PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

Bel, Michiel Van; Diels, Tim; Vancaester, Emmelien; Kreft, Łukasz; Botzki, Alexander; Peer, Yves Van de; Coppens, Frederik; Vandepoele, Klaas

doi:10.1093/nar/gkx1002

Cited by 410 publications

(372 citation statements)

References 32 publications

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“…This situation is not unexpected as recent estimates suggest that vascular plants and bryophytes started to diverge from one another more than 400 million years ago, many million years earlier than the estimated evolutionary origin of the common ancestor of vascular and/or seed plants (Morris et al , ). Similar degradation of collinearity can be seen between monocot and dicot lineages, whereas greater collinearity can be observed within dicot and monocot genomes (Murat et al , ; Van Bel et al , ; Zhao and Schranz, ).…”

Section: Discussionmentioning

confidence: 78%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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Summary Marchantia polymorpha has recently become a prime model for cellular, evo‐devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule‐scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high‐density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map‐based cloning, feasible.

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Section: Discussionmentioning

confidence: 78%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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“…The PTM data were accompanied with various protein and experimental metadata. Protein identifiers were cross-referenced using UniProtKB (UniProt Consortium, 2018) and the plant comparative genomics platform PLAZA (Van Bel et al, 2018) for identical protein sequences. For the original MS studies, the respective PubMed identifier and the PRIDE (Vizca ıno et al, 2016) accession data of the raw MS data, if deposited, were incorporated.…”

Section: Ptm Data and Metadata Collection And Processingmentioning

confidence: 99%

The Plant PTM Viewer, a central resource for exploring plant protein modifications

et al. 2019

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Summary Post‐translational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site‐specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry‐based PTM data to remain at pace with future PTM plant studies.

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“…The coding sequences and annotations for Morus notabilis were downloaded from the NCBI, reference RefSeq assembly accession GCF_000414095.1 [66]. The coding sequences and annotations for Ziziphus jujube [67] were downloaded from the Plaza4 database [68]. The headers of the .fasta files, as well as the 9 th columns of the .gff3 files were edited to make the datasets compatible with the software packages used for downstream analysis.…”

Section: Ks-distribution Analysismentioning

confidence: 99%

Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Sahu¹,

Liu²,

Yssel

et al. 2019

Preprint

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Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 100 pounds). To date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2,822 and 2,034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch-and sucrose metabolism, photosynthesis and others. The copy number of several starch synthesis related genes were found increased in jackfruit and breadfruit compared to closely related species, and the tissue specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.

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PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

Cited by 410 publications

References 32 publications

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

The Plant PTM Viewer, a central resource for exploring plant protein modifications

Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

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