4.8 Article

PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)

Liming Cai et al.

Summary: Despite significant differences in genome size among angiosperms, key features of genome architecture are largely conserved. The highly modified genome of Sapria himalayana Griff. demonstrates high levels of gene loss compared to other vascular plants and extreme disparity in intron size among retained genes. Furthermore, at least 1.2% of the Sapria genome is inferred to be derived from host-to-parasite horizontal gene transfers, highlighting the value of HGTs as DNA fossils to study extinct symbioses.

CURRENT BIOLOGY (2021)

Article Biochemistry & Molecular Biology

GreenPhylDB v5: a comparative pangenomic database for plant genomes

Guignon Valentin et al.

Summary: Comparative genomics is the analysis of genomic relationships among different species, with GreenPhylDB providing a database for exploring gene families and homologous relationships among plant genomes. By harnessing multiple genome sequences by species, GreenPhylDBv5 introduces the concept of comparative pangenomics to predict homologous relationships and support community curation efforts.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

The Gene Ontology resource: enriching a GOld mine

Seth Carbon et al.

Summary: The Gene Ontology Consortium has made advancements in the last two years, such as improving the GO-CAM annotation framework, increasing the number of annotations and annotated gene products, and reviewing older annotations for consistency.

NUCLEIC ACIDS RESEARCH (2021)

Review Agronomy

Chromosome-level de novo genome assemblies of over 100 plant species

Kenta Shirasawa et al.

Summary: Genome sequence analysis in higher plants began with Arabidopsis thaliana, and has advanced with the sequencing of over 400 plant species. Long-read sequencing technologies and sequence scaffolding have allowed for chromosome-level genome sequence assemblies, enhancing comparative analysis of multiple plant genomes.

BREEDING SCIENCE (2021)

Article Biochemistry & Molecular Biology

The InterPro protein families and domains database: 20 years on

Matthias Blum et al.

Summary: InterPro database offers a comprehensive classification of protein sequences and is a widely used resource for protein family annotation. Its software InterProScan allows users to search protein and nucleic acid sequences against InterPro's signatures.

NUCLEIC ACIDS RESEARCH (2021)

Review Plant Sciences

Building near-complete plant genomes

Todd P. Michael et al.

CURRENT OPINION IN PLANT BIOLOGY (2020)

Article Multidisciplinary Sciences

Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors

Xiaoyu Tu et al.

NATURE COMMUNICATIONS (2020)

Review Biochemical Research Methods

Interactive and coordinated visualization approaches for biological data analysis

Antonio Cruz et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Review Plant Sciences

Gene space completeness in complex plant genomes

Michiel Van Bel et al.

CURRENT OPINION IN PLANT BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism

Satoko Yoshida et al.

CURRENT BIOLOGY (2019)

Review Plant Sciences

Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes

Hyungtaek Jung et al.

TRENDS IN PLANT SCIENCE (2019)

Article Biochemistry & Molecular Biology

MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis

Rainer Schwacke et al.

MOLECULAR PLANT (2019)

Article Biochemistry & Molecular Biology

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

Michiel Van Bel et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Genetics & Heredity

The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond et al.

NATURE GENETICS (2018)

Review Plant Sciences

Why we need more non-seed plant models

Stefan A. Rensing

NEW PHYTOLOGIST (2017)

Article Genetics & Heredity

First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Nee (Fagaceae)

Victoria L. Sork et al.

G3-GENES GENOMES GENETICS (2016)

Article Biochemistry & Molecular Biology

The GOA database: Gene Ontology annotation updates for 2015

Rachael P. Huntley et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Klaus F. X. Mayer et al.

SCIENCE (2014)

Article Plant Sciences

The reference genome of the halophytic plant Eutrema salsugineum

Ruolin Yang et al.

FRONTIERS IN PLANT SCIENCE (2013)

Article Biochemistry & Molecular Biology

Phytozome: a comparative platform for green plant genomics

David M. Goodstein et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Plant Sciences

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

Michiel Van Bel et al.

PLANT PHYSIOLOGY (2012)

Review Biochemistry & Molecular Biology

Operons

Anne E. Osbourn et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2009)

Article Biochemistry & Molecular Biology

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

Sebastian Proost et al.

PLANT CELL (2009)

Article Biochemistry & Molecular Biology

Genomic gene clustering analysis of pathways in eukaryotes

JM Lee et al.

GENOME RESEARCH (2003)