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You searched for: Journal name Genomics Remove constraint Journal name: Genomics Publication year rev 7979-2021 Remove constraint Publication year rev: 7979-2021 Source 2021 v.113 no.3 Remove constraint Source: 2021 v.113 no.3
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1. A comprehensive transcriptome analysis of contrasting rice cultivars highlights the role of auxin and ABA responsive genes in heat stress response

Author:
Eshan Sharma; Pratikshya Borah; Amarjot Kaur; Akanksha Bhatnagar; Trilochan Mohapatra; Sanjay Kapoor; Jitendra P. Khurana
Source:
Genomics 2021 v.113 no.3 pp. 1247-1261
ISSN:
0888-7543
Subject:
ambient temperature; auxins; climate change; cold; cultivars; genes; genomics; heat; heat shock response; heat tolerance; microarray technology; red rice; transcriptome; transcriptomics; wheat
Abstract:
... Sensing a change in ambient temperature is key to survival among all living organisms. Temperature fluctuations due to climate change are a matter of grave concern since it adversely affects growth and eventually the yield of crop plants, including two of the major cereals, i.e., rice and wheat. Thus, to understand the response of rice seedlings to elevated temperatures, we performed microarray-ba ...
DOI:
10.1016/j.ygeno.2021.03.007

2. ASDB: A comprehensive omics database for Anopheles sinensis

Author:
Yu-Juan Zhang; Yang Lan; Bin Chen
Source:
Genomics 2021 v.113 no.3 pp. 976-982
ISSN:
0888-7543
Subject:
Anopheles sinensis; amino acid sequences; databases; filariasis; genes; genetic variation; humans; malaria; metagenomics; microRNA; non-coding RNA; nucleotide sequences; sequence alignment; transcriptome; China; South East Asia
Abstract:
... Anopheles sinensis is a key disease vector for human malaria and parasitic diseases such as malayan filariasis, and it is considered to be one of the most important malaria vectors in China and Southeast Asia. As high-throughput sequencing and assembly technology are widely used in An. sinensis, a lot of omics data have been generated, and abundant genome, mRNA transcriptome, miRNA transcriptome a ...
DOI:
10.1016/j.ygeno.2021.02.005

3. Aberrant methylation modifications reflect specific drug responses in small cell lung cancer

Author:
Peixin Chen; Haoyue Guo; Yu Liu; Bin Chen; Sha Zhao; Shengyu Wu; Wei Li; Lei Wang; Keyi Jia; Hao Wang; Minlin Jiang; Xuzhen Tang; Hui Qi; Chunlei Dai; Junyan Ye; Yayi He
Source:
Genomics 2021 v.113 no.3 pp. 1114-1126
ISSN:
0888-7543
Subject:
DNA methylation; drug therapy; drugs; genomics; lung neoplasms; microRNA; precipitin tests; transcription initiation site
Abstract:
... In the study, Methylated DNA immunoprecipitation sequencing, RNA sequencing, and whole-exome sequencing were employed to clinical small cell lung cancer (SCLC) patients. Then, we verified the therapeutic predictive effects of differentially methylated genes (DMGs) in 62 SCLC cell lines. Of 4552 DMGs between chemo-sensitive and chemo-insensitive group, coding genes constituted the largest percentag ...
DOI:
10.1016/j.ygeno.2020.12.045

4. Comparative profile of exosomal microRNAs in postmenopausal women with various bone mineral densities by small RNA sequencing

Author:
Dece Kong; Tianning Chen; Xinhui Zheng; Tieyi Yang; Yan Zhang; Jin Shao
Source:
Genomics 2021 v.113 no.3 pp. 1514-1521
ISSN:
0888-7543
Subject:
bone density; exosomes; gene ontology; genomics; microRNA; osteopenia; osteoporosis; postmenopause; prediction; quantitative polymerase chain reaction
Abstract:
... To explore the role of plasma miRNAs in exosomes in early postmenopausal women. Small RNA sequencing was implemented to clarify the expression of miRNA in plasma exosomes obtained from 15 postmenopausal women, divided into groups of osteoporosis, osteopenia, and normal bone mass based on bone mineral density. Differentially expressed miRNAs (DEMs) were identified by comparing miRNA expression prof ...
DOI:
10.1016/j.ygeno.2021.03.028

5. Comparative proteomic analysis provides insight into the molecular mechanism of vegetative growth advantage in allotriploid Populus

Author:
Jiang Li; Yi Wang; Hairong Wei; Xiangyang Kang
Source:
Genomics 2021 v.113 no.3 pp. 1180-1192
ISSN:
0888-7543
Subject:
Calvin cycle; Populus; biomass; carbon dioxide fixation; diploidy; gene expression regulation; genomics; lumber; photorespiration; protein degradation; protein synthesis; proteomics; starch; sucrose; vegetative growth
Abstract:
... Though allotriploid poplar shows a salient vegetative growth advantage that impacts biomass and lumber yield, the proteomic data of Populus allotriploids have not been scrutinized for identifying the underlying molecular mechanisms. We conducted a large-scale label-free proteomics profiling of the 5th, 10th, and 25th leaves of allotriploids and diploids, and identified 4587 protein groups. Among 9 ...
DOI:
10.1016/j.ygeno.2021.03.002

6. De novo full length transcriptome analysis of Arachis glabrata provides insights into gene expression dynamics in response to biotic and abiotic stresses

Author:
Chuanzhi Zhao; Liangqiong He; Han Xia; Ximeng Zhou; Yun Geng; Lei Hou; Pengcheng Li; Guanghui Li; Shuzhen Zhao; Changle Ma; Ronghua Tang; Manish K. Pandey; Rajeev K. Varshney; Xingjun Wang
Source:
Genomics 2021 v.113 no.3 pp. 1579-1588
ISSN:
0888-7543
Subject:
Arachis glabrata; catechol oxidase; cold; drought; flowers; forage; forage crops; gene expression; gene expression regulation; genomics; leaf spot; leaves; peanuts; sequence analysis; transcriptome; transcriptomics
Abstract:
... The perennial ornamental peanut Arachis glabrata represents one of the most adaptable wild Arachis species. This study used PacBio combined with BGISEQ-500 RNA-seq technology to study the transcriptome and gene expression dynamics of A. glabrata. Of the total 109,747 unique transcripts obtained, >90,566 transcripts showed significant homology to known proteins and contained the complete coding seq ...
DOI:
10.1016/j.ygeno.2021.03.030

7. Evidence for discrete modes of YAP1 signaling via mRNA splice isoforms in development and diseases

Author:
Jan Vrbský; Vladimir Vinarský; Ana Rubina Perestrelo; Jorge Oliver De La Cruz; Fabiana Martino; Antonio Pompeiano; Valerio Izzi; Ota Hlinomaz; Vladimir Rotrekl; Marius Sudol; Stefania Pagliari; Giancarlo Forte
Source:
Genomics 2021 v.113 no.3 pp. 1349-1365
ISSN:
0888-7543
Subject:
cell proliferation; genes; genomics; heart; organogenesis; protein isoforms; protein-protein interactions; transcription (genetics)
Abstract:
... Yes-associated protein 1 (YAP1) is a transcriptional co-activator downstream of Hippo pathway. The pathway exerts crucial roles in organogenesis and its dysregulation is associated with the spreading of different cancer types. YAP1 gene encodes for multiple protein isoforms, whose specific functions are not well defined. We demonstrate the splicing of isoform-specific mRNAs is controlled in a stag ...
DOI:
10.1016/j.ygeno.2021.03.009

8. Genetic dissection of soybean partial resistance to sclerotinia stem rot through genome wide association study and high throughout single nucleotide polymorphisms

Author:
Yan Jing; Weili Teng; Lijuan Qiu; Hongkun Zheng; Wenbin Li; Yingpeng Han; Xue Zhao
Source:
Genomics 2021 v.113 no.3 pp. 1262-1271
ISSN:
0888-7543
Subject:
Glycine max; Sclerotinia; alleles; dissection; genome-wide association study; genomics; haplotypes; linkage disequilibrium; quantitative polymerase chain reaction; quantitative traits; soybeans; stem rot
Abstract:
... Sclerotinia stem rot (SSR) is a disease of soybean [Glycine max (L.) Merr] that causes severe yield losses. We studied 185 representative soybean accessions to evaluate partial SSR resistance and sequenced these by the specific-locus amplified fragment sequencing method. In total, 22,048 single-nucleotide polymorphisms (SNPs), with minor allele frequencies (MAF) ≥5% and missing data <3%, were deve ...
DOI:
10.1016/j.ygeno.2020.10.042

9. Genetic predictors of gene expression associated with psychiatric comorbidity in patients with inflammatory bowel disease – A pilot study

Author:
Allan Bruinooge; Qian Liu; Ye Tian; Wenxin Jiang; Yao Li; Wei Xu; Charles N. Bernstein; Pingzhao Hu
Source:
Genomics 2021 v.113 no.3 pp. 919-932
ISSN:
0888-7543
Subject:
apolipoprotein B; cerebellum; cohort studies; comorbidity; databases; drugs; frontal lobe; gene expression; genes; genomics; humans; inflammatory bowel disease; phosphorylation; pigmentation; skeletal muscle; tyrosine; Manitoba
Abstract:
... Inflammatory bowel disease (IBD) affects millions of people in North America, and patients with IBD have a high incidence of psychiatric comorbidities (PC). The genetic mechanisms underlying the link are, in general, poorly understood. A transcriptome-wide association study (TWAS) was performed using genetically regulated gene expression profiles imputed from the genetic profiles of 240 IBD patien ...
DOI:
10.1016/j.ygeno.2021.02.001

10. Genome resequencing reveals DNA polymorphisms associated with seed size/weight determination in chickpea

Author:
Mohan Singh Rajkumar; Rohini Garg; Mukesh Jain
Source:
Genomics 2021 v.113 no.3 pp. 1458-1468
ISSN:
0888-7543
Subject:
DNA; cell growth; chickpeas; genomics; genotyping; seed size; sequence analysis; transcription factors
Abstract:
... Crop productivity in legumes is determined by number and size/weight of seeds. To understand the genetic basis of seed size/weight in chickpea, we performed genome resequencing of 13 small- and 5 large-seeded genotypes using Illumina platform. Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) differentiating small- and large-seeded genotypes were identified. A total of 17,90 ...
DOI:
10.1016/j.ygeno.2021.03.020

11. Genome-wide association study-based identification genes influencing agronomic traits in rice (Oryza sativa L.)

Author:
Aijun Wang; Yuqi Jiang; Xinyue Shu; Zhongping Zha; Desuo Yin; Yao Liu; Danhua Zhang; Deze Xu; Chengzhi Jiao; Xiaomei Jia; Xiaoying Ye; Shuangcheng Li; Qiming Deng; Shiquan Wang; Jun Zhu; Yueyang Liang; Ting Zou; Huainian Liu; Lingxia Wang; Jianqing Zhu; Ping Li; Zaijun Zhang; Aiping Zheng
Source:
Genomics 2021 v.113 no.3 pp. 1396-1406
ISSN:
0888-7543
Subject:
Oryza sativa; cultivars; food intake; genomics; haplotypes; human population; linkage disequilibrium; phenotype; prediction; rice
Abstract:
... Rice is one of the most important cereal crops, providing the daily dietary intake for approximately 50% of the global human population. Here, we re-sequenced 259 rice accessions, generating 1371.65 Gb of raw data. Furthermore, we performed genome-wide association studies (GWAS) on 13 agronomic traits using 2.8 million single nucleotide polymorphisms (SNPs) characterized in 259 rice accessions. Ph ...
DOI:
10.1016/j.ygeno.2021.03.016

12. Genomic dissection of ROS detoxifying enzyme encoding genes for their role in antioxidative defense mechanism against Tomato leaf curl New Delhi virus infection in tomato

Author:
Namisha Sharma; Mehanathan Muthamilarasan; Priya Dulani; Manoj Prasad
Source:
Genomics 2021 v.113 no.3 pp. 889-899
ISSN:
0888-7543
Subject:
DNA; Tomato leaf curl New Delhi virus; catalase; cultivars; cytoplasm; disease susceptibility; dissection; enzyme activity; genes; genomics; glutathione transferase; glutathione-disulfide reductase; peroxidase; superoxide dismutase; tomatoes; viruses
Abstract:
... In the present study, genes encoding for six major classes of enzymatic antioxidants, namely superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), Peroxidase (Prx) and glutathione S-transferase (GST) are identified in tomato. Their expression was studied in tomato cultivars contrastingly tolerant to ToLCNDV during virus infection and different hormone treatments. Significant upre ...
DOI:
10.1016/j.ygeno.2021.01.022

13. Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds

Author:
K.A. Saravanan; Manjit Panigrahi; Harshit Kumar; Subhashree Parida; Bharat Bhushan; G.K. Gaur; Triveni Dutt; B.P. Mishra; R.K. Singh
Source:
Genomics 2021 v.113 no.3 pp. 955-963
ISSN:
0888-7543
Subject:
cattle; cattle breeds; disease susceptibility; domestication; genetic variation; genomics; genotyping; haplotypes; heat stress; homozygosity; sample size
Abstract:
... Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotyp ...
DOI:
10.1016/j.ygeno.2021.02.009

14. Identification of hub genes through co-expression network of major QTLs of fiber length and strength traits in multiple RIL populations of cotton

Author:
Abdul Hafeez; Abdul Razzaq; Aijaz Ahmed; Aiying Liu; Ge Qun; Li Junwen; Yuzhen Shi; Xiaoying Deng; Muhammad Mubashar Zafar; Arfan Ali; Wankui Gong; Youlu Yuan
Source:
Genomics 2021 v.113 no.3 pp. 1325-1337
ISSN:
0888-7543
Subject:
cotton; fiber quality; gene expression; genes; genomics; sequence analysis
Abstract:
... The present study demonstrated a de novo correlation among fiber quality genes in multiple RIL populations including sGK9708 × 0–153, LMY22 × LY343 and Lumianyan28 × Xinluzao24. The current study was conducted to identify the major common QTLs including fiber length and strength, and to identify the co-expression networks of fiber length and strength QTLs harbored genes to target the hub genes. Th ...
DOI:
10.1016/j.ygeno.2021.02.023

15. Integrated analysis of virus and host transcriptomes in cervical cancer in Asian and Western populations

Author:
Qiongzi Qiu; Qing Zhou; Aoran Luo; Xufan Li; Kezhen Li; Wenfeng Li; Mengqian Yu; Md Amanullah; Bingjian Lu; Weiguo Lu; Pengyuan Liu; Yan Lu
Source:
Genomics 2021 v.113 no.3 pp. 1554-1564
ISSN:
0888-7543
Subject:
genomics; immunotherapy; macrophages; prognosis; sequence analysis; transcriptome; uterine cervical neoplasms; viruses; China
Abstract:
... Race may influence vulnerability to HPV variants in viral infection and perisistence. Integrated analysis of the virus and host transcriptomes from different populations provides an unprecedented opportunity to understand these racial disparities in the prevalence of HPV and cervical cancers. We performed RNA-Seq analysis of 90 tumors and 39 adjacent normal tissues from cervical cancer patients at ...
DOI:
10.1016/j.ygeno.2021.03.029

16. Integrated genomic selection for rapid improvement of crops

Author:
Gopalareddy Krishnappa; Siddanna Savadi; Bhudeva Singh Tyagi; Sanjay Kumar Singh; Harohalli Masthigowda Mamrutha; Satish Kumar; Chandra Nath Mishra; Hanif Khan; Krishnappa Gangadhara; Govindareddy Uday; Gyanendra Singh; Gyanendra Pratap Singh
Source:
Genomics 2021 v.113 no.3 pp. 1070-1086
ISSN:
0888-7543
Subject:
animals; food production; genetic improvement; genomics; genotyping; marker-assisted selection; phenotype; prediction
Abstract:
... An increase in the rate of crop improvement is essential for achieving sustained food production and other needs of ever-increasing population. Genomic selection (GS) is a potential breeding tool that has been successfully employed in animal breeding and is being incorporated into plant breeding. GS promises accelerated breeding cycles through a rapid selection of superior genotypes. Numerous empi ...
DOI:
10.1016/j.ygeno.2021.02.007

17. Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle

Author:
Xiuge Wang; Zhihua Ju; Qiang Jiang; Jifeng Zhong; Chengkun Liu; Jinpeng Wang; Jesse L. Hoff; Robert D. Schnabel; Han Zhao; Yaping Gao; Wenhao Liu; Lingling Wang; Yundong Gao; Chunhong Yang; Minghai Hou; Ning Huang; Luciana C.A. Regitano; Laercio R. Porto-Neto; Jared E. Decker; Jeremy F. Taylor; Jinming Huang
Source:
Genomics 2021 v.113 no.3 pp. 1491-1503
ISSN:
0888-7543
Subject:
Bos javanicus; CRISPR-Cas systems; altitude; domestication; genetic variation; genomics; genotype; hypoxia; immunohistochemistry; introgression; liver; quantitative polymerase chain reaction; yaks; zebu
Abstract:
... Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of B ...
DOI:
10.1016/j.ygeno.2021.03.023

18. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing

Author:
Yanci Yang; Tao Zhou; Zengqiang Qian; Guifang Zhao
Source:
Genomics 2021 v.113 no.3 pp. 1438-1447
ISSN:
0888-7543
Subject:
Ilex; Quercus; genomics; introgression; monophyly; paleoclimatology; plastid genome; China; Himalayan region
Abstract:
... China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree s ...
DOI:
10.1016/j.ygeno.2021.03.013

19. Placental DNA methylation profiles in opioid-exposed pregnancies and associations with the neonatal opioid withdrawal syndrome

Author:
Uppala Radhakrishna; Sangeetha Vishweswaraiah; Lavanya V. Uppala; Marta Szymanska; Jacqueline Macknis; Sandeep Kumar; Fozia Saleem-Rasheed; Buket Aydas; Ariadna Forray; Srinivas B. Muvvala; Nitish K. Mishra; Chittibabu Guda; David J. Carey; Raghu P. Metpally; Richard C. Crist; Wade H. Berrettini; Ray O. Bahado-Singh
Source:
Genomics 2021 v.113 no.3 pp. 1127-1135
ISSN:
0888-7543
Subject:
DNA methylation; artificial intelligence; bioinformatics; genomics; pathophysiology; placenta; prediction; pregnancy; statistics; therapeutics
Abstract:
... Opioid abuse during pregnancy can result in Neonatal Opioid Withdrawal Syndrome (NOWS). We investigated genome-wide methylation analyses of 96 placental tissue samples, including 32 prenatally opioid-exposed infants with NOWS who needed therapy (+Opioids/+NOWS), 32 prenatally opioid-exposed infants with NOWS who did not require treatment (+Opioids/-NOWS), and 32 prenatally unexposed controls (-Opi ...
DOI:
10.1016/j.ygeno.2021.03.006

20. Single-cell RNA sequencing reveals the sustained immune cell dysfunction in the pathogenesis of sepsis secondary to bacterial pneumonia

Author:
Teng Wang; Xianglong Zhang; Zhanguo Liu; Tong Yao; Dongying Zheng; Jianwei Gan; Shuang Yu; Lin Li; Peng Chen; Jian Sun
Source:
Genomics 2021 v.113 no.3 pp. 1219-1233
ISSN:
0888-7543
Subject:
Orthomyxoviridae; RNA; Severe acute respiratory syndrome coronavirus 2; bacterial pneumonia; disease course; genomics; interferon-gamma; monocytes; mortality; pathogenesis
Abstract:
... Sepsis is a leading cause of mortality in intensive care unit worldwide, it's accompanied by immune cell dysfunction induced by multiple factors. However, little is known about the specific alterations in immune cells in the dynamic pathogenesis of sepsis secondary to bacterial pneumonia. Here, we used single cell RNA sequencing (scRNA-seq) to profile peripheral blood mononuclear cells (PBMCs) in ...
DOI:
10.1016/j.ygeno.2021.01.026