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ERX3663473: Illumina MiSeq paired end sequencing; Plant and Fungal Trees of Life (PAFTOL)
1 ILLUMINA (Illumina MiSeq) run: 826,193 spots, 497.4M bases, 299.2Mb downloads

Submitted by: Royal Botanical Gardens, Kew
Study: A phylogenomic analysis of Nepenthes (Nepenthaceae)
show Abstracthide Abstract
Nepenthaceae is one of the largest carnivorous plant families and features ecological and morphological adaptations indicating an impressive adaptive radiation. However, investigation of evolutionary and taxonomic questions is hindered by poor phylogenetic understanding, with previous molecular studies based on limited loci and taxa. We use high-throughput sequencing with a target-capture methodology based on a 353-loci, probe set to recover sequences for 197 samples, representing 151 described or putative Nepenthes species. Phylogenetic analyses were performed using supermatrix and maximum quartet species tree approaches. Our analyses confirm five Western outlier taxa, followed by N. danseri, as successively sister to the remainder of the group. We also find mostly consistent recovery of two major Southeast Asian clades. The first contains common or widespread lowland species plus a Wallacean–New Guinean clade. Within the second clade, sects. Insignes and Tentaculatae are well supported, while geographically defined clades representing Sumatra, Indochina, Peninsular Malaysia, Palawan, Mindanao and Borneo are also consistently recovered. However, we find considerable conflicting signal at the site and locus level, and often unstable backbone relationships. A handful of Bornean taxa are inconsistently placed and require further investigation. We make further suggestions for a modified infra-generic classification of genus Nepenthes.
Sample: Frankenia corymbosa
SAMEA6237218 • ERS4036909 • All experiments • All runs
Library:
Name: Target-enriched library of Frankenia corymbosa
Instrument: Illumina MiSeq
Strategy: WGS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Construction protocol: NEBNext Ultra II DNA Library Prep Kit for Illumina and enriched with Angiosperm-353 bait kit (Johnson et al. 2019; doi:10.1093/sysbio/syy086)
Runs: 1 run, 826,193 spots, 497.4M bases, 299.2Mb
Run# of Spots# of BasesSizePublished
ERR3672068826,193497.4M299.2Mb2019-11-21

ID:
9449386

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