Phylogenetic tree building in the genomic age

P Kapli, Z Yang, MJ Telford - Nature Reviews Genetics, 2020 - nature.com
Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …

Phylogenomics and the flowering plant tree of life

C Guo, Y Luo, LM Gao, TS Yi, HT Li… - Journal of Integrative …, 2023 - Wiley Online Library
The advances accelerated by next‐generation sequencing and long‐read sequencing
technologies continue to provide an impetus for plant phylogenetic study. In the past …

TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining

C Chen, Y Wu, J Li, X Wang, Z Zeng, J Xu, Y Liu… - Molecular plant, 2023 - cell.com
Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020, its
superior functionality in data analysis has been demonstrated by its widespread adoption by …

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

D Kuznetsov, F Tegenfeldt, M Manni… - Nucleic acids …, 2023 - academic.oup.com
OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of
eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of …

Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

Y Huang, J He, Y Xu, W Zheng, S Wang, P Chen… - Nature Genetics, 2023 - nature.com
The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide,
such as sweet orange and lemon. The origin of Citrus species has long been debated and …

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

B Amos, C Aurrecoechea, M Barba… - Nucleic acids …, 2022 - academic.oup.com
Abstract The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB,
https://veupathdb. org) represents the 2019 merger of VectorBase with the EuPathDB …

[HTML][HTML] The Chinese pine genome and methylome unveil key features of conifer evolution

S Niu, J Li, W Bo, W Yang, A Zuccolo, S Giacomello… - Cell, 2022 - cell.com
Conifers dominate the world's forest ecosystems and are the most widely planted tree
species. Their giant and complex genomes present great challenges for assembling a …

[HTML][HTML] Pan-genome of wild and cultivated soybeans

Y Liu, H Du, P Li, Y Shen, H Peng, S Liu, GA Zhou… - Cell, 2020 - cell.com
Soybean is one of the most important vegetable oil and protein feed crops. To capture the
entire genomic diversity, it is needed to construct a complete high-quality pan-genome from …

The giant diploid faba genome unlocks variation in a global protein crop

M Jayakodi, AA Golicz, J Kreplak, LI Fechete, D Angra… - Nature, 2023 - nature.com
Increasing the proportion of locally produced plant protein in currently meat-rich diets could
substantially reduce greenhouse gas emissions and loss of biodiversity. However, plant …

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

A Song, J Su, H Wang, Z Zhang, X Zhang… - Nature …, 2023 - nature.com
Abstract Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important
ornamental plant with great economic, cultural, and symbolic value. However, research on …