An update on bioinformatics resources for plant genomics research

Basantani, Mahesh Kumar; Gupta, Divya; Mehrotra, Rajesh; Mehrotra, Santosh; Vaish, Swati; Singh, Anjali

doi:10.1016/j.cpb.2017.12.002

Cited by 9 publications

(3 citation statements)

References 108 publications

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“…The presence of gaps in a linkage map needs to be analyzed carefully, because they could indicate an assembly problem in the reference genome. Plant genomes have proved to be difficult to assemble because of high heterozygosity, large numbers of repeat sequences and being large and complex [59]. Eichler et al, [60] suggested that genome duplication will be the most important cause of gaps in a physical and genetic map because they are difficult to assemble due to mapping of markers to multiple regions.…”

Section: Discussionmentioning

confidence: 99%

Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling

Carrasco¹,

González²,

Gebauer³

et al. 2018

PLoS ONE

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This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. “Angeleno” (An) as maternal line and cv. “Aurora” (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.

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Section: Discussionmentioning

confidence: 99%

Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling

Carrasco¹,

González²,

Gebauer³

et al. 2018

PLoS ONE

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show abstract

“…Next-generation sequencing as well as traditional Sanger sequencing methods are of great significance in unraveling the complexity of plant genomes. These are constantly generating heaps of sequence data to be analyzed, annotated and stored, thus creating a revolutionary demand for resources and tools to manage and handle these necessities (Basantani et al 2017). Here we present a brief compilation of web resources that are either specific for grape or encompass a variety of species including Vitis sp ( Table 2).…”

Section: Resourcesmentioning

confidence: 99%

Status and Prospects of Systems Biology in Grapevine Research

Matus

Ruggieri

Romero

et al. 2019

Compendium of Plant Genomes

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The cultivated grapevine, Vitis vinifera L., has gathered a vast amount of omics data throughout the last two decades, driving the imperative use of computational resources for its analysis and integration. Molecular systems biology arises from this need allowing to model and predict the emergence of phenotypes or responses in biological systems. Beyond single omics networks, integrative approaches associate the molecular components of an organism and combine them into higher order networks to model dynamic behaviors. Application of network-based methods in multi-omics data is providing additional resources to address important questions regarding grapevine fruit quality and composition. Here we review the recent history of systems biology in this species. We highlight the most relevant aspects of the discipline and describe important integrative studies that have helped in the global understanding of how this species responds to the environment and how it triggers the fruit ripening developmental program. We also highlight the latest resources that are available for the grapevine community to exploit and take advantage of all the omics data that its being generated.

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“…Transcription factor binding sites were also found using JASPAR and confirmed using CONSITE [ 24 ]. The knowledge of such cis- regulatory elements in plant stresses will further help understand the plant genome structure [ 25 ]. With the use of such information, synthetic modules can be created to increase crop yield [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

In Silico Analysis of CCGAC and CATGTG Cis-regulatory Elements Across Genomes Reveals their Roles in Gene Regulation under Stress

Bhadouriya

Suresh

Gupta

et al. 2021

Self Cite

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Background: Plant yield closely depends on its environment and is negatively affected by abiotic stress conditions like drought, salinity, heat, and cold. Analysis of the stress-inducible genes in Arabidopsis has previously shown that CCGAC and CATGTG play a crucial role in controlling the gene expression through the binding of DREB/CBF and NAC TFs under various stress conditions, mainly drought and salinity. Methods: The pattern of these motifs is conserved, which has been analyzed in this study to find the mechanism of gene expression through spacer specificity, inter motif distance preference, functional analysis, and statistical analysis for four different plants, namely Oryza sativa, Triticum aestivum, Arabidopsis thaliana, and Glycine max. Results: The spacer frequency analysis has shown a preference for particular spacer lengths among four genomes. The spacer specificity at all the spacer lengths which predicts dominance of particular base pairs over others, was analyzed to find the preference of the sequences in the flanking region. Functional analysis on stress-regulated genes for saline, osmotic, and heat stress clearly shows that these motif frequencies with inter motif distance (0-30) in the promoter region of Arabidopsis are highest in genes which are upregulated by saline and osmotic stress and downregulated by heat stress. Conclusion: Microarray data were analyzed to confirm the role of both motifs in stress response pathways. Transcription factors seem to prefer larger motif size with repeated CCGAC and CATGTG elements. The common preference for one spacer was further validated through Box and Whisker’s statistical analysis.

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An update on bioinformatics resources for plant genomics research

Cited by 9 publications

References 108 publications

Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling

Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling

Status and Prospects of Systems Biology in Grapevine Research

In Silico Analysis of CCGAC and CATGTG Cis-regulatory Elements Across Genomes Reveals their Roles in Gene Regulation under Stress

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