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- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.03.004
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.02.001
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.04.015
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.02.010
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.02.016
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.09.015
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.08.013
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.05.005
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.06.004
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.04.010
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.02.009
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.06.015
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.02.002
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.04.013
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.12.012
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.02.005
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.02.012
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.02.013
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.05.018
- 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
-
https://dx.doi.org/10.1016/j.ygeno.2019.05.010