Selection constraints determine preference for A/U-ending codons in Taxus contorta

Unequal utilization of synonymous codons is a well-known phenomenon among living organisms. This phenomenon plays a major role in the enhancement of the accuracy and efficiency of translation. Gymnosperms are rarely paid attention in this aspect. Understanding the degree of and determining the forces influencing codon usage bias (CUB) in Taxus contorta, an endangered Himalayan gymnosperm, will prove useful in interpreting the evolutionary characteristics of this species. Using RNAseq data, 93 790 assembled transcripts were clustered into 32 701 unigenes. Around 13 061 full-length sequences were utilized for the analysis of CUB. Compositional properties showed that GC-content ranged from 28.76% to 65.22%, with an average value of 44.28%, suggesting an AT-rich genome. The mean effective number of codons (ENC) value revealed that CUB is not strong in T. contorta. The preferred codons tended to be A/U ending, whereas the avoided codons tended to be G/C ending. A P2 index of 0.54 and a Mutation Responsive Index (MRI) value of –0.02 in addition to the results revealed by the neutrality, ENC, and parity plots showed that natural selection is a predominating factor governing CUB. Mutational pressure, gene length, hydropathiciy, aromaticity, and nucleotide composition influence CUB weakly.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Transcripts_RA

The Trinity unigenes assembled from RNA seq of leaf and flower tissue were clustered (95% identity) and filtered to obtain a master file containing only non-redundant transcripts (>500bp)

Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

Rhododendron arboreum, an ecologically prominent species, also lends commercial and medicinal benefits in the form of palatable juices and useful herbal-drugs. The local abundance and survival of the species under highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered the additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illuminaâ s platform facilitated the generation of ~100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out shorter transcripts predicted 113,167 non-redundant transcripts with an average length of 1164.6 bases. 71,961 transcripts were categorized based on the functional annotations in the Gene Ontology database, whereby 5,710 were grouped into 141 pathways and 23,746 encoded for different transcription factors. Transcriptome screening further identified 35,419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Cancer Screening Differences Among Muslims and Non-Muslims: Insights from the Chicago Multiethnic Prevention and Surveillance Study.

BACKGROUND: While cancer screening disparities along socioeconomic and racial/ethnic lines are well studied, differences based on religious affiliation are under-researched. Though diverse in terms of race/ethnicity, Muslim Americans appear to share values and beliefs that similarly inform their health and healthcare seeking behaviors. Cancer screening disparities among Muslim Americans are also understudied. METHODS: To examine differences in cancer screening behaviors based on Muslim affiliation, we analyzed data from a longitudinal cohort study examining lifestyle, healthcare access, environmental, and genetic factors on the health of Chicagoans. RESULTS: Of 7552 participants, 132 (1.7%) were Muslim. Between Muslim and non-Muslims, there were no significant differences in prostate, cervical, and breast cancer screening rates, but Muslims were less likely to undergo colorectal cancer screening. When differences in obesity and insurance status were accounted for in a multivariate regression model, religious affiliation was no longer significantly associated with screening rates. DISCUSSION: Religious values can influence cancer screening behaviors; hence, tracking cancer screening along religious lines may illuminate previously unknown disparities. Our analysis of a predominately African American cohort of Chicagoans, however, did not reveal religious affiliation to predict cancer screening disparities