Plant organellar genomes: much done, much more to do

J Wang, S Kan, X Liao, J Zhou, LR Tembrock… - Trends in Plant …, 2024 - cell.com
Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic
origin. In recent decades, advances in sequencing technologies have contributed to a …

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 …

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

M Uliano-Silva, JGRN Ferreira, K Krasheninnikova… - BMC …, 2023 - Springer
Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb)
and highly accurate (> Q20). Because of these properties, they have revolutionised genome …

CPGView: A package for visualizing detailed chloroplast genome structures

S Liu, Y Ni, J Li, X Zhang, H Yang… - Molecular Ecology …, 2023 - Wiley Online Library
Chloroplast genomes have been widely used in studying plant phylogeny and evolution.
Several chloroplast genome visualization tools have been developed to display the …

Plastid phylogenomic insights into relationships of all flowering plant families

HT Li, Y Luo, L Gan, PF Ma, LM Gao, JB Yang, J Cai… - BMC biology, 2021 - Springer
Background Flowering plants (angiosperms) are dominant components of global terrestrial
ecosystems, but phylogenetic relationships at the familial level and above remain only …

Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding

Y Zhang, M Zhao, J Tan, M Huang, X Chu, Y Li… - Nature Genetics, 2024 - nature.com
To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-
to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus …

A comprehensive phylogenomic platform for exploring the angiosperm tree of life

WJ Baker, P Bailey, V Barber, A Barker… - Systematic …, 2022 - academic.oup.com
The tree of life is the fundamental biological roadmap for navigating the evolution and
properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering …

PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data

C Bi, F Shen, F Han, Y Qu, J Hou, K Xu, L Xu… - Horticulture …, 2024 - academic.oup.com
Complete mitochondrial genomes (mitogenomes) of plants are valuable resources for
nucleocytoplasmic interactions, plant evolution, and plant cytoplasmic male sterile line …

An updated tribal classification of Lamiaceae based on plastome phylogenomics

F Zhao, YP Chen, Y Salmaki, BT Drew, TC Wilson… - BMC biology, 2021 - Springer
Background A robust molecular phylogeny is fundamental for develo** a stable
classification and providing a solid framework to understand patterns of diversification …