Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana

Yang, Jianhua; Osman, Kim; Iqbal, Mudassar; Stekel, Dov J.; Luo, Zewei; Armstrong, Susan J.; Franklin, F. Christopher H.

doi:10.3389/fpls.2012.00297

Cited by 18 publications

(19 citation statements)

References 68 publications

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“…The public B. rapa interactome [ 42 ] was downloaded and we computed for each class of gene copies (LF, MF1, MF2, LF–MF1, LF–MF2, LF–MF1–MF2, B. rapa -specific genes) the proportion of genes that are connected with at least one partner within networks.…”

Section: Methodsmentioning

confidence: 99%

Understanding Brassicaceae evolution through ancestral genome reconstruction

Murat

Louis

Maumus³

et al. 2015

Genome Biol

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BackgroundBrassicaceae is a family of green plants of high scientific and economic interest, including thale cress (Arabidopsis thaliana), cruciferous vegetables (cabbages) and rapeseed.ResultsWe reconstruct an evolutionary framework of Brassicaceae composed of high-resolution ancestral karyotypes using the genomes of modern A. thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula. The ancestral Brassicaceae karyotype (Brassicaceae lineages I and II) is composed of eight protochromosomes and 20,037 ordered and oriented protogenes. After speciation, it evolved into the ancestral Camelineae karyotype (eight protochromosomes and 22,085 ordered protogenes) and the proto-Calepineae karyotype (seven protochromosomes and 21,035 ordered protogenes) genomes.ConclusionsThe three inferred ancestral karyotype genomes are shown here to be powerful tools to unravel the reticulated evolutionary history of extant Brassicaceae genomes regarding the fate of ancestral genes and genomic compartments, particularly centromeres and evolutionary breakpoints. This new resource should accelerate research in comparative genomics and translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0814-y) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Understanding Brassicaceae evolution through ancestral genome reconstruction

Murat

Louis

Maumus³

et al. 2015

Genome Biol

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“…E. salsugineum is closely related to the model species A. thaliana and the agronomically important Brassica species (e.g., Oilseed rape). The availability of whole-genome sequences of several species in Brassicaceae has opened a new era of comparative genomics in Brassicaceae for a better understanding of genome evolution of this plant family (Dassanayake et al, 2011; Hu et al, 2011; Wang et al, 2011; Cheng et al, 2012; Fang et al, 2012; Hatje and Kollmar, 2012; Tang and Lyons, 2012; Wu et al, 2012; Yang et al, 2012). Because of these relationships, many of the genetic and genomic tools available for A. thaliana can be used to facilitate functional and comparative studies of the two species.…”

Section: Introductionmentioning

confidence: 99%

The Reference Genome of the Halophytic Plant Eutrema salsugineum

et al. 2013

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Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Eutrema salsugineum is a halophytic species in the Brassicaceae that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, including extreme salinity and cold. It has been widely used as a laboratorial model for stress biology research in plants. Here, we present the reference genome sequence (241 Mb) of E. salsugineum at 8× coverage sequenced using the traditional Sanger sequencing-based approach with comparison to its close relative Arabidopsis thaliana. The E. salsugineum genome contains 26,531 protein-coding genes and 51.4% of its genome is composed of repetitive sequences that mostly reside in pericentromeric regions. Comparative analyses of the genome structures, protein-coding genes, microRNAs, stress-related pathways, and estimated translation efficiency of proteins between E. salsugineum and A. thaliana suggest that halophyte adaptation to environmental stresses may occur via a global network adjustment of multiple regulatory mechanisms. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of halophytic plants to salinity and that might be bioengineered in related crop species.

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“…In recent years, gene co-expression networks have been used to unravel important biological processes and their regulatory mechanisms. There has been a growing trend in using large-scale protein-protein interaction (PPI) networks in plant systems (Yang et al 2012b); however, the datasets cover only a limited range of PPI data. Furthermore, PPI networks are not static but dynamic entity and expression of protein is intrinsically controlled by different regulatory mechanisms (Liang and Li 2007).…”

Section: Discussionmentioning

confidence: 99%

Computational Analysis of “-omics” Data to Identify Transcription Factors Regulating Secondary Metabolism in Rauvolfia serpentina

Pathania

Acharya

2015

Plant Mol Biol Rep

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Rauvolfia serpentina has been known to produce therapeutically important indole alkaloids used in treatment of various diseases. Despite its medicinal importance, complete understanding of its secondary metabolism is challenging due to complex interplay among various transcription factors (TFs) and genes. However, weighted co-expression analysis of transcriptome along with integration of metabolomics data has proficiency to elucidate topological properties of complex regulatory interactions in secondary metabolism. We aimed to implement an integrative strategy using B-omicsd ata to identify TFs of Bunknown function^and exemplify their role in regulation of valuable metabolites as well as metabolic traits. A total of 69 TFs were identified through significant thresholds and removal of false positives based on cisregulatory motif analysis. Network-biology inspired analysis of co-expression network lead to generation of four statistically significant and biologically robust modules. Similar to known regulatory roles of WRKY and AP2-EREBP TF families in Catharanthus roseus, this study presented them to regulate synthesis of alkaloids in R. serpentina as well.Moreover, TFs in module 4 were observed to be regulating connecting steps between primary and secondary metabolic pathways in the synthesis of terpenoid indole alkaloids. Integration of metabolomics data further highlight the significance of module 1 since it was statistically predicted to be involved in synthesis of specialized metabolites, and associated genes may physically clustered on genome. Importantly, putative TFs in module 1 may modulate the major indole alkaloids synthesis in response to various environmental stimuli. The methodology implemented herein may provide a better reference to identify and explore functions of transcriptional regulators.

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Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana

Cited by 18 publications

References 68 publications

Understanding Brassicaceae evolution through ancestral genome reconstruction

Understanding Brassicaceae evolution through ancestral genome reconstruction

The Reference Genome of the Halophytic Plant Eutrema salsugineum

Computational Analysis of “-omics” Data to Identify Transcription Factors Regulating Secondary Metabolism in Rauvolfia serpentina

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