De novoassembly and functional annotation of blood transcriptome of loggerhead turtle, andin silicocharacterization of peroxiredoxins and thioredoxins

Abstract

The aim of this study was to generate and analyze the atlas of the loggerhead turtle blood transcriptome by RNA-seq, as well as identify and characterize thioredoxin (Tnxs) and peroxiredoxin (Prdxs) antioxidant enzymes of the greatest interest in the control of peroxide levels and other biological functions. The transcriptome of loggerhead turtle was sequenced using the Illumina Hiseq 2000 platform and de novo assembly was performed using the Trinity pipeline. The assembly comprised 515,597 contigs with an N50 of 2,631 bp. Contigs were analyzed with CD-Hit obtaining 374,545 unigenes, of which 165,676 had ORFs encoding putative proteins longer than 100 amino acids. A total of 52,147 (31.5%) of these transcripts had significant homology matches in at least one of the five databases used. From the enrichment of GO terms, 180 proteins with antioxidant activity were identified, among these 28 Prdxs and 50 putative Tnxs. The putative proteins of loggerhead turtles encoded by the genes Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip were predicted and characterized in silico. When comparing Prdxs and Txns of loggerhead turtle with homologous human proteins, they showed 18 (9%), 52 (18%) 94 (43%), 36 (16%), 35 (33%) and 74 (19%) amino acid mutations respectively. However, they showed high conservation in active sites and structural motifs (98%), with few specific modifications. Of these, Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip presented 0, 25, 18, three, six and two deleterious changes. This study provides a high quality blood transcriptome and functional annotation of loggerhead sea turtles.

Comparison of Microbial Populations in the Blood of Patients With Myocardial Infarction and Healthy Individuals

“…The upregulation of these pathways was correlated with Huntington's disease, followed by Parkinson's disease, oxidative phosphorylation, Alzheimer's disease, and microbial metabolism in diverse environment signaling pathways (Zhou et al, 2020 ). Furthermore, our study found that posttranslational modifications, protein turnover, chaperones, amino acid transport, and metabolism were significantly increased in MI patients, and similar findings were reported in previous studies on different diseases (Liu et al, 2015 ; Wang et al, 2017 ; Hernández-Fernández et al, 2021 ), although the direct role of these pathways in MI is still not clear. According to our knowledge, the predicted functional metabolic COG pathway in MI patients was explored for the first time in our study.…”