PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics
Michiel Van Bel,Tim Diels,Emmelien Vancaester,Lukasz Kreft,Alexander Botzki,Yves Van de Peer,Frederik Coppens,Klaas Vandepoele +7 more
TLDR
PLAZA 4.0 is presented, the latest iteration of the PLAZA framework, providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes.Abstract:
PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.read more
Citations
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Journal Article
Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix
TL;DR: FastTree as mentioned in this paper uses sequence profiles of internal nodes in the tree to implement neighbor-joining and uses heuristics to quickly identify candidate joins, then uses nearest-neighbor interchanges to reduce the length of the tree.
Journal ArticleDOI
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Jaime Huerta-Cepas,Damian Szklarczyk,Davide Heller,Ana Hernández-Plaza,Sofia K. Forslund,Helen Cook,Daniel R. Mende,Ivica Letunic,Thomas Rattei,Lars Juhl Jensen,Christian von Mering,Peer Bork +11 more
TL;DR: eggNOG as discussed by the authors is a public database of orthology relationships, gene evolutionary histories and functional annotations, with a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes.
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An overview of sucrose synthases in plants.
Ofer Stein,David Granot +1 more
TL;DR: The current knowledge regarding plant SuSy is summarized, including newly discovered possible developmental roles for SuSy in meristem functioning that involve sugar and hormonal signaling are summarized.
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Phylogenetic tree building in the genomic age.
TL;DR: The principles, steps and computational tools for phylogenetic tree building are discussed, including identification of orthologous genes or proteins, multiple sequence alignment, and choice of substitution models and inference methodologies.
Journal ArticleDOI
The hornwort genome and early land plant evolution
Jian Zhang,Xin Xing Fu,Rui Qi Li,Xiang Zhao,Yang Liu,Ming He Li,Arthur Zwaenepoel,Hong Ma,Bernard Goffinet,Yan Long Guan,Jia Yu Xue,Yi Ying Liao,Qing-Feng Wang,Qing‐Hua Wang,Jie Yu Wang,Jie Yu Wang,Guo-Qiang Zhang,Zhi Wen Wang,Yu Jia,Mei Zhi Wang,Shan-Shan Dong,Jian Fen Yang,Yuannian Jiao,Ya-Long Guo,Hongzhi Kong,An Ming Lu,Huanming Yang,Shou Zhou Zhang,Yves Van de Peer,Zhong-Jian Liu,Zhong-Jian Liu,Zhi-Duan Chen +31 more
TL;DR: A draft genome sequence of the hornwort Anthoceros augustus confirms the phylogenetic relationships among the three clades of bryophytes and provides insight into the unique characteristics of hornworts and their adaptations to live on land.
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