[HTML][HTML] Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa …

K Debray, J Marie-Magdelaine, T Ruttink… - BMC Evolutionary …, 2019 - Springer
Background With an ever-growing number of published genomes, many low levels of the
Tree of Life now contain several species with enough molecular data to perform shallow …

Comparative plastid genome analyses of Rosa: Insights into the phylogeny and gene divergence

C Zhang, SQ Li, HH Xie, JQ Liu, XF Gao - Tree Genetics & Genomes, 2022 - Springer
The genus Rosa comprises more than 150 species spread across three subgenera,
Hesperhodos, Hulthemia, and Rosa, most of which have high economic and ecological …

[HTML][HTML] Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers

A Cabrera, A Kozik, W Howad, P Arus, AF Iezzoni… - Bmc Genomics, 2009 - Springer
Background Detailed comparative genome analyses within the economically important
Rosaceae family have not been conducted. This is largely due to the lack of conserved gene …

Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa

K Debray, MC Le Paslier, A Bérard… - Systematic …, 2022 - academic.oup.com
Reticulation, caused by hybridization and allopolyploidization, is considered an important
and frequent phenomenon in the evolution of numerous plant lineages. Although both …

Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids

PR Steele, M Guisinger-Bellian, CR Linder… - Molecular Phylogenetics …, 2008 - Elsevier
Angiosperm systematics has progressed to the point where it is now expected that multiple,
independent markers be used in phylogenetic studies. Universal primers for amplifying …

Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids

L Zhao, X Li, N Zhang, SD Zhang, TS Yi, H Ma… - Molecular phylogenetics …, 2016 - Elsevier
The Rosids is one of the largest groups of flowering plants, with 140 families and∼ 70,000
species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes …

[HTML][HTML] Rosaceae phylogenomic studies provide insights into the evolution of new genes

L Jiang, X Li, K Lyu, H Wang, Z Li, W Qi, L Zhang… - Horticultural Plant …, 2024 - Elsevier
Rosa banksiae, known as Lady Banks' rose, is a perennial ornamental crop and a versatile
herb in traditional Chinese medicine. Given the lack of genomic resources, we assembled a …

[HTML][HTML] Genome assembly and phylogenomic data analyses using plastid data: Contrasting species tree estimation methods

DJP Gonçalves, BB Simpson, GH Shimizu, RK Jansen… - Data in brief, 2019 - Elsevier
Phylogenomics has become increasingly popular in recent years mostly due to the
increased affordability of next generation sequencing techniques. Phylogenomics has …

[HTML][HTML] Identifying genetic markers for a range of phylogenetic utility–From species to family level

B Choi, MD Crisp, LG Cook, K Meusemann… - PLoS …, 2019 - journals.plos.org
Resolving the phylogenetic relationships of closely related species using a small set of loci
is challenging as sufficient information may not be captured from a limited sample of the …

[HTML][HTML] The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose

S Li, G Yang, S Yang, J Just, H Yan, N Zhou, H Jian… - Scientific reports, 2019 - nature.com
Roses are important woody plants featuring a set of important traits that cannot be
investigated in traditional model plants. Here, we used the restriction-site associated DNA …