial genomes from two Alpheidae species and insights into the phylogeny of Caridea

Author:
Wang, Qi; Wang, Ziqian; Tang, Dan; Xu, Xinyi; Tao, Yitao; Ji, Chenyao; Wang, Zhengfei
Source:
Genomics 2020 v.112 no.1 pp. 65-70
ISSN:
0888-7543
Subject:
Bayesian theory; Decapoda; amino acids; data collection; gene order; gene rearrangement; genetic structure; genomics; mitochondrial genes; mitochondrial genome; monophyly; nucleotides; shrimp; statistical analysis; topology; transfer RNA
Abstract:
... The mitochondrial genome (mitogenome) has been widely used in phylogenetics and molecular evolution as a parameter, due to its simple genetic structure, high evolutionary rate, and compositional heterogeneity properties. Alpheidae is a large and highly diverse family of the Caridea infraorder, currently containing about 600 species dispersed all over the world. However, only a few shrimps in Alphe ...
DOI:
10.1016/j.ygeno.2019.08.013

8. Characterization of Dof family in Pyrus bretschneideri and role of PbDof9.2 in flowering time regulation

Author:
Liu, Xueying; Liu, Zhe; Hao, Ziwei; Chen, Guodong; Qi, Kaijie; Zhang, Hao; Jiao, Huijun; Wu, Xiao; Zhang, Shaoling; Wu, Juyou; Wang, Peng
Source:
Genomics 2020 v.112 no.1 pp. 712-720
ISSN:
0888-7543
Subject:
Arabidopsis; DNA; Pyrus bretschneideri; circadian clocks; flowering date; pears; phylogeny; transcription factors
Abstract:
... DNA binding with One Finger (Dof) proteins are plant-specific transcription factors with highly conserved Dof domain, including C2-C2 type zinc finger motifs. In this study, we identified 45 PbDofs in pear (Pyrusbretschneideri). PbDofs were classified into eight subfamilies by phylogenetic analysis. Conserved motifs of PbDof proteins were analyzed by MEME. PbDofs in subfamily D₁ werehomologous to ...
DOI:
10.1016/j.ygeno.2019.05.005

9. Characterization of the complete mitochondrial genome of Uca lacteus and comparison with other Brachyuran crabs

Author:
Wang, Ziqian; Shi, Xuejia; Guo, Huayun; Tang, Dan; Bai, Yuze; Wang, Zhengfei
Source:
Genomics 2020 v.112 no.1 pp. 10-19
ISSN:
0888-7543
Subject:
Uca; ancestry; crabs; gene order; gene rearrangement; genes; mitochondrial genome; monophyly; paraphyly; transfer RNA
Abstract:
... Brachyuran crabs comprise the most species-rich clade among the crustacean order Decapoda and are divided into several major superfamilies. However, the monophyly of the superfamilies Ocypodoidea and Grapsoidea in their current compositions within the Brachyura remains inconclusive. In this study, the complete mitochondrial genome (mitogenome) of Uca lacteus (Ocypodoidea, Ocypodidae) was sequenced ...
DOI:
10.1016/j.ygeno.2019.06.004

10. Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots

Author:
Abdullah,; Mehmood, Furrukh; Shahzadi, Iram; Waseem, Shahid; Mirza, Bushra; Ahmed, Ibrar; Waheed, Mohammad Tahir
Source:
Genomics 2020 v.112 no.1 pp. 581-591
ISSN:
0888-7543
Subject:
Hibiscus rosa-sinensis; Hibiscus syriacus; RNA editing; amino acids; chloroplast genome; genes; nucleotide sequences; phylogeny; ribosomal RNA; transfer RNA
Abstract:
... Previous studies to resolve phylogenetic and taxonomic discrepancies of Hibiscus remained inconclusive. Here, we report chloroplast genome sequence of Hibiscus rosa-sinensis. Hibiscus rosa-sinensis chloroplast genome was 160,951 bp, comprising of large single copy (89,509 bp) and small single copy (20,246 bp) regions, separated by IRa and IRb (25,598 bp each). The genome contained 130 genes includ ...
DOI:
10.1016/j.ygeno.2019.04.010

11. Chromosomal breakpoints in a cohort of head and neck squamous cell carcinoma patients

Author:
Ribeiro, I.P.; Carreira, I.M.; Esteves, L.; Caramelo, F.; Liehr, T.; Melo, J.B.
Source:
Genomics 2020 v.112 no.1 pp. 297-303
ISSN:
0888-7543
Subject:
DNA; chromosome breakage; gene amplification; head; neck; nucleotide sequences; patients; squamous cell carcinoma; telomeres
Abstract:
... Head and neck squamous cell carcinoma (HNSCC) presents complex chromosomal rearrangements, however, the molecular mechanisms behind HNSCC development remain elusive. The identification of the recurrent chromosomal breakpoints could help to understand these mechanisms. Array-CGH was performed in HNSCC patients and the chromosomal breakpoints involved in gene amplification/loss were analyzed. Freque ...
DOI:
10.1016/j.ygeno.2019.02.009

12. Close encounters between Trypanosoma cruzi and the host mammalian cell: Lessons from genome-wide expression studies

Author:
Oliveira, Antonio Edson R.; Grazielle-Silva, Viviane; Ferreira, Ludmila R.P.; Teixeira, Santuza M.R.
Source:
Genomics 2020 v.112 no.1 pp. 990-997
ISSN:
0888-7543
Subject:
Chagas disease; Trypanosoma cruzi; animal models; biomarkers; disease progression; energy metabolism; etiological agents; genes; immune response; mammals; microarray technology; parasites; pathogenesis; patients; sequence analysis; tissues; transcriptome
Abstract:
... Trypanosoma cruzi is the etiologic agent of Chagas disease, a life-threatening disease that affects different tissues. Within its mammalian host, T. cruzi develops molecular strategies for successful invasion of different cell types and adaptation to the intracellular environment. Conversely, the host cell responds to the infection by activating intracellular pathways to control parasite replicati ...
DOI:
10.1016/j.ygeno.2019.06.015

13. CodSeqGen: A tool for generating synonymous coding sequences with desired GC-contents

Author:
Al-Ssulami, Abdulrakeeb M.; Azmi, Aqil M.; Hussain, Muhammad
Source:
Genomics 2020 v.112 no.1 pp. 237-242
ISSN:
0888-7543
Subject:
amino acid sequences; amino acids; gene expression; probability; regulatory sequences; stochastic processes; transcription (genetics); transcription factors
Abstract:
... Identification of regulatory elements is essential for understanding the mechanism behind regulating gene expression. These regulatory elements—located in or near gene—bind to proteins called transcription factors to initiate the transcription process. Their occurrences are influenced by the GC-content or nucleotide composition. For generating synthetic coding sequences with pre-specified amino ac ...
DOI:
10.1016/j.ygeno.2019.02.002
PubMed:
30738198
PubMed Central:
PMC7127556

14. Comparative genomics analysis of Mycoplasma capricolum subsp. capripneumoniae 87001

Author:
Li, Yuan; Wang, Rui; Sun, Wenjing; Song, Zhiqiang; Bai, Fan; Zheng, Huajun; Xin, Jiuqing
Source:
Genomics 2020 v.112 no.1 pp. 615-620
ISSN:
0888-7543
Subject:
Mycoplasma; Mycoplasma capricolum subsp. capripneumoniae; Mycoplasma mycoides; cattle; chromosomes; contagious caprine pleuropneumonia; farms; genes; genomics; goats; hemolysins; host specificity; lipoproteins; open reading frames; pathogens; vaccines; virulence; China
Abstract:
... Mycoplasma capricolum subsp. capripneumoniae (Mccp), belongs to Mycoplasma mycoides cluster and is a causal pathogen of contagious caprine pleuropneumonia (CCPP). This paper presents the complete annotated genome sequence of Mccp Strain 87001—a strain that was isolated from pneumonia affected goats on a farm in China, and comparative genomics analysis of five Mccp genomes in addition to comparativ ...
DOI:
10.1016/j.ygeno.2019.04.013

15. Comparative mitochondrial genomic analysis of Macrophthalmus pacificus and insights into the phylogeny of the Ocypodoidea & Grapsoidea

Author:
Wang, Qi; Tang, Dan; Guo, Huayun; Wang, Jie; Xu, Xinyi; Wang, Zhengfei
Source:
Genomics 2020 v.112 no.1 pp. 82-91
ISSN:
0888-7543
Subject:
Varunidae; aquaculture; fisheries; gene order; gene rearrangement; genes; genomics; mitochondrial genome; monophyly; paraphyly; taxonomy
Abstract:
... Grapsoidea and Ocypodoidea, two of the most abundant and economically important groups in Brachyura, are of great commercial value to fisheries and aquaculture. However, the taxonomy of Ocypodoidea and Grapsoidea has long been highly disputed. Previous studies have investigated this problem through phylogenetic analysis based on limited taxonomic sampling, with different reports proposing either m ...
DOI:
10.1016/j.ygeno.2019.12.012

16. Comparative phylogenetic analysis of aquaporins provides insight into the gene family expansion and evolution in plants and their role in drought tolerant and susceptible chickpea cultivars

Author:
Hussain, Athar; Tanveer, Rabbia; Mustafa, Ghulam; Farooq, Muhammed; Amin, Imran; Mansoor, Shahid
Source:
Genomics 2020 v.112 no.1 pp. 263-275
ISSN:
0888-7543
Subject:
Arabidopsis; Cicer arietinum; Liliopsida; algae; animal tissues; aquaporins; chickpeas; corn; cultivars; drought tolerance; genes; mosses and liverworts; phylogeny; regulatory sequences; reverse transcriptase polymerase chain reaction; soybeans; water stress
Abstract:
... Aquaporins (AQPs) are water channel proteins that play a significant role in drought stress. Although the AQPs identified in multiple plant species, there is no detailed evolutionary and comparative study of AQPs regarding chickpea plant. The current study involved evolutionary analyses coupled with promoter and expression analyses of chickpea AQPs (CaAQPs). A total of 924 non-redundant AQPs were ...
DOI:
10.1016/j.ygeno.2019.02.005

17. Comparative profiling of ovarian and testicular piRNAs in the mud crab Scylla paramamosain

Author:
Waiho, Khor; Fazhan, Hanafiah; Zhang, Yin; Li, Shengkang; Zhang, Yueling; Zheng, Huaiping; Ikhwanuddin, Mhd; Ma, Hongyu
Source:
Genomics 2020 v.112 no.1 pp. 323-331
ISSN:
0888-7543
Subject:
DNA repair; RNA; Scylla paramamosain; animal ovaries; biogenesis; crabs; gametogenesis; gene expression regulation; genes; germ cells; ribosomes; testes
Abstract:
... PIWI-interacting RNAs (piRNAs) are abundantly found in germ cells and involved in gametogenesis and gonadal development. Information on the regulatory roles of piRNAs in crustacean reproduction, however, is scarce. Thus, we identified gonadal piRNAs of mud crab Scylla paramamosain. Of the 115,491 novel piRNAs, 596 were differentially expressed. Subsequently, 389,887 potential piRNA-target genes we ...
DOI:
10.1016/j.ygeno.2019.02.012

18. Comparative study on seasonal hair follicle cycling by analysis of the transcriptomes from cashmere and milk goats

Author:
Zhang, Yanjun; Wu, Kejing; Wang, Lele; Wang, Zhiying; Han, Wenjing; Chen, Dong; Wei, Yaxun; Su, Rui; Wang, Ruijun; Liu, Zhihong; Zhao, Yanhong; Wang, Zhixin; Zhan, Leilei; Zhang, Yi; Li, Jinquan
Source:
Genomics 2020 v.112 no.1 pp. 332-345
ISSN:
0888-7543
Subject:
Cashmere (goat breed); Western blotting; dairy goats; gene expression; genes; hair follicles; immunohistochemistry; information sources; mitogen-activated protein kinase; quantitative polymerase chain reaction; sequence analysis; signal transduction; transcriptome; transforming growth factor beta; wool production
Abstract:
... Guard hair and cashmere undercoat are developed from primary and secondary hair follicle, respectively. Little is known about the gene expression differences between primary and secondary hair follicle cycling. In this study, we obtained RNA-seq data from cashmere and milk goats grown at four different seasons. We studied the differentially expressed genes (DEGs) during the yearly hair follicle cy ...
DOI:
10.1016/j.ygeno.2019.02.013

19. Comparative transcriptome analysis of different stages of Plasmodium falciparum to explore vaccine and drug candidates

Author:
Guleria, Vandana; Jaiswal, Varun
Source:
Genomics 2020 v.112 no.1 pp. 796-804
ISSN:
0888-7543
Subject:
Plasmodium falciparum; infectious diseases; malaria; pathogens; protein synthesis; proteins; transcriptome; transcriptomics; vaccines
Abstract:
... Malaria is a life-threatening disease causes huge burden on human health. Every year >200 million cases of malaria are reported globally. Researchers have carried out research on transcriptome of different stages of Plasmodium species to understand complex pathology of pathogens and to discover therapeutics. Researchers are targeting different stages of Plasmodium falciparum separately. Hence, to ...
DOI:
10.1016/j.ygeno.2019.05.018

20. Complete genome sequence provides insights into the quorum sensing-related spoilage potential of Shewanella baltica 128 isolated from spoiled shrimp

Author:
Li, Jianpeng; Yu, Honglei; Yang, Xiaoyuan; Dong, Ruyue; Liu, Zunying; Zeng, Mingyong
Source:
Genomics 2020 v.112 no.1 pp. 736-748
ISSN:
0888-7543
Subject:
Shewanella baltica; biochemical pathways; biofilm; genes; in vitro studies; metabolism; nucleotide sequences; proteins; putrescine; refrigeration; serine proteinases; shrimp; spoilage; sulfur; trimethylamine
Abstract:
... Shewanella baltica 128 is a specific spoilage organism (SSO) isolated from the refrigerated shrimp that results in shrimp spoilage. This study reported the complete genome sequencing of this strain, with the primary annotations associated with amino acid transport and metabolism (8.66%), indicating that S. baltica 128 has good potential for degrading proteins. In vitro experiments revealed Shewane ...
DOI:
10.1016/j.ygeno.2019.05.010