in-silico-identification-characterization-circrnas-during-host

<em>In Silico</em> Identification and Characterization of circRNAs During Host-Pathogen Interactions

Circular RNAs (circRNAs) are a class of non-coding RNAs that are formed via back-splicing. These circRNAs are predominantly studied for their roles as ...

Universiti Malaya

Although plants and animals are evolutionarily distant, the structure and function of their chromosomes are largely conserved. This allowed the establishment of a human-Arabidopsis hybrid cell line in which a neo-chromosome was formed by insertion of segments of Arabidopsis chromosomes into human chromosome 15. We used this unique system to investigate how the introgressed part of a plant genome was maintained in human genetic background. The analysis of the neo-chromosome in 60- and 300-day-old cell cultures by next-generation sequencing and molecular cytogenetics suggested its origin by fusion of DNA fragments of different sizes from Arabidopsis chromosomes 2, 3, 4, and 5, which were randomly intermingled rather than joined end-to-end. The neo-chromosome harbored Arabidopsis centromeric repeats and terminal human telomeres. Arabidopsis centromere wasn't found to be functional. Most of the introgressed Arabidopsis DNA was eliminated during the culture, and the Arabidopsis genome in 300-day-old culture showed significant variation in copy number as compared with the copy number variation in the 60-day-old culture. Amplified Arabidopsis centromere DNA and satellite repeats were localized at particular loci and some fragments were inserted into various positions of human chromosome. Neo-chromosome reorganization and behavior in somatic cell hybrids between the plant and animal kingdoms are discussed.

Molecular organization of recombinant human-Arabidopsis chromosomes in hybrid cell lines.

Gene prediction is a laborious and time-consuming task. The advancement of sequencing technologies and bioinformatics tools, coupled with accelerated rate of ribosome profiling and mass spectrometry development, have made identification of small open reading frames (sORFs) (< 100 codons) in various plant genomes possible. The past 50 years have seen sORFs being isolated from many organisms. However, to date, a comprehensive sORF annotation pipeline is as yet unavailable, hence, addressed in our review. Here, we also provide current information on classification and functions of plant sORFs and their potential applications in crop improvement programs.

Small open reading frames in plant research: from prediction to functional characterization.

A novel glufosinate-tolerant  sp. LA21, was isolated from soil samples of an oil palm plantation with a long history of glufosinate application. The genome of  sp. LA21 was sequenced with 150 bp paired-end conducted using Illumina sequencing technology. De novo genome assembly was performed using SPAdes, ABySS, and Velvet assemblers. Phylogenetic analysis using 16S rRNA gene sequence showed that  sp. LA21 was closely related to  ATCC 33634. Multilocus sequence analysis (MLSA) based on four bacterial housekeeping genes (16S rRNA,  ,  , and  ) was conducted together with 138 reference genomes of  species. The phylogenetic tree derived from MLSA analysis using concatenated 16S rRNA- sequences grouped  sp. LA21 under  group and  subgroup. Detailed phylogenomic analysis using average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC) approaches showed that  sp. LA21 could be classified as a novel  species.

Whole genome sequencing and phylogenomic analyses of a novel glufosinate-tolerant  species.

Flooding caused or exacerbated by climate change has threatened plant growth and food production worldwide. The lack of knowledge on how crops respond and adapt to flooding stress imposes a major barrier to enhancing their productivity. Hence, understanding the flooding-responsive mechanisms of crops is indispensable for developing new flooding-tolerant varieties. Here, we examined the banana ( cv. Berangan) responses to soil waterlogging for 1, 3, 5, 7, 14, and 24 days. After waterlogging stress, banana root samples were analyzed for their molecular and biochemical changes. We found that waterlogging treatment induced the formation of adventitious roots and aerenchyma with conspicuous gas spaces. In addition, the antioxidant activities, hydrogen peroxide, and malondialdehyde contents of the waterlogged bananas increased in response to waterlogging stress. To assess the initial response of bananas toward waterlogging stress, we analyzed the transcriptome changes of banana roots. A total of 3508 unigenes were differentially expressed under 1-day waterlogging conditions. These unigenes comprise abiotic stress-related transcription factors, such as ethylene response factors, basic helix-loop-helix, myeloblastosis, plant signal transduction, and carbohydrate metabolisms. The findings of the study provide insight into the complex molecular events of bananas in response to waterlogging stress, which could later help develop waterlogging resilient crops for the future climate.

Article	Year
Molecular organization of recombinant human-Arabidopsis chromosomes in hybrid cell lines. Scientific reports\| PubMed ID: 33785802	2021
Small open reading frames in plant research: from prediction to functional characterization. 3 Biotech\| PubMed ID: 35251879	2022
Whole genome sequencing and phylogenomic analyses of a novel glufosinate-tolerant species. 3 Biotech\| PubMed ID: 35547011	2022
Waterlogging Stress Induces Antioxidant Defense Responses, Aerenchyma Formation and Alters Metabolisms of Banana Plants. Plants (Basel, Switzerland)\| PubMed ID: 35956531	2022

Chee How Teo

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