PlantRGDB: A Database of Plant Retrocopied Genes

Wang, Yi

doi:10.1093/pcp/pcw210

Cited by 5 publications

(3 citation statements)

References 46 publications

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“…We had observed some intronless genes in the different TaHSP sub-families, but none of the TaHSP60 and TaHSP90 sub-family genes were intronless. Usually, newly evolved genes or pseudogenes arising from retro-transposition 25 are intronless, which arise by copy-paste type mechanism 24 . TaSHSP sub-family had the maximum number of intronless genes followed by TaHSP40 sub-family.…”

Section: Hsp Gene Identification Chromosome Mapping Gene Duplicatiomentioning

confidence: 99%

Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L.

Kumar

Sharma

Chunduri

et al. 2020

Sci Rep

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Heat shock proteins (HSPs) have a significant role in protein folding and are considered as prominent candidates for development of heat-tolerant crops. Understanding of wheat HSPs has great importance since wheat is severely affected by heat stress, particularly during the grain filling stage. In the present study, efforts were made to identify HSPs in wheat and to understand their role during plant development and under different stress conditions. HSPs in wheat genome were first identified by using Position-Specific Scoring Matrix (PSSMs) of known HSP domains and then also confirmed by sequence homology with already known HSPs. Collectively, 753 TaHSPs including 169 TaSHSP, 273 TaHSP40, 95 TaHSP60, 114 TaHSP70, 18 TaHSP90 and 84 TaHSP100 were identified in the wheat genome. Compared with other grass species, number of HSPs in wheat was relatively high probably due to the higher ploidy level. Large number of tandem duplication was identified in TaHSPs, especially TaSHSPs. The TaHSP genes showed random distribution on chromosomes, however, there were more TaHSPs in B and D sub-genomes as compared to the A sub-genome. Extensive computational analysis was performed using the available genomic resources to understand gene structure, gene expression and phylogentic relationship of TaHSPs. Interestingly, apart from high expression under heat stress, high expression of TaSHSP was also observed during seed development. The study provided a list of candidate HSP genes for improving thermo tolerance during developmental stages and also for understanding the seed development process in bread wheat. The sessile nature of plants makes them vulnerable to various kinds of biotic and abiotic stresses. Plants have sophisticated mechanisms to recognize and respond to these stresses. High-temperature stress is common abiotic stress, which significantly reduces the crop yield worldwide. Simulation modeling has predicted that every 1 °C rise in temperature above 30 °C reduces the grain filling duration by 0.30-0.60% and grain yield by 1.0-1.6% 1. In response to high-temperature stress, plants synthesize many stress-responsive proteins including a family of proteins called heat shock proteins (HSPs). Enhanced production of HSPs has also been reported under other stress conditions like salinity, heavy metal, and drought 2,3. Some HSPs are also involved in the development of viral infections too, in both plants and animals 4,5. HSPs function as chaperones and assist in the refolding of denatured proteins, folding of nascent polypeptides and resolubilization of denatured protein aggregates 6,7. With increasing concerns about global warming and climate change, many laboratories across the world have used HSPs to create thermo-tolerant plants 8,9. There are reports describing the direct or indirect involvement of HSPs in different developmental stages of the plant 10. Various HSPs show tissue-specific and developmental stage specific

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Section: Hsp Gene Identification Chromosome Mapping Gene Duplicatiomentioning

confidence: 99%

Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L.

Kumar

Sharma

Chunduri

et al. 2020

Sci Rep

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“…The criteria for judging retrocopies are based mainly on the core definition that the sequences of retrocopies and their parental genes are highly similar but the parental genes lose multiple introns. Current retrocopy identification pipelines are based on the TBLASTN, BLAT, and paralog methods, and we selected representative studies in these pipelines to compare with RetroScan: RetrogeneDB (Rosikiewicz et al, 2017) for TBLASTN, PlantRGDB (Wang, 2017) for BLAT and the study of Abdelsamad and Pecinka (2014) and Zhang et al (2005) for paralog (Supplementary Table 3). The results between these methods vary greatly, so we used Arabidopsis thaliana as an example to explain the reasons for these differences.…”

Section: Comparison With Previous Studiesmentioning

confidence: 99%

“…This is not conducive to further evolutionary analysis because the BLAT method cannot get the proteins mutations information between parental genes and retrocopies. Navarro and Galante (2015) used the BLAT method to scan for retrocopies in seven primate genomes, and the PlantRGDB database provides annotations for the retrocopies of 49 plant genomes (Wang, 2017). Moreover, a new method developed by Abdelsamad and Pecinka (2014) divides the annotated genes into two types, intron-free genes and intron-containing genes, and then aligns them using paralogs to identify retrocopies.…”

Section: Introductionmentioning

confidence: 99%

RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization

Wei

Sun

et al. 2021

Front. Genet.

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Retrocopies, which are considered “junk genes,” are occasionally formed via the insertion of reverse-transcribed mRNAs at new positions in the genome. However, an increasing number of recent studies have shown that some retrocopies exhibit new biological functions and may contribute to genome evolution. Hence, the identification of retrocopies has become very meaningful for studying gene duplication and new gene generation. Current pipelines identify retrocopies through complex operations using alignment programs and filter scripts in a step-by-step manner. Therefore, there is an urgent need for a simple and convenient retrocopy annotation tool. Here, we report the development of RetroScan, a publicly available and easy-to-use tool for scanning, annotating and displaying retrocopies, consisting of two components: an analysis pipeline and a visual interface. The pipeline integrates a series of bioinformatics software programs and scripts for identifying retrocopies in just one line of command. Compared with previous methods, RetroScan increases accuracy and reduces false-positive results. We also provide a Shiny app for visualization. It displays information on retrocopies and their parental genes that can be used for the study of retrocopy structure and evolution. RetroScan is available at https://github.com/Vicky123wzy/RetroScan.

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Computational Methods for Pseudogene Annotation Based on Sequence Homology

Harrison

2021

Methods in Molecular Biology

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PlantRGDB: A Database of Plant Retrocopied Genes

Cited by 5 publications

References 46 publications

Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L.

Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L.

RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization

Computational Methods for Pseudogene Annotation Based on Sequence Homology

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