Genome-Wide Transcriptome Profiling Revealed Cotton Fuzz Fiber Development Having a Similar Molecular Model as Arabidopsis Trichome

AbstractCerebral amyloid angiopathy (CAA) contributes to accelerated cognitive decline in Alzheimer’s disease (AD) dementia and is a common finding at autopsy. The APOEε4 allele and male sex have previously been reported to associate with increased CAA in AD. To inform biomarker and therapeutic target discovery, we aimed to identify additional genetic risk factors and biological pathways involved in this vascular component of AD etiology. We present a genome-wide association study of CAA pathology in AD cases and report sex- and APOE-stratified assessment of this phenotype. Genome-wide genotypes were collected from 853 neuropathology-confirmed AD cases scored for CAA across five brain regions, and imputed to the Haplotype Reference Consortium panel. Key variables and genome-wide genotypes were tested for association with CAA in all individuals and in sex and APOEε4 stratified subsets. Pathway enrichment was run for each of the genetic analyses. Implicated loci were further investigated for functional consequences using brain transcriptome data from 1,186 samples representing seven brain regions profiled as part of the AMP-AD consortium. We confirmed association of male sex, AD neuropathology and APOEε4 with increased CAA, and identified a novel locus, LINC-PINT, associated with lower CAA amongst APOEε4-negative individuals (rs10234094-C, beta = −3.70 [95% CI −0.49—−0.24]; p = 1.63E-08). Transcriptome profiling revealed higher LINC-PINT expression levels in AD cases, and association of rs10234094-C with altered LINC-PINT splicing. Pathway analysis indicates variation in genes involved in neuronal health and function are linked to CAA in AD patients. Further studies in additional and diverse cohorts are needed to assess broader translation of our findings.

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A comparative genome‐wide analysis of the ABC transporter gene family among three Gossypium species and the evidence for a role of some GhABCs in fiber development and response to stresses

Crop Science ◽

10.1002/csc2.20525 ◽

2021 ◽

Author(s):

Baolu Cui ◽

Yan Li ◽

Yanjie Zhang

Keyword(s):

Gene Family ◽

Abc Transporter ◽

Fiber Development ◽

Transporter Gene ◽

Comparative Genome ◽

Genome Wide Analysis ◽

Gossypium Species ◽

Genome Wide

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Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate

BMC Biotechnology ◽

10.1186/s12896-021-00668-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Victoria Yu Shtratnikova ◽

Mikhail I. Sсhelkunov ◽

Victoria V. Fokina ◽

Eugeny Y. Bragin ◽

Andrey A. Shutov ◽

...

Keyword(s):

Dehydrogenase Activity ◽

Transcriptome Profiling ◽

Comparative Investigation ◽

Mycolic Acid ◽

Gene Organization ◽

Expression Level ◽

Bacterial Degradation ◽

Genome Wide ◽

Steroid Catabolism

Abstract Background Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq. Results Although the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N. simplex. Unlike phytosterol, cortisone 21-acetate does not provide induction of the genes with predicted KstR and KstR2 sites. Superior 3-ketosteroid-Δ1-dehydrogenase activity of N. simplex VKM Ac-2033D is due to the kstDs redundancy in the genome, with the highest expression level of the gene KR76_27125 orthologous to kstD2, in response to cortisone 21-acetate. The substrate spectrum of N. simplex 3-ketosteroid-Δ1-dehydrogenase was expanded in this study with progesterone and its 17α-hydroxylated and 11α,17α-dihydroxylated derivatives, that effectively were 1(2)-dehydrogenated in vivo by the whole cells of the N. simplex VKM Ac-2033D. Conclusion The results contribute to the knowledge of biocatalytic features and diversity of steroid modification capabilities of actinobacteria, defining targets for further bioengineering manipulations with the purpose of expansion of their biotechnological applications.

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Genome-wide transcriptome profiling of black poplar ( Populus nigra L.) under boron toxicity revealed candidate genes responsible in boron uptake, transport and detoxification

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2016.09.015 ◽

2016 ◽

Vol 109 ◽

pp. 146-155 ◽

Cited By ~ 10

Author(s):

Kubilay Yıldırım ◽

Senem Uylaş

Keyword(s):

Candidate Genes ◽

Transcriptome Profiling ◽

Populus Nigra ◽

Boron Toxicity ◽

Boron Uptake ◽

Black Poplar ◽

Genome Wide

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Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms

EvoDevo ◽

10.1186/s13227-018-0110-5 ◽

2018 ◽

Vol 9 (1) ◽

Cited By ~ 9

Author(s):

Peter D. Olson ◽

Magdalena Zarowiecki ◽

Katherine James ◽

Andrew Baillie ◽

Georgie Bartl ◽

...

Keyword(s):

Transcriptome Profiling ◽

Spatial Expression ◽

Genome Wide

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Genome-wide transcriptome profiling of transgenic hop (Humulus lupulus L.) constitutively overexpressing HlWRKY1 and HlWDR1 transcription factors

BMC Genomics ◽

10.1186/s12864-018-5125-8 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Ajay Kumar Mishra ◽

Ganesh Selvaraj Duraisamy ◽

Mudra Khare ◽

Tomáš Kocábek ◽

Jernej Jakse ◽

...

Keyword(s):

Transcription Factors ◽

Transcriptome Profiling ◽

Humulus Lupulus ◽

Genome Wide ◽

Humulus Lupulus L

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Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

10.1101/2021.05.12.443750 ◽

2021 ◽

Author(s):

Tanzeem Fatima ◽

Rangachari Krishnan ◽

Ashutosh Srivastava ◽

Vageeshbabu S. Hanur ◽

M. Srinivasa Rao

Keyword(s):

Transcriptome Profiling ◽

Santalum Album ◽

Rna Seq ◽

Improvement Program ◽

East Indian ◽

Kegg Pathways ◽

Oil Biosynthesis ◽

Genome Wide ◽

A Genome ◽

Santalum Album L

East Indian Sandalwood (Santalum album L.) is highly valued for its heartwood and its oil. There have been no efforts to comparative study of high and low oil yielding genetically identical sandalwood trees grown in similar climatic condition. Thus we intend to study a genome wide transcriptome analysis to identify the corresponding genes involved in high oil biosynthesis in S. album. In this study, 15 years old S. album (SaSHc and SaSLc) genotypes were targeted for analysis to understand the contribution of genetic background on high oil biosynthesis in S. album. A total of 28,959187 and 25,598869 raw PE reads were generated by the Illumina sequencing. 2.12 million and 1.811 million coding sequences were obtained in respective accessions. Based on the GO terms, functional classification of the CDS 21262, & 18113 were assigned into 26 functional groups of three GO categories; (4,168; 3,641) for biological process (5,758;4,971) cellular component and (5,108;4,441) for molecular functions. Total 41,900 and 36,571 genes were functionally annotated and KEGG pathways of the DEGs resulted 213 metabolic pathways. In this, 14 pathways were involved in secondary metabolites biosynthesis pathway in S. album. Among 237 cytochrome families, nine groups of cytochromes were participated in high oil biosynthesis. 16,665 differentially expressed genes were commonly detected in both the accessions (SaHc and SaSLc). The results showed that 784 genes were upregulated and 339 genes were downregulated in SaHc whilst 635 upregulated 299 downregulated in SaSLc S. album. RNA-Seq results were further validated by quantitative RT-PCR. Maximum Blast hits were found to be against Vitis vinifera. From this study we have identified additional number of cytochrome family in SaHc. The accessibility of a RNA-Seq for high oil yielding sandalwood accessions will have broader associations for the conservation and selection of superior elite samples/populations for further genetic improvement program.

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Genome-wide analysis of CrRLK1L genes and their expression profiling during fiber development in cotton

10.21203/rs.3.rs-44129/v1 ◽

2020 ◽

Author(s):

Dongyun Zuo ◽

Javaria Ashraf ◽

Hailiang Cheng ◽

Shang Liu ◽

Youping Zhang ◽

...

Keyword(s):

Stress Responses ◽

Plant Immunity ◽

Fiber Development ◽

The Other ◽

Element Analysis ◽

Specific Expression ◽

Group Iii ◽

Group I ◽

Genome Wide ◽

Specific Expression Pattern

Abstract Background: Catharanthus roseus receptor-like kinase 1-like (CrRLK1Ls) proteins play important roles in cell growth, plant morphogenesis, reproduction, hormone signaling, plant immunity and stress responses in Arabidopsis. However, not much information is available about their functions during cotton fiber development.Results: We identified a total of 125, 73 and 71 full-length putative CrRLK1L genes in G. hirsutum, G. arboreum and G. raimondii, which are much greater than that of the other plants. The phylogenetic and gene structure analysis divided the cotton CrRLK1L genes into six major groups, among which only group I and II contained AtCrRLK1Ls of Arabidopsis, suggesting that other groups (group III-VI) were expanded by gene duplication during cotton evolution. Genome collinearity analysis revealed that half of the At02 genes in G. hirsutum derived from A02 of G. arboreum, while the other half (GhCrRLK1L6 and GhCrRLK1L7) originated from Dt03 and Dt02 of G. raimondii, indicating segmental duplication between noncorresponding chromosomes during polyploidization of G. hirsutum. In addition, expression and cis-element analysis revealed that only 22 GhCrRLK1Ls showed specific expression pattern during fiber development which are mainly due to the presence of binding sites for NAC, MYB and WRKY transcription factors.Conclusions: This study provides a strong foundation to further explore the molecular mechanism of CrRLK1L genes during fiber development in upland cotton.

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Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferase (HAT) Gene Family in Response to Hormonal Applications, Metal and Abiotic Stresses in Cotton

International Journal of Molecular Sciences ◽

10.3390/ijms20215311 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5311 ◽

Cited By ~ 3

Author(s):

Muhammad Imran ◽

Sarfraz Shafiq ◽

Muhammad Ansar Farooq ◽

Muhammad Kashif Naeem ◽

Emilie Widemann ◽

...

Keyword(s):

Fiber Quality ◽

Purifying Selection ◽

Fiber Development ◽

Amino Acid Sequences ◽

Environmental Cues ◽

Post Translational Modifications ◽

Cellular Processes ◽

Genome Wide ◽

Selection Gene ◽

Almost All

Post-translational modifications are involved in regulating diverse developmental processes. Histone acetyltransferases (HATs) play vital roles in the regulation of chromation structure and activate the gene transcription implicated in various cellular processes. However, HATs in cotton, as well as their regulation in response to developmental and environmental cues, remain unidentified. In this study, 9 HATs were identified from Gossypium raimondi and Gossypium arboretum, while 18 HATs were identified from Gossypium hirsutum. Based on their amino acid sequences, Gossypium HATs were divided into three groups: CPB, GNAT, and TAFII250. Almost all the HATs within each subgroup share similar gene structure and conserved motifs. Gossypium HATs are unevenly distributed on the chromosomes, and duplication analysis suggests that Gossypium HATs are under strong purifying selection. Gene expression analysis showed that Gossypium HATs were differentially expressed in various vegetative tissues and at different stages of fiber development. Furthermore, all the HATs were differentially regulated in response to various stresses (salt, drought, cold, heavy metal and DNA damage) and hormones (abscisic acid (ABA) and auxin (NAA)). Finally, co-localization of HAT genes with reported quantitative trait loci (QTL) of fiber development were reported. Altogether, these results highlight the functional diversification of HATs in cotton growth and fiber development, as well as in response to different environmental cues. This study enhances our understanding of function of histone acetylation in cotton growth, fiber development, and stress adaptation, which will eventually lead to the long-term improvement of stress tolerance and fiber quality in cotton.

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