MG2C: a user-friendly online tool for drawing genetic maps

Chao, Jiangtao; Li, Zhiyuan; Sun, Yuqiang; Aluko, Oluwaseun Olayemi; Wu, Xinru; Wang, Qian; Liu, Guanshan

doi:10.1186/s43897-021-00020-x

Cited by 121 publications

(83 citation statements)

References 5 publications

(6 reference statements)

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“…For each candidate PLATZ family member, we assessed the transcript and protein sequence of each member based on the full-length ginkgo transcript dataset, and the longest isoform was selected for downstream analysis. TBtools ( Chen et al, 2020 ) was used to analyze the basic information of ginkgo genome chromosomes, and MG2C ( Chao et al, 2021 ) was used to draw the chromosome location map according to the location of GbPLATZ s, which were named according to the chromosome order. TBtools was also used to visualize the SeqLogo of GbPLATZ amino acid sequences.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification of PLATZ Transcription Factors in Ginkgo biloba L. and Their Expression Characteristics During Seed Development

Han

Rong²,

Tian³

et al. 2022

Front. Plant Sci.

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Plant AT-rich protein and zinc-binding protein (PLATZ) is a class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. PLATZ plays an important role in seed development, water tolerance, and cell proliferation in early plant growth. In this study, 11 GbPLATZs were identified from the ginkgo genome with complete PLATZ-conserved domains, which represents a smaller number compared with angiosperms. Multi-species phylogenetic analysis showed that PLATZ genes were conserved in seed plants, and the 11 members were represented by four groups, among which groups I and II were closely related. Analysis of gene structures, sequence module characteristics, and expression patterns showed that GbPLATZs were similar within and differed between groups. RNA-seq and qRT-PCR results showed that GbPLATZs had distinct expression patterns. Most genes were associated with seed development, among which six genes were highly related. Subcellular localization experiments showed that six GbPLATZ proteins related to seed development were localized in the nucleus, suggesting that they might function as traditional transcription factors. This study provides a basis for understanding the structural differentiation, evolutionary characteristics, expression profile, and potential functions of PLATZ transcription factors in Ginkgo biloba.

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Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification of PLATZ Transcription Factors in Ginkgo biloba L. and Their Expression Characteristics During Seed Development

Han

Rong²,

Tian³

et al. 2022

Front. Plant Sci.

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“…Genome mapping of SiPOD (peroxidase genes) and SiLAC (laccase genes) was rendered using MG2C V2.1 [ 54 ] based on the annotation information. Sesame-to-sesame and sesame-to-Arabidopsis synteny blocks were investigated with the MCScanX toolkit [ 55 ].…”

Section: Methodsmentioning

confidence: 99%

Characterization of Peroxidase and Laccase Gene Families and In Silico Identification of Potential Genes Involved in Upstream Steps of Lignan Formation in Sesame

Zoclanclounon

Rostás

Chung

et al. 2022

Life

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Peroxidases and laccases are oxidative enzymes involved in physiological processes in plants, covering responses to biotic and abiotic stress as well as biosynthesis of health-promoting specialized metabolites. Although they are thought to be involved in the biosynthesis of (+)-pinoresinol, a comprehensive investigation of this class of enzymes has not yet been conducted in the emerging oil crop sesame and no information is available regarding the potential (+)-pinoresinol synthase genes in this crop. In the present study, we conducted a pan-genome-wide identification of peroxidase and laccase genes coupled with transcriptome profiling of diverse sesame varieties. A total of 83 and 48 genes have been identified as coding for sesame peroxidase and laccase genes, respectively. Based on their protein domain and Arabidopsis thaliana genes used as baits, the genes were classified into nine and seven groups of peroxidase and laccase genes, respectively. The expression of the genes was evaluated using dynamic transcriptome sequencing data from six sesame varieties, including one elite cultivar, white vs black seed varieties, and high vs low oil content varieties. Two peroxidase genes (SiPOD52 and SiPOD63) and two laccase genes (SiLAC1 and SiLAC39), well conserved within the sesame pan-genome and exhibiting consistent expression patterns within sesame varieties matching the kinetic of (+)-pinoresinol accumulation in seeds, were identified as potential (+)-pinoresinol synthase genes. Cis-acting elements of the candidate genes revealed their potential involvement in development, hormonal signaling, and response to light and other abiotic triggers. Transcription factor enrichment analysis of promoter regions showed the predominance of MYB binding sequences. The findings from this study pave the way for lignans-oriented engineering of sesame with wide potential applications in food, health and medicinal domains.

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“…The collinearity of HDACs in different genomes was analyzed by McscanX as above. Chromosomal location of RoHDACs and total length of chromosomes were extracted from a genome annotation gff file and a genome sequence, and they were marked by MG2C_v2.0 ( , accessed on 13 August 2021) [ 78 ].…”

Section: Methodsmentioning

confidence: 99%

HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume

Meng

Wen

et al. 2022

IJMS

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Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant Prunus mume is poorly understood. Here, we identify 121 RoHDACs from eight Rosaceae plants of which 13 PmHDACs genes are from P. mume. A phylogenetic analysis suggests that the RoHDACs family is classified into three subfamilies, HDA1/RPD3, HD2, and SIR2. We identify 11 segmental duplication gene pairs of RoHDACs and find, via a sequence alignment, that the HDACs gene family, especially the plant-specific HD2 family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three HDACs subfamilies has its own conserved domains. The expression of PmHDACs in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all PmHDACs genes—especially PmHDA1/6/14, PmHDT1, and PmSRT1/2—significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the HDACs family in Rosaceae plants. Expression profiles of PmHDACs in response to cold stress could provide an important clue to improve the cold hardiness of mei.

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MG2C: a user-friendly online tool for drawing genetic maps

Cited by 121 publications

References 5 publications

Genome-Wide Identification of PLATZ Transcription Factors in Ginkgo biloba L. and Their Expression Characteristics During Seed Development

Genome-Wide Identification of PLATZ Transcription Factors in Ginkgo biloba L. and Their Expression Characteristics During Seed Development

Characterization of Peroxidase and Laccase Gene Families and In Silico Identification of Potential Genes Involved in Upstream Steps of Lignan Formation in Sesame

HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume

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