Current trends in chloroplast genome research

Chloroplast is an important cellular organelle of autotrophs which has an independent, circular, doublestranded DNA molecule termed as chloroplast genome. The chloroplast DNA (cpDNA) contains essential genes for its maintenance and operation. Several components of the photosystems andproteins involved in biosynthetic pathways are also encoded by the chloroplast genome. Exploring the genetic repository of this organelle is vital due to its conserved nature, small size, persistent gene organization and promising ability for transgenic expression. Therefore, cpDNA sequence information has been instrumental in phylogenetic studies and molecular taxonomy of plants. Chloroplast genome sequencing efforts have being initiated with conventional cloning and chain-termination sequencing technologies. Dedicated databases such as CGDB and GOBASE among others have been established as more and more complete cpDNA sequences are being reported. Presently, elegant molecular biologytechniques including shotgun sequencing, rolling circle amplification (RCA), Amplification, Sequencing and Annotation of Plasteome (ASAP) and Next generation sequencing are being used to accelerate data output. Owing to many fold increase in submission of cpDNA sequences in nucleotide databases, challenges of in-depth data analysis stimulated the emergence of devoted annotation, assembling and phylogenetic software. Recently, reported bioinformatics software for chloroplast genome studiescomprise of DOGMA for annotation, SCAN-SE, ARAGON and PREP suit for RNA analyses and CG viewer for circular map construction/comparative analysis. Faster algorithms for gene-order based phylogenetic reconstruction and bootstrap analysis have attracted the attention of research community. Current trends in sequencing strategies and bioinformatics with reference to chloroplast genomes hold great potential to illuminate more hidden corners of this ancient cell organelle

Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard.

This is the final version of the article. Available from the publisher via the DOI in this record.We analyzed the genome sequence of an endophytic bacterial strain Pseudomonas putida TJI51 isolated from mango bark tissues. Next generation DNA sequencing and short read de novo assembly generated the 5,805,096 bp draft genome of P. putida TJI51. Out of 6,036 protein coding genes in P. putida TJI51 sequences, 4,367 (72%) were annotated with functional specifications, while the remaining encoded hypothetical proteins. Comparative genome sequence analysis revealed that the P. putida TJI51genome contains several regions, not identified in so far sequenced P. putida genomes. Some of these regions were predicted to encode enzymes, including acetylornithine deacetylase, betaine aldehyde dehydrogenase, aldehyde dehydrogenase, benzoylformate decarboxylase, hydroxyacylglutathione hydrolase, and uroporphyrinogen decarboxylase. The genome of P. putida TJI51 contained three nonribosomal peptide synthetase gene clusters. Genome sequence analysis of P. putidaTJI51 identified this bacterium as an endophytic resident. The endophytic fitness might be linked with alginate, which facilitates bacterial colonization in plant tissues. Genome sequence analysis shed light on the presence of a diverse spectrum of metabolic activities and adaptation of this isolate to various niches.This research was financially supported by the Higher Education Commission, Islamabad Pakistan

Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids

Background: Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information. Results: The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of three different stages of fruit ripening (pre-climacteric, climacteric and post-climacteric) were also analyzed. The analysis of the RNAseqatlas presented here reveals strong differences in gene expression patterns between different organs, especially between root and flower, but also reveals similarities among the gene expression patterns in other organs, such as stem, leaves and aerial buds (vegetative organs) or seed and fruit (storage organs). Important regulators, functional categories, and differentially expressed genes involved in avocado fruit ripening were identified. Additionally, to demonstrate the utility of the avocado gene expression atlas, we investigated the expression patterns of genes implicated in fatty acid metabolism and fruit ripening. Conclusions: A description of transcriptomic changes occurring during fruit ripening was obtained in Mexican avocado, contributing to a dynamic view of the expression patterns of genes involved in fatty acid biosynthesis and the fruit ripening process

Depressive symptoms associated with COVID-19 preventive practice measures, daily activities in home quarantine and suicidal behaviors: findings from a large-scale online survey in Bangladesh

Background: The world is facing a public health emergency situation caused by the COVID-19 pandemic. Psychological wellbeing among individuals worldwide has been negatively affected by the pandemic especially in low- and middle-income countries such as Bangladesh. The present study aimed to assess the estimate of depressive symptoms and investigated its associations with COVID-19 preventive practice measures, daily activities in home quarantine, and suicidal behaviors in a large-scale Bangladeshi online survey. Methods: An online-based cross-sectional survey was widely distributed to Bangladeshi citizens. A total of 13,654 participants (61.0% male; mean age = 24.0 years [SD = 6.0]; age range 18–65 years) completed the survey between May and June (2020). The survey included socio-demographics and COVID-19-related questions, along with lifestyle, suicidal, and psychometric measures. Hierarchical regression was performed to determine significant associations between depression and examined variables. Results: The estimate of depressive symptoms during the COVID-19 pandemic was 43.5%. Based on hierarchical regression analysis, depression was significantly associated with not engaging in COVID-19 preventive measures, daily activities in home quarantine (e.g., playing videogames), and suicidal behaviors. Conclusions: Depressive symptoms appeared to be high during the COVID-19 pandemic in Bangladesh. To fight against the pandemic, mental health issues as well as physical health issues need to be taken into consideration