Identification of tandem repeat families from long-read sequences of Humulus lupulus

Repeat-mediated recombination results in Complex DNA structure of the mitochondrial genome of Trachelospermum jasminoides

BACKGROUND

Trachelospermum jasminoides has medicinal and ornamental value and is widely distributed in China. Although the chloroplast genome has been documented, the mitochondrial genome has not yet been studied.

RESULTS

The mitochondrial genome of T. jasminoides was assembled and functionally annotated using Illumina and nanopore reads. The mitochondrial genome comprises a master circular molecular structure of 605,764 bp and encodes 65 genes: 39 protein-coding genes, 23 transfer RNA (tRNA) genes and 3 ribosomal RNA genes. In addition to the single circular conformation, we found many alternative conformations of the T. jasminoides mitochondrial genome mediated by 42 repetitive sequences. Six repetitive sequences (DRS01-DRS06) were supported by nanopore long reads, polymerase chain reaction (PCR) amplifications, and Sanger sequencing of the PCR products. Eleven homologous fragments were identified by comparing the mitochondrial and chloroplast genome sequences, including three complete tRNA genes. Moreover, 531 edited RNA sites were identified in the protein-coding sequences based on RNA sequencing data, with nad4 having the highest number of sites (54).

CONCLUSION

To our knowledge, this is the first description of the mitochondrial genome of T. jasminoides. Our results demonstrate the existence of multiple conformations. These findings lay a foundation for understanding the genetics and evolutionary dynamics of Apocynaceae.

Hop (Humulus lupulus L.) extract reverts glycaemic imbalance and cognitive impairment in an animal model of obesity

The rates of overweight and obesity around the world have increased in past years. The body's adipose tissue stimulates the antioxidant and oxidation imbalance capacity at the cellular level. This scenario favors an inflammatory low-grade systemic condition starting with insulin resistance, which in turn may involve diabetes mellitus type 2 and cognitive decline afterward. Neurological diseases have been correlated to senile age diseases over time. This scenario calls for a change in the incidence of obesity in the younger generation. An unhealthy dietary consumption together with sedentary habits might lead to poor gut absorption of nutrients. Several plants and foods have bioactive compounds that can reduce or inhibit radical scavengers, reactive oxygen species, and metal ion complexes that threaten the cerebral defense system. The bitter acids from hops (Humulus lupulus L.) have been demonstrated to have promising effects on lipid and carbohydrate metabolism improvement, reducing inflammatory responses through alpha acids, beta acids, and analogs action. Therefore, the current study aimed to investigate the bioactivity of hop bitter acids in obese and lean mice. For that, a dry hop extract (DHE) was obtained by applying carbon dioxide as the fluid of supercritical extraction. Afterward, seventy-eight male mice of the C57BL/6J strain were weighed and randomly distributed into six groups of 13 animals each according to the diet offered: (NO) normolipidic diet, (NO1) normolipidic diet containing 0.35% alpha acids, (NO2) normolipidic diet containing 3.5% alpha acids, (HP) hyperlipidic diet, (HP1) hyperlipidic diet containing 0.35% alpha acids, and (HP2) hyperlipidic diet containing 3.5% alpha acids. After applying the glycemic tolerance and insulin tolerance tests, a better stabilization of glycemia levels and weight gain among those animals fed with DHE (NO2 and HP2) were observed in comparison to the obese control group (HP) (p < 0.05). There was also an amelioration of antioxidant capacity observed by checking the enzymatic profile by SOD and an apparent mitigation of brain degeneration by checking GSK3β and p-IRS1 proteins expression (p < 0.05). The y-maze cognitive test applied to highlight possible obesity-harmful animal brains did not indicate a statistical difference between the groups. Although the weekly dietary intake between the obese HP2 group (33.32 ± 4.11, p < 0.05) and control HP (42.3 ± 5.88, p < 0.05) was different. The bioactive compounds present in DHE have demonstrated relevant effects on glycemic control, insulin signaling, and the consequent modulatory action of the obesity-related markers with the brain's inflammatory progression.

Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

Simple Summary

The evolutionary patterns and phylogenetic utility of duplicate control regions (CRs) in 72 individuals of Varanus salvator macromaculatus and other varanids have been observed. Divergence of the two CRs from each individual revealed a pattern of independent evolution in CRs of varanid lineage. This study is a first step towards developing new phylogenetic evolutionary models of the varanid lineage, with accurate evolutionary inferences to provide basic insights into the biology of mitogenomes.

Abstract

Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.