Characterization of the complete chloroplast genome of Helicteres hirsuta Lour. 1790 (Helicteriodeae: Malvaceae).

Helicteres hirsuta Lour. 1790 is a precious medicinal plant species, especially for treating chronic liver diseases. Genomic data on H. hirsuta are limited. Therefore, this current study aimed to characterize the chloroplast genome of H. hirsuta and reconstruct the phylogenetic relationship among Helicteroideae taxa. Consequently, the complete chloroplast genome of H. hirsuta was 163,404 bp in length and contained 113 unique genes (79 protein-coding genes, 30 tRNA genes, and four rRNA genes). Notably, two introns of clpP gene of H. hirsuta were lost in comparison to that of other Helicteroideae species. The phylogenetic tree based on chloroplast genomes of eleven Helicteroideae species revealed that H. hirsuta was closely related to Reevesia species. In conclusion, our study described the first complete chloroplast genome of H. hirsuta, which is essential for tracing evolutionary history in the Helicteroideae subfamily.

Rapid identification of SARS-CoV-2 strains via isothermal enzymatic recombinase amplification and nanopore sequencing.

Surveillance of the SARS-CoV-2 genome has become a crucial technique in the management of COVID-19, aiding the pandemic response and supporting effective public health interventions. Typically, whole-genomic sequencing is used along with PCR-based target enrichment techniques to identify SARS-CoV-2 variants, which is a complicated and time-consuming process that requires central laboratory facilities. Thus, there is an urgent need to develop rapid and cost-effective tools for precise on-site detection and identification of SARS-CoV-2 strains. In this study, we demonstrate the rapid diagnosis of COVID-19 and identification of SARS-CoV-2 variants by amplification and sequencing of the entire SARS-CoV-2 S gene using isothermal enzymatic recombinase amplification combined with the advanced Oxford nanopore sequencing technique. The entire procedure, from sampling to sequencing, takes less than 8 hours and can be performed with limited resources. The newly developed method has noteworthy implications for examining the transmission dynamics of the virus, detecting novel genetic variants, and assessing the effect of mutations on diagnostic approaches, antiviral treatments, and vaccines.

The complete mitochondrial genome of Siganus virgatus Valenciennes (Siganidae: Acanthuriformes).

Siganus virgatus Valenciennes 1835 is an essential species for examining reef ecosystems; however, its mitochondrial genome has not been studied. In this research, the mitogenome of S. virgatus was sequenced and characterized. The results revealed a circular genome of 16,505 bp that was composed of A (28.1%), C (31.3%), G (14%), and T nucleotides (26.6%). The genome contained 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. Most genes of the mitogenome were transcribed on the heavy strand (H-strand), whereas ND6 and eight tRNA genes (including tRNA-Ala, -Asn, -Cys, -Gln, -Glu, -Ser (1), -Pro, and -Tyr) were transcribed on the light strand (L-strand). Comparative analysis revealed a high degree of conservation of gene content and order among the Siganus mitogenomes. Phylogenetic analysis inferred from whole mitogenomes exhibited a close relationship between S. virgatus and S. guttatus. The newly completed mitogenome of S. virgatus provides essential genomic data for further studies on population genetics and the evolution of the Siganus genus and the Siganidae family.

The complete mitochondrial genome of Mystus gulio Hamilton (Siluriformes: Bagridae) and its phylogenetic implication.

Mystus gulio Hamilton, also called long whiskers catfish, is an endemic fish and a common food in some Asian countries. In this study, the complete mitochondrial genome of M. gulio was sequenced using the MinION system (Oxford Nanopore Technologies). The mitochondrial genome is 16,518 bp in length (41.1% [G + C] content) and consists of 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The results of phylogenetic analysis inferred from whole mitochondrial genomes of Mystus and related species in the family Bagridae revealed that M. gulio is closely related to Mystus cavasius.

Soil Mineral Composition and Salinity Are the Main Factors Regulating the Bacterial Community Associated with the Roots of Coastal Sand Dune Halophytes.

Soil salinity and mineral deficiency are major problems in agriculture. Many studies have reported that plant-associated microbiota, particularly rhizosphere and root microbiota, play a crucial role in tolerance against salinity and mineral deficiency. Nevertheless, there are still many unknown parts of plant-microbe interaction, especially regarding their role in halophyte adaptation to coastal ecosystems. Here, we report the bacterial community associated with the roots of coastal sand dune halophytes Spinifex littoreus and Calotropis gigantea, and the soil properties that affect their composition. Strong correlations were observed between root bacterial diversity and soil mineral composition, especially with soil Calcium (Ca), Titanium (Ti), Cuprum (Cu), and Zinc (Zn) content. Soil Ti and Zn content showed a positive correlation with bacterial diversity, while soil Ca and Cu had a negative effect on bacterial diversity. A strong correlation was also found between the abundance of several bacterial species with soil salinity and mineral content, suggesting that some bacteria are responsive to changes in soil salinity and mineral content. Some of the identified bacteria, such as Bacillus idriensis and Kibdelosporangium aridum, are known to have growth-promoting effects on plants. Together, the findings of this work provided valuable information regarding bacterial communities associated with the roots of sand dune halophytes and their interactions with soil properties. Furthermore, we also identified several bacterial species that might be involved in tolerance against stresses. Further work will be focused on isolation and transplantation of these potential microbes, to validate their role in plant tolerance against stresses, not only in their native hosts but also in crops.

A Novel CO2-Based Insect Sampling Device and Associated Field Method Evaluated in a Strawberry Agroecosystem.

There is high demand for accurate insect sampling methods to inform integrated pest management strategies. Despite widespread application, existing sampling methods, such as portable aspirating and sweep netting, can result in overrepresentation of prominent pests, underrepresentation of natural enemies, and damage to plants. In this study, we test a novel device for insect sampling via anesthetization. Specifically, we test the effect of CO2 (application pressure and duration of exposure) on Lygus hesperus Knight (Hemiptera: Miridae) anesthetization in the laboratory and on insect community density in a strawberry agroecosystem. Carbon dioxide application proves an effective means of anesthetization compared to negative controls, and an increase in net CO2 exposure results in a decrease in time until L. hesperus anesthetization. Field results indicate the CO2 method collects more parasitoids and thrips than a portable aspirator, and at the 50 PSI application pressure and 15-s exposure, the CO2 method results in a comparable number of pests collected as the research standard, a portable aspirator with 8-s aspiration time. Benefits of the CO2 method include minimal plant damage, highly explicit spatial and temporal data, and scalability.