U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

ERX9058766: Illumina HiSeq X paired end sequencing
1 ILLUMINA (Illumina HiSeq X) run: 1.6M spots, 475.1M bases, 172.6Mb downloads

Submitted by: freie universitaet berlin, botanic garden and botanical museum berlin (freie universitaet berlin, botanic garden and bota)
Study: Relationships within Scorzonerinae using Hyb-Seq
show Abstracthide Abstract
Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains twelve main lineages and approximately 300 species. Relationships within the subtribe either at inter-or intrageneric levels were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear conserved ortholog loci designed for Asteraceae and obtains obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach on resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analysed three nuclear datasets: exon only excluding all potentially paralogous loci, exon only including loci that were only potentially paralogous in 1–-3 samples, exon plus intron regions (supercontigs), and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages and were successful in fully resolving the backbone phylogeny of the subtribe, while internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but, some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. In light of the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.
Sample: Plant sample from Gelasia tomentosa
SAMEA13856401 • ERS11456922 • All experiments • All runs
Library:
Instrument: Illumina HiSeq X
Strategy: Targeted-Capture
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 1.6M spots, 475.1M bases, 172.6Mb
Run# of Spots# of BasesSizePublished
ERR95172241,623,241475.1M172.6Mb2022-06-30

ID:
22624990

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...