Biology subjects

Haider, W.

Publications and source records attributed to Haider, W..

3 recordsLinked to original sources

bioRxiv2023

De novo Genome Assembly, Functional Annotation and SSR Mining of Citrus reticulata (Kinnow) from Pakistan

Citrus reticulata (Blanco) fruit is native to South East Asia which owns many of the nutritional, medicinal and economic advantages, locally known as "Kinnow" and one of the priced mandarin varieties (Dancy, Fuetrells Early and Honey) of Citrus genera renowned for its exclusive taste, vitamin richness, thin peel, long shelf-life and seedless characteristics in Pakistan. However, genetic improvement and breeding strategies of this valued variety are lacking due to the in-housed insufficient genomic and technical resources. Therefore, the current research was initiated to provide the base-line de-novo genome assembly of C. reticulata (seedless kinnow) at a depth of 151x with Illumina paired-end short-read sequencing technology using HiSeq 2500. Whole-genome sequencing resulted in 139,436,350 raw reads ([~]20.09 GB) of data, however, after removing the low-quality reads (1.08%), duplicated sequences (10.5%) and Illumina adaptors, 137,901,462 clean reads were obtained with ([~]18.87 GB) of clean data which was further used for downstream variant calling analysis. In total, 348,861 scaffolds were generated with N50 value of 4827 which constitute 263,018,9 contigs ranging from 71-36,213 with total of 179,984,763 nucleotides. The GC content of the final draft assembly at 71-mer was 34.1%. Moreover, annotation was performed with "Hayai-Annotation Plants" tool which marked the whole-genome mapping with three main functional databases of interpro, Pfam and gene ontology. Additionally, in-silico identification of 111,032 Simple Sequence Repeats (SSR) was also accomplished with the help of GMATA tool, which may be used for further screening and genetic improvement of the citrus varieties by means of this current assembly as a resource of local reference genome.

bioinformatics↗

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↗

bioRxiv2017

Ecological, angler and spatial heterogeneity drive social and ecological outcomes in an integrated landscape model of freshwater recreational fisheries

Freshwater recreational fisheries constitute complex adaptive social-ecological systems (SES) where mobile anglers link spatially structured ecosystems. We present a general social-ecological model of a spatial recreational fishery for northern pike (Esox lucius) that included an empirically measured mechanistic utility model driving angler behaviors. We studied emergent properties at the macro-scale (e.g., region) as a result of local-scale fish-angler interactions, while systematically examining key heterogeneities (at the angler and ecosystem level) and sources of uncertainty. We offer three key insights. First, the angler population size and the resulting latent reginal angling effort exerts a much greater impact on the overall regional-level overfishing outcome than any residential pattern (urban or rural), while the residential patterns strongly affects the location of local overfishing pockets. Second, simplifying a heterogeneous angler population to a homogenous one representing the preference and behaviours of an average angler risks severely underestimating landscape-level effort and regional overfishing. Third, we did not find that ecologically more productive lakes were more systematically overexploited than lower-productive lakes. We conclude that understanding regional-level outcomes depends on considering four key ingredients: regional angler population size, the angler population composition, the specific residential pattern in place and spatial ecological variation. Simplification of any of these may obscure important dynamics and render the system prone to collapse.

ecology↗