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Lerner, Ariel [1], Lee, Aaron [2], Gilman, Ian S. [3], Srivastav, Mansa [4], Donoghue, Michael [5], Clement, Wendy [1].

Reconstructing a plastid phylogeny of the Dipsacales from off-target Angiosperms353 Hyb-Seq data.

Recent advances in genomics, such as target enrichment or Hyb-Seq, are being employed more frequently and as a result increasing the representation of nuclear data in phylogenomics. Often, the plastome can be assembled from off-target reads from Hyb-Seq data, readily allowing a comparison of nuclear and plastid phylogenies. Here we reconstruct the plastid phylogeny of Dipsacales, a clade of ca. 1,100 species, using off-target reads from a Hyb-Seq data set generated using the Angiosperms353 probe set. We sampled 94 Dipsacales species and two outgroups representing the phylogenetic diversity of the group. Plastid reads were first filtered from the raw data using Bowtie2; these filtered data were then used in a reference based assembly in Bowtie2 against a closely related and publicly available reference genome (25 different reference genomes used in total). We were able to assemble 85 of the 96 species sampled. Nearly 90% of the assembled genomes accounted for >50% of the total length of the reference plastome. Genome alignments were conducted in several different ways using MAFFT. First, the whole plastomes of the species were aligned simultaneously. Second, we took a two-step approach to alignment. To facilitate this, species were initially assigned to one of eight major Dipsacales clades and each of these clades were aligned individually; then, the eight alignments were simultaneously aligned using the merge function in MAFFT to preserve within clade alignments. Third, genes and intergenic regions were extracted from each plastid assembly and aligned by locus. Aligned loci were concatenated to form three data sets: genic, intergenic, and genic+intergenic loci. Each of the five alignments were analyzed using maximum likelihood (ML) in RAxML using a GTR+GAMMA model with 500 bootstrap replicates. Matrices that resulted from concatenating loci were partitioned by gene region in ML analyses. The resulting trees were largely congruent with a few important differences. For example, in the Caprifolieae clade, the clade-based alignment recovered Leycesteria+Triosteum. The genome, genic, intergenic, and genic+intergenic analyses recovered Leycesteria+Symphoricarpos. When comparing plastid and nuclear topologies, both strongly supported Heptacodium as sister to Caprifolieae, but discordances were detected regarding the placement of Zabelia and Morinioideae as well as relationships within the Linnaeeae. This study presents the most comprehensive plastid genome dataset for the Dipsacales, and demonstrates the potential for using off-target reads to reconstruct plastid genomes and assessing cytonuclear discordance when implementing a Hyb-Seq approach.

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1 - The College of New Jersey, Biology, 2000 Pennington Road, Ewing, New Jersey, 08618, United States
2 - University of Minnesota, Twin Cities, Department of Plant and Microbial Biology, 712 Biological Sciences, 1445 Gortner Avenue, Saint Paul, MN, 55108, USA
3 - Yale University, Ecology and Evolutionary Biology, 165 Prospect St, Osborn Memorial Labs, New Haven, CT, 06511, USA
4 - Yale University, Ecology And Evolutionary Biology, 420 Temple Street, Helen Hadley Hall, Environmental Science Center, Room Number 356, New Haven, CT, 06511, United States
5 - Yale University, Department Of Ecology And Evolutionary Biology, 21 Sachem St., New Haven, CT, 06511, United States

none specified

Presentation Type: Poster
Session: P3, Phylogenomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PL021
Abstract ID:792
Candidate for Awards:None

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