Magdy S AlabadyUniversity of Georgia | UGA · Department of Plant Biology
Magdy S Alabady
PhD [Genomic and transcriptomic computational Biologist]
About
53
Publications
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1,506
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Introduction
Magdy Alabady currently is an Associate Research Faculty at the Department of Plant Biology, and Director of the Georgia Genomics and Bioinformatics Core Lab at the University of Georgia.
Additional affiliations
July 2017 - August 2017
January 2013 - present
October 2008 - March 2013
Education
October 2002 - October 2007
Field of study
- Plant Functional Genomics (Single cell development at the transcriptional level)
September 1999 - October 2001
October 1990 - May 1994
Publications
Publications (53)
Objective:
To use RNA sequencing (RNAseq) to characterize renal transcriptional activities of genes associated with proinflammatory and profibrotic pathways in ischemia-induced chronic kidney disease (CKD) in cats.
Samples:
Banked renal tissues from 6 cats with experimentally induced CKD (renal ischemia [RI] group) and 9 healthy cats (control gr...
Background
The Beet curly top virus C4 oncoprotein is a pathogenic determinant capable of inducing extensive developmental abnormalities. No studies to date have investigated how the transcriptional profiles differ between plants expressing or not expressing the C4 oncoprotein.
Results
We investigated early transcriptional changes in Arabidopsis a...
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and ch...
Soil-based microorganisms assume a direct and crucial role in the promotion of soil health, quality and fertility, all factors known to contribute heavily to the quality and yield of agricultural products. Cover cropping, used in both traditional and organic farming, is a particularly efficient and environmentally favorable tool for manipulating mi...
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We used long read technologies and an optical map based approach to produce a maize genome assembly composed of only 63 contigs. The B73-Ab10 genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), multip...
Next-generation DNA sequencing (NGS) offers many benefits, but major factors limiting NGS include reducing costs of: 1) start-up (i.e., doing NGS for the first time); 2) buy-in (i.e., getting the smallest possible amount of data from a run); and 3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in...
The study of carnivorous plants can afford insight into their unique evolutionary adaptations and their interactions with prokaryotic and eukaryotic species. For Sarracenia (pitcher plants), we identified 64 quantitative trait loci (QTL) for insect- capture traits of the pitchers, providing the genetic basis for differences between the pitfall and...
Maize abnormal chromosome 10 (Ab10) encodes a classic example of true meiotic drive that converts heterochromatic regions called knobs into motile neocentromeres that are preferentially transmitted to egg cells. Here, we identify a cluster of eight genes on Ab10, called the Kinesin driver (Kindr) complex, that are required for both neocentromere mo...
The critically endangered elkhorn coral (Acropora palmata) is affected by white pox disease (WPX) throughout the Florida Reef Tract and wider Caribbean. The bacterium Serratia marcescens was previously identified as one etiologic agent of WPX but is no longer consistently detected in contemporary outbreaks. It is now believed that multiple etiologi...
Background:
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant speci...
Gossypium barbadense L. (Egyptian and Pima) produces single celled fiber trichomes that are the longest and richest in cellulosic contents in the plant kingdom. Developmental dissection of fiber at the transcriptional level is crucial to unveiling the genetic mechanisms underpinning fiber morphogenesis. We profiled the transcriptome of developing P...
To understand the variation in genomic patterning of DNA methylation we compared methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and r...
Base J, beta-D-glucosyl-hydroxymethyluracil, is a chromatin modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. In Trypanosoma brucei, J is enriched, along with histone H3 variant (H3.V), at sites involved in RNA Polymerase (RNAP) II termination and telomeric sites involved in regulating variant surface g...
Chromosome maps.
Whole chromosomes (Chr. 1–11, T. brucei Lister 427 version 9.0 genome) and the localization of base J (blue), H3.V (red), and mRNA coding genes (black lines; top strand is indicated by a line in the top half of the panel, bottom strand by a line in the bottom half) are shown. Genes on the top strand are transcribed from left to rig...
RT-qPCR analysis of ES associated ESAGs.
RT-qPCR analysis of the indicated ESAGs was performed as described in Fig 3D. P values were calculated using Student’s t test. *, p value ≤ 0.05; **, p value ≤ 0.01.
(TIFF)
Working model for H3.V regulating RNAP II transcription and mRNA and siRNA expression.
O-linked glycosylation of DNA (base J) is indicated by black line and dot. Nucleosomes are indicated by circles where green represents canonical histones and red represents histone H3 variant and an additional histone variant found at termination sites in T. bruc...
Regulation of siRNAs by H3.V at other loci.
Mapping of small RNAs to SLACS, INGI, CIR147 and IR3.
(TIFF)
Genomic context of genes downregulated in the H3.V KO.
(A) The EP/PAG1 loci. Small arrow indicates the RNAP I transcription start site in the promoter region. Genes in bold are downregulated in the H3.V KO. Genes in blue are transcribed by RNAP II on the top strand and EP and PAG genes in red are transcribed by RNAP I. MARP: microtubule-associated...
Small RNA-seq RPM and statistical significance at cSSRs.
The average small RNA-seq RPM of triplicate libraries at cSSRs is listed. Chromosome number and the 5’ and 3’ position of regions quantified are included. Statistical significance was assessed using pairwise Fisher’s Exact test on both total reads and specifically 21-27bp reads. Yellow highli...
Regulation of siRNAs by H3.V.
(A) Mapping of 23-26nt small RNAs to cSSR 11.9 in WT and H3.V KO. (B) Phasing of siRNAs mapping to a cSSR on chromosome 5 in WT cells. Position is indicated in kb. Colors indicate nucleotide: green, A; red, T; blue, C; and orange, G.
(TIFF)
Regulation of termination and gene expression by H3.V.
(A-C) Localization of H3.V, J, ORFs, and mRNA-seq reads from wild type T. brucei are plotted for cSSR 9.2 (position 1110–1190 kb is shown). (D-F) Gene expression changes and termination defects are analyzed as described in Fig 3. P values were calculated using Student’s t test. *, p value ≤ 0.0...
Confirmation of mRNA-seq transcript changes in T. brucei by RT-qPCR.
RT-qPCR was performed as described in Fig 3D. 5350: Tb427tmp.160.5350; 1960: Tb427.07.1960; 1565: Tb427tmp.02.1565; 1580: Tb427tmp.02.1580; 5384: Tb427.02.5384; and 6820: Tb427.07.6820. P values were calculated using Student’s t test. *, p value ≤ 0.05; **, p value ≤ 0.01.
(TIFF)
Enrichment of genes adjacent to H3.V and J following the loss of H3.V and/or J.
(A) Genes were defined as adjacent to H3.V or J if located within 10 kb of an H3.V and J enriched region, respectively, and are indicated in grey. Genes not adjacent to H3.V or J are indicated in white [13, 14]. 2463 (27%) genes are adjacent to H3.V and 2837 (31%) are a...
T. brucei gene expression changes following H3.V and/or J loss.
mRNAs found up or downregulated by 2-fold or more by mRNA-seq are listed, along with available gene descriptions, RPKM, fold change, and an indication of whether the genes are located within 10kb of H3.V and/or J. P values determined by Cuffdiff are listed for each condition compared t...
High-throughput sequencing information.
Information about all sequencing experiments performed in this study is listed. Also indicates the figures in which the data are presented.
(XLSX)
T. brucei upregulated genes following H3.V and/or J loss.
Similar to S1 Table, but upregulated genes are organized according to their location within PTUs. Genes sharing the same number are located in the same PTU and genes with different numbers are located in different PTUs.
(XLSX)
Regulation of termination and gene expression by H3.V.
(A-C) Localization of H3.V, J, ORFs and mRNA-seq reads from wild type T. brucei are ploted for cSSR 10.5 (1120–1140). (D) mRNA-seq transcript fold changes of the genes indicated in the ORF map in B, as described in Fig 5E. White bars: Wild type; grey bars: Wild type+DMOG; dark grey bars: H3.V K...
We describe restriction site associated RNA sequencing (RARseq), an RNAseq-based genotype by sequencing (GBS) method. It includes the construction of RNAseq libraries from double stranded cDNA digested with selected restriction enzymes. To test this, we constructed six single-and six-dual-digested RARseq libraries from six F2 pitcher plant individu...
Populus species are widely distributed across the Northern Hemisphere. The genetic diversity makes the genus an ideal study system for traits of ecological or agronomic significance. However, sequence variation between the genome-sequenced Populus trichocarpa Nisqually-1 and many other Populus species and hybrids poses significant challenges for re...
Figure S1. Comparisons of bark and xylem RNA-Seq data analysis using the variant-substituted P. tremula x abla 717 (sPta717) genome or the P. trichocarpa (Ptr_v3) reference genome. (a-b) Transcript abundance in bark (a) and xylem (b). Genes with significantly different FPKM values are highlighted in red (higher in sPta717) or blue (higher in Ptr_v3...
Table S1. Tissue sources of total RNA used for cDNA-primed genome amplification. Table S2. List of NGS datasets used in this study. Table S3. Identification of 717 genomic variants. Table S4. Number of expressed genes detected using the two different genomes. Table S5. Mapping rates of DNA-Seq and ChIP-Seq reads. Table S6. Re-annotation of Affymetr...
The genetic diversity of Populus species makes the genus a rich resource for functional genomic studies and agronomic trait improvement. However, sequence variation between the reference (P. trichocarpa) genome and that of the routinely transformed genotype (P. tremula x alba 717-1B4) poses significant challenges for research. Techniques such as qu...
Pima cotton (Gossypium barbadense L.) produces single-celled fiber seed trichomes (fibers) that are characterized by cellulosic-rich cell walls and desirable properties of long, strong and fine fibers,the longest and richest in cellulosic contents in the plant kingdom. To identify regulatory networks that likely govern these fiber quality traits, t...
The Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. However, few genomic resources exist for Miscanthus, which limits understanding of its interesting biology and future genetic improvement. A comprehensive catalog of expressed sequences were generated from a variety of Miscanthus species and tissue...
Gossypium barbadense L. (Egyptian and Pima) produces single-celled fiber trichomes that are the longest and richest in cellulosic content in the plant kingdom. Developmental dissection of fiber at the transcriptional level is crucial to unveil the genetic mechanisms underpinning fiber morphogenesis. This book describes the transcriptome of developi...
To gain novel insights into the molecular mechanisms underlying Pima cotton fiber quality, expression profiling of the Pima fiber transcriptome was performed as a function of development. The profiling was performed at 6 developmental time points: 8, 11, 14, 17, 21, and 24dpa. The expression profiling using long oligonucleotide microarray showed dy...
In order to study gene expression at the genomic level during elongation and secondary cell wall synthesis of upland cotton fiber, oligonucleotide microarrays were employed. RNA was isolated from fibers in 7 different time points beginning prior to peak fiber expansion, continuing through termination of fiber expansion and ending at peak cellulose...
Background
MAP is a suspected zoonotic pathogen and the causative agent of Johne’s Disease in cattle and other ruminant animals. With over $1 billion dollars in loss to the dairy industry due to Johne’s Disease, efforts to eliminate or reduce MAP from cattle are of importance. The purpose of this study was to determine if daily intake of probiotics...
Pseudomonas aeruginosa, which causes serious infections in immunocompromised patients, produces numerous virulence factors, including exotoxin A and the siderophore pyoverdine. As production of these virulence factors is influenced by the host environment, we examined the effect serum has on global transcription within P. aeruginosa strain PAO1 at...
Discovering the molecular mechanisms controlling biomass traits could accelerate the development of sustainable bioenergy from feedstock grasses. Small RNA (sRNA) play crucial roles in the regulation of plant genes important in development, responses to stress, and genome evolution. Regulatory networks of sRNAs and mRNAs are known to control plant...
Flow cytometric histogram of M. × giganteus nuclei stained with propidium iodide.
Estimates of nuclear DNA content in several Miscanthus accessions, by flow cytometry.
A table (tab delimited text format) of all repetitive sequences detected in the Miscanthus genome.
Miscanthus x giganteus (Mxg) is a perennial grass that produces superior biomass yields in temperate environments. The essentially uncharacterized triploid genome (3n = 57, x = 19) of Mxg is likely critical for the rapid growth of this vegetatively propagated interspecific hybrid.
A survey of the complex Mxg genome was conducted using 454 pyroseque...
Two different techniques for the molecular typing of Pseudomonas aeruginosa were used to study the epidemiology of P. aeruginosa strains. Colonization with P. aeruginosa was studied by taking samples of human origin collected from urine, sputum samples of patients suffering from lung manifestations and patients exposed to third-degree burns. In add...
Cotton fiber is an economically important seed trichome and the world's leading natural fiber used in the manufacture of textiles. As a step toward elucidating the genomic organization and distribution of gene networks responsible for cotton fiber development, we investigated the distribution of fiber genes in the cotton genome. Results revealed th...
Microarray expression data for Set 1 genes (125). The normalized expression values for Set 1 genes from Pima and TM1 developmental relative to the expression at 5 dpa. Genes are ordered according to the cluster number (as shown in Table 2). Functional descriptions were developed by BLASTing against NR unigene set (Genbank) and Arabidopsis (TAIR7) d...
Cotton fiber is a single-celled seed trichome of major biological and economic importance. In recent years, genomic approaches such as microarray-based expression profiling were used to study fiber growth and development to understand the developmental mechanisms of fiber at the molecular level. The vast volume of microarray expression data generat...
There is an immediate need for a high-density genetic map of cotton anchored with fiber genes to facilitate marker-assisted selection (MAS) for improved fiber traits. With this goal in mind, genetic mapping with a new set of microsatellite markers [comprising both simple (SSR) and complex (CSR) sequence repeat markers] was performed on 183 recombin...
Questions
Questions (4)
Raw RNA-seq data are discrete data but normalized RNA-seq data (RPM or RPKM or FPKM) are not discrete, i.e. continuous data. Shouldn't this change in the data's nature change our understanding of the data? In other words, why can't the microarray analysis tools be used to analyze the normalized RNA-seq data-both are continuous data types?
From a statistical viewpoint, is it necessary to maintain the discreteness or continuity of datasets? If yes, should we round the normalized RNA-seq data to maintain its discreteness?
It annoys me to see gene expression value reported in a real number. For instance, what does it mean when a gene expression value is 10.5987 RPM/RPKM/FPKM. How is the fraction "0.5987" is expressed in reality?
Why RNA-seq data are always modeled as negative binomial distribution? What are the parameters or the assumptions that make RNA-seq data fit the negative binomial distribution?
We measured the expression of two genes before and after DSN normalization of the full-length cDNA library. These two genes are Ubi4, which is highly abundant, and Pr1.1, which is not. Unfortunately, the expression ratio before and after DSN normalization is very similar. One would expect the high abundant gene will become in the range as the the low abundant gene. Any suggestion? Explanations?
Has anyone compared Trinity with Abyss-trans for de novo assembly of the same data sets? I'd like to see the stats of both assemblies as well as any other assessment measures. Which algorithms deal with the isoforms and repeats issues better?
