IBS 2.0: an upgraded illustrator for the visualization of biological sequences

Xie, Yubin; Zuo, Zhixiang; Ren, Jian

doi:10.1093/nar/gkac373

Cited by 48 publications

(25 citation statements)

References 17 publications

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“…The three residues of the catalytic triad and their positions are shown on top of each domain diagram. These diagrams were generated using IBS 2.0 (Xie et al . 2022).…”

Section: Resultsmentioning

confidence: 99%

A high-quality reference genome for the fission yeastSchizosaccharomyces osmophilus

Jia

Zhang

Liang

et al. 2022

Preprint

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Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organismSchizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes ofS. pombeand three other fission yeast speciesS. japonicus,S. octosporus, andS. cryophilushas enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast speciesS. osmophilusand obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed thatS. osmophilusis most closely related toS. octosporusand these two species diverged around 16 million years ago. To demonstrate the utility of thisS. osmophilusreference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of two types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of two types of mitochondrial selfish elements.

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“…The three residues of the catalytic triad and their positions are shown on top of each domain diagram. These diagrams were generated using IBS 2.0 (Xie et al . 2022).…”

Section: Resultsmentioning

confidence: 99%

A high-quality reference genome for the fission yeastSchizosaccharomyces osmophilus

Jia

Zhang

Liang

et al. 2022

Preprint

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“…Phosphorylation data was extracted from (Olsen et al ., 2010)and (Mergner et al ., 2020). Results are represented using Illustrator for Biological Sequences (IBS) tool (Xie et al ., 2022) and Jmol. (A) NTMC2T5 proteins at ER-Chloroplast CS; (B and C) SYT1 to 5 and CLB1 proteins located at ER-PM CS; (D to F) SYT6, TEX2 and NTMC2T6 proteins located at ER-TGN CS.…”

Section: Resultsmentioning

confidence: 99%

Identification of plant exclusive lipid transfer SMP proteins at membrane contact sites in Arabidopsis and Tomato

Huercano

Percio

Sánchez-Vera

et al. 2022

Preprint

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Membrane contact sites (MCS) are regions where two membranes of different organelles are close but not fused; they coordinate non-vesicular communication between organelles and are involved in a wide variety of physiological functions, including membrane lipid homeostasis. Amongst proteins localized at MCS are those containing a lipid transport domain known as synaptotagmin-like mitochondrial-lipid binding protein (SMP), being the mammalian Extended Synaptotagmins, the yeast Tricalbins and the plant Synaptotagmin 1 (SYT1) the best SMP proteins characterized so far. They are all localized at endoplasmic reticulum-plasma membrane contact sites (ER-PM CS). We have carried outin-silicogenome-wide identification of genes encoding SMP proteins in Arabidopsis and tomato. We have identified the plant exclusive NTMC2T5 proteins as ER-chloroplast CS components which make them extremely interesting as the route for lipid trafficking into and out of chloroplasts remains unknown. Additionally,NTMC2T5over-expressions caused a significant clustering of chloroplast around nucleus. Moreover, SYT6, NTMC2T6 and TEX2 have been identified as ER-Trans-Golgi Network CS proteins. These proteins associated between them and with the exocytosis related proteins VAMP721 and VAMP727. Since the functional roles of many of these genes are unknown, this gene collection provides a useful resource for future studies.HIGHLIGHTPlant exclusive lipid transport proteins were identified at membrane contact sites. SYT6, TEX2 and NTMC2T6 proteins are localized at ER-TGN. NTMC2T5 proteins are localized at ER-Chloroplast and induced chloroplast-nucleus clustering.

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“…NCBI CDD ( Structure/cdd/wrpsb.cgi last accessed: 14 May 2022) and SMART ( last accessed: 14 May 2022) were used to identify conserved protein domains. DGAT gene structures were generated with the IBS tools [ 55 ]. Conserved amino acid sequences for CsDGATs were identified using MEME SUITE (minimum width ≥ 6, maximum width = 50) [ 56 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification, Classification, and Expression Analyses of the CsDGAT Gene Family in Cannabis sativa L. and Their Response to Cold Treatment

Yan

Chang²,

Gu³

et al. 2023

IJMS

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Hempseed is a nutrient-rich natural resource, and high levels of hempseed oil accumulate within hemp seeds, consisting primarily of different triglycerides. Members of the diacylglycerol acyltransferase (DGAT) enzyme family play critical roles in catalyzing triacylglycerol biosynthesis in plants, often governing the rate-limiting step in this process. As such, this study was designed to characterize the Cannabis sativa DGAT (CsDGAT) gene family in detail. Genomic analyses of the C. sativa revealed 10 candidate DGAT genes that were classified into four families (DGAT1, DGAT2, DGAT3, WS/DGAT) based on the features of different isoforms. Members of the CsDGAT family were found to be associated with large numbers of cis-acting promoter elements, including plant response elements, plant hormone response elements, light response elements, and stress response elements, suggesting roles for these genes in key processes such as development, environmental adaptation, and abiotic stress responses. Profiling of these genes in various tissues and varieties revealed varying spatial patterns of CsDGAT expression dynamics and differences in expression among C. sativa varieties, suggesting that the members of this gene family likely play distinct functional regulatory functions CsDGAT genes were upregulated in response to cold stress, and significant differences in the mode of regulation were observed when comparing roots and leaves, indicating that CsDGAT genes may play positive roles as regulators of cold responses in hemp while also playing distinct roles in shaping the responses of different parts of hemp seedlings to cold exposure. These data provide a robust basis for further functional studies of this gene family, supporting future efforts to screen the significance of CsDGAT candidate genes to validate their functions to improve hempseed oil composition.

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IBS 2.0: an upgraded illustrator for the visualization of biological sequences

Cited by 48 publications

References 17 publications

A high-quality reference genome for the fission yeastSchizosaccharomyces osmophilus

A high-quality reference genome for the fission yeastSchizosaccharomyces osmophilus

Identification of plant exclusive lipid transfer SMP proteins at membrane contact sites in Arabidopsis and Tomato

Genome-Wide Identification, Classification, and Expression Analyses of the CsDGAT Gene Family in Cannabis sativa L. and Their Response to Cold Treatment

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