Target‐enrichment sequencing reveals for the first time a well‐resolved phylogeny of the core Bromelioideae (family Bromeliaceae)

Abstract

A phylogenomic analysis of the so far phylogenetically unresolved subfamily Bromelioideae (Bromeliaceae) was performed to infer species relationships as the basis for future taxonomic treatment, stabilization of generic concept, and further analyses of evolution and biogeography of the subfamily. A target‐enrichment approach was chosen, using the Angiosperms353 v.4 kit RNA‐baits and including 86 Bromelioideae species representing previously identified major evolutionary lineages. Phylogenetic analyses were based on 125 target nuclear loci, assembled off‐target plastome as well as mitogenome reads. A Bromelioideae phylogeny with a mostly well‐resolved backbone is provided based on nuclear (194 kbp), plastome (109 kbp), and mitogenome data (34 kbp). For the nuclear markers, a coalescent‐based analysis of single‐locus gene trees was performed as well as a supermatrix analysis of concatenated gene alignments. Nuclear and plastome datasets provide well‐resolved trees, which showed only minor topological incongruences. The mitogenome tree is not sufficiently resolved. A total of 26 well‐supported clades were identified. The genera Aechmea, Canistrum, Hohenbergia, Neoregelia, and Quesnelia were revealed polyphyletic. In core Bromelioideae, Acanthostachys is sister to the remainder. Among the 26 recognized clades, 12 correspond with currently employed taxonomic concepts. Hence, the presented phylogenetic framework will serve as an important basis for future taxonomic revisions as well as to better understand the evolutionary drivers and processes in this exciting subfamily.

Expansions and contractions of the inverted repeat, as well as gene loss and potential pseudogenization shape plastome evolution in Hechtioideae (Bromeliaceae, Poales)

“…As in previous phylogenetic studies, clade F is characterized herein by short internodes with low to moderate statistical support. Thus, even with complete plastid genome sequence data, support for relationships at shallower phylogenetic divergences within that clade remains low to moderate, pointing to the need to seek more variable molecular markers such as low‐copy nuclear loci, as has been explored recently for other rapidly radiating bromeliad lineages (Loiseau et al, 2021; Yardeni et al, 2022; Bratzel et al, 2023).…”

“…Next‐generation sequencing (NGS) techniques have recently been proven to be a powerful source of data to examine phylogenetic relationships at different taxonomic scales in Bromeliaceae (Machado et al, 2020; Paule et al, 2020; Chávez‐Galarza et al, 2021a, 2021b; Loiseau et al, 2021; Möbus et al, 2021, Liu et al, 2022; Vera‐Paz et al, 2022, 2023; Yardeni et al, 2022; Bratzel et al, 2023). Phylogenetic analyses based on complete plastome sequences derived from NGS have improved phylogenetic resolution and statistical support within the bromeliad subfamilies Puyoideae (Liu et al, 2022) and Tillandsioideae (Vera‐Paz et al, 2022, 2023), when compared with previous single‐ and multilocus studies based on Sanger sequenced markers.…”

Young evolutionary origins of dioecy in the genus Asparagus

“…Plastome sequences were extracted from either whole‐genome sequencing (WGS) or mining off‐target Hyb‐Seq reads from experiments with Angiosperms353 (Johnson et al, 2018) or Asparagaceae1726—a recently developed probe set for Hyb‐Seq and phylogenomics in Asparagaceae (P. C. Bentz and J. Leebens‐Mack, University of Georgia, unpublished data). Mining off‐target reads from target‐enriched sequencing data is possible due to the high copy number of organellar genomes in sequencing data (Graham et al, 2006; Bratzel et al, 2023). In sum, DNA was isolated from silica‐dried or flash‐frozen leaf tissue using Quick‐DNA Plant/Seed Miniprep Kit (Zymo Research, Irvine, CA, USA), DNeasy Plant Mini Kit (Qiagen, Nordic, Copenhagen, Denmark), or Biomarker Plant DNA Kit (Beijing Biomarker Biotechnology, Beijing, China) according to the manufacturer's protocol.…”

Phylogenomics and the rise of the angiosperms

“…The standardized panel of nuclear genes in our dataset paves the way for more collaborations and data integration 17 , 51 , while the open availability of universal tools to sequence them (that is, Angiosperms353 probes 8 ) has made nuclear genomic data more accessible at relatively low cost. The accelerating uptake of this approach 52 – 54 , which is readily applicable to herbarium collections 16 , indicates that large volumes of data will soon become available for a wide range of applications in plant diversity, systematic and macroevolutionary research.…”