Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms
Improvements in long read DNA sequencing and related techniques facilitated the
generation of complex eukaryotic genomes. Despite these advances, the quality of …
generation of complex eukaryotic genomes. Despite these advances, the quality of …
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome
Whereas de novo assemblies of RNA-Seq data are being published for a growing number of
species across the tree of life, there are currently no broadly accepted methods for …
species across the tree of life, there are currently no broadly accepted methods for …
Genome-guided transcriptome assembly in the age of next-generation sequencing
LD Florea, SL Salzberg - IEEE/ACM transactions on …, 2013 - ieeexplore.ieee.org
Next generation sequencing technologies provide unprecedented power to explore the
repertoire of genes and their alternative splice variants, collectively defining the …
repertoire of genes and their alternative splice variants, collectively defining the …
Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage
The Zingiberales are an iconic order of monocotyledonous plants comprising eight families
with distinctive and diverse floral morphologies and representing an important ecological …
with distinctive and diverse floral morphologies and representing an important ecological …
Tools and strategies for long-read sequencing and de novo assembly of plant genomes
The commercial release of third-generation sequencing technologies (TGSTs), giving long
and ultra-long sequencing reads, has stimulated the development of new tools for …
and ultra-long sequencing reads, has stimulated the development of new tools for …
Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus
SF Li, J Wang, R Dong, HW Zhu, LN Lan… - Horticulture …, 2020 - academic.oup.com
Asparagus setaceus is a popular ornamental plant cultivated in tropical and subtropical
regions globally. Here, we constructed a chromosome-scale reference genome of A …
regions globally. Here, we constructed a chromosome-scale reference genome of A …
Angiosperm phylogeny based on 18S/26S rDNA sequence data: constructing a large data set using next-generation sequence data
VH Maia, MA Gitzendanner, PS Soltis… - … Journal of Plant …, 2014 - journals.uchicago.edu
The utility of 18S and 26S in broad phylogenetic analyses has been much maligned due in
large part to the low signal in both genes. However, few analyses have employed complete …
large part to the low signal in both genes. However, few analyses have employed complete …
A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (Brassica napus)
B Li, Q Yang, L Yang, X Zhou, L Deng, L Qu… - Horticulture …, 2023 - academic.oup.com
Allopolyploid oilseed rape (Brassica napus) is an important oil crop and vegetable.
However, the latest version of its reference genome, with collapsed duplications, gaps, and …
However, the latest version of its reference genome, with collapsed duplications, gaps, and …
Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 …
A Bräutigam, T Mullick, S Schliesky… - Journal of …, 2011 - academic.oup.com
Next-generation sequencing enables the study of species without a sequenced genome at
the 'omics' level. Custom transcriptome databases are generated and global expression …
the 'omics' level. Custom transcriptome databases are generated and global expression …
Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes
F Han, Y Peng, L Xu, P Xiao - BMC genomics, 2014 - Springer
Background Single copy genes are common across angiosperm genomes. With the
sufficiently high quality sequenced genomes, the identification of large-scale single copy …
sufficiently high quality sequenced genomes, the identification of large-scale single copy …