Biology subjects

Abdullah,

Publications and source records attributed to Abdullah,.

7 recordsLinked to original sources

bioRxiv2025

CGAS (Chloroplast Genome Analysis Suite): An Automated Python Pipeline for Comprehensive Comparative Chloroplast Genomics

BackgroundChloroplast genome analysis underpins plant phylogenetics, comparative genomics, and molecular marker development. Although high-quality chloroplast genomes are now routinely generated, downstream comparative analyses still rely on fragmented toolchains requiring separate tools for annotation, codon analysis, and SNP detection, extensive manual curation, and ad hoc scripting, which limit reproducibility and scalability. ResultsWe present the Chloroplast Genome Analysis Suite (CGAS), an automated Python-based pipeline designed as a comprehensive solution for comparative chloroplast genomics. CGAS integrates nine core analytical modules into a single, reproducible workflow operating directly on annotated GenBank files and pre-aligned FASTA datasets. The pipeline performs automated gene content analysis, publication-ready gene table generation, chloroplast structural characterization (LSC/SSC/IR boundaries and GC content), codon usage and amino acid composition analyses enabling batch processing of 10-50+ genomes, SNP detection with transition/transversion statistics, intron feature characterization, simple sequence repeat identification, and nucleotide diversity profiling. Unlike existing tools, CGAS emphasizes biologically informed handling of edge cases, including trans-spliced genes (e.g., rps12), IR-mediated gene duplication, and annotation artifacts. All outputs are generated in standardized, publication-ready Excel and Word formats with timestamped provenance. ConclusionsCGAS provides a unified, automated, and biologically robust framework for comparative chloroplast genome analysis. By minimizing manual intervention and emphasizing batch processing, the suite substantially accelerates methodologically consistent analyses. The pipeline is openly available at https://github.com/abdullah30/Chloroplast-Genome-Analysis-Suite-CGAS and readily extensible, supporting its adoption as a standardized analytical backend for chloroplast comparative genomics.

bioinformatics↗

bioRxiv2021

Phosphate transporter genes: genome-wide identification and characterization in Camelina sativa

Phosphorus is known as a key element associated with growth, energy, and cell signaling. In plants, phosphate transporters (PHTs) are responsible for moving and distributing phosphorus in cells and organs. PHT genes have been genome-wide identified and characterized in various plant species, however, these genes have not been widely identified based on available genomic data in Camellia sativa, which is an important oil seed plant. In the present study, we found 66 PHT genes involved in phosphate transporter/translocate in C. sativa. The recognized genes belonged to PHTs1, PHTs2, PHTs4, PHOs1, PHO1 homologs, glycerol-3-PHTs, sodium dependent PHTs, inorganic PHTs, xylulose 5-PHTs, glucose-6-phosphate translocators, and phosphoenolpyruvate translocators. Our finding revealed that PHT proteins are divers based on their physicochemical properties such as Isoelectric point (pI), molecular weight, GRAVY value, and exon-intron number(s). Besides, the expression profile of PHT genes in C. sativa based on RNA-seq data indicate that PHTs are involved in response to abiotic stresses such as cold, drought, salt, and cadmium. The tissue specific expression high expression of PHO1 genes in root tissues of C. sativa. In additions, four PHTs, including a PHT4;5 gene, a sodium dependent PHT gene, and two PHO1 homolog 3 genes were found with an upregulation in response to aforementioned studied stresses. In the current study, we found that PHO1 proteins and their homologs have high potential to post-translation modifications such as N-glycosylation and phosphorylation. Besides, different cis-acting elements associated with response to stress and phytohormone were found in the promoter region of PHT genes. Overall, our results show that PHT genes play various functions in C. Sativa and regulate Camellia responses to external and intracellular stimuli. The results can be used in future studies related to the functional genomics of C. sativa.

plant biology↗

bioRxiv2021

Pseudogenization of trnT-GGU in chloroplast genomes of the plant family Asteraceae

The chloroplast genome evolves through the course of evolution. Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The pseudogenization of the trnT-GGU gene was previously reported in the Cryptomeria japonica (Cupressaceae), Pelargonium x hortorum (Geraniaceae), and in the two species of the tribe Gnaphalieae (Asteroideae, Asteraceae). Here, we performed a broad analysis of the trnT-GGU gene among the species of twelve subfamilies of Asteraceae and found pseudogenization of this gene is not limited to the two species of Gnaphalieae or the tribe Gnaphalieae. We report for the first time that this gene is pseudo in the species of three subfamilies of Asteraceae, including Gymnarrhenoideae, Cichorioideae and Asteroideae. The analyses of the species of 78 genera of Asteroideae revealed that this pseudogenization event is linked to the insertion within the 5' acceptor stem and not linked to the habit, habitat, and geographical distribution of the plant.

evolutionary biology↗

bioRxiv2021

The GASA Gene Family in Theobroma cacao: Genome Wide Identification and Expression Analyses

The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20-25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.

plant biology↗

bioRxiv2020

Agro-morphological, yield, and genotyping-by-sequencing data of selected wheat germplasm

Wheat (Triticum aestivum) is the most important staple food in Pakistan. Knowledge of its genetic diversity is critical for designing effective crop breeding programs. Here we report agro-morphological and yield data for 112 genotypes (including 7 duplicates) of wheat (Triticum aestivum) cultivars, advance lines, landraces and wild relatives, collected from several research institutes and breeders across Pakistan. We also report genotyping-by-sequencing (GBS) data for a selected sub-set of 52 genotypes. Sequencing was performed using Illumina HiSeq 2500 platform using the PE150 run. Data generated per sample ranged from 1.01 to 2.5 Gb; 90% of the short reads exhibited quality scores above 99.9%. TGACv1 wheat genome was used as a reference to map short reads from individual genotypes and to filter single nucleotide polymorphic loci (SNPs). On average, 364,074{+/-}54479 SNPs per genotype were recorded. The sequencing data has been submitted to the SRA database of NCBI (accession number SRP179096). The agro-morphological and yield data, along with the sequence data and SNPs will be invaluable resources for wheat breeding programs in future.

genetics↗

bioRxiv2020

Comparison among the first representative chloroplast genomes of Orontium, Lisa, Zamioculcas, and Stylochaeton of the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of the first representatives of four genera representing three subfamilies: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using the plastomes. The size of the chloroplast genomes ranged from 163,770-169,982 bp. These genomes comprise 114 unique genes, including 80 protein-coding, 4 rRNA, and 30 tRNA genes. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The junctions JSB (IRb/SSC) and JSA (SSC/IRa) are highly variable, as is oligonucleotide repeats content among the genomes. The patterns of inverted repeats contraction and expansion were shown to be homoplasious and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were shown for several genes in S. bogneri. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

plant biology↗

bioRxiv2020

Complete chloroplast genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): unique inverted repeat expansion and contraction affect rate of evolution

The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae: Anthurium huixtlense (163,116 bp) and Pothos scandens (164,719 bp). The chloroplast genome of P. scandens showed unique inverted repeats (IRs) contraction and expansion, which increases the size of the large single copy (102,956) region and decreases the size of the small single-copy (6779 bp) region. This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as opposed to IRs. We found a 2.3-fold increase of oligonucleotide repeats in P. scandens when compared with A. huixtlense, whereas amino acid frequency and codon usage revealed similarities. We recorded higher transition substitutions than transversion substitutions. The transition/transversion ratio was 2.26 in P. scandens and 2.12 in A. huixtlense. We also found a higher rate of transversion substitutions linked with non-synonymous substitutions than synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.

genomics↗