A dedicated target capture approach reveals variable genetic markers across micro‐ and macro‐evolutionary time scales in palms

Abstract

Understanding the genetics of biological diversification across micro-and macroevolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations.In palms, an emblematic, economically and ecologically important plant family with high diversity in the tropics, studies of diversification at the population and species levels are still hampered by a lack of genomic markers suitable for the genotyping of large numbers of recently diverged taxa. To fill this gap, we used a whole genome sequencing approach to develop target sequencing for molecular markers in 4,184 genome regions, including 4,051 genes and 133 non-genic putatively neutral regions. These markers were chosen to cover a wide range of evolutionary rates allowing future studies at the family, genus, species and population levels. Special emphasis was given to the avoidance of copy number variation during marker selection. In addition, a set of 149 well-known sequence regions previously used as phylogenetic markers by the palm biological research community were included in the target regions, to open the possibility to combine and jointly analyse already available data sets with genomic data to be produced with this new toolkit. The bait set was effective for species belonging to all three palm subfamilies tested (Arecoideae, Ceroxyloideae and Coryphoideae), with high mapping rates, specificity and efficiency. The number of high-quality single nucleotide polymorphisms (SNPs) detected at both the sub-family and population levels facilitates efficient analyses of genomic diversity across micro-and macro-evolutionary time scales.

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae

“…This step was omitted for samples with degraded DNA. Library preparations were performed following de La Harpe et al (2019). Briefly, sample cleaning, end repair and A-tailing steps were carried out with a KAPA LTP library preparation kit (Roche, Basel, Switzerland), and adaptor ligation and adaptor fill-in reactions steps (Meyer and Kircher, 2010).…”

“…In this context, the recent development of several sequence capture kits for the Arecaceae (Heyduk et al, 2015; de La Harpe et al, 2019) represents an ideal opportunity to fill the gaps in palm phylogenomics. Here, using the bait kit developed by de La Harpe et al (2019), we sequenced 4,184 genomic regions for 85% of the species of tribe Geonomateae, including 84% of the species of Geonoma and applied both standard and coalescent-based methods to reconstruct the phylogenetic relationships within the tribe. Using substantial intraspecific sampling, we assessed the validity of the species delimitations proposed by Henderson (2011) for the widespread and highly morphologically variable species complexes.…”

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

“…Our genome skims allow for the design of purpose primers and/or capture probes [57][58][59]. For example, Li et al [20] suggest a two-step barcode process, where the plastid genome is used in a second step for designing within-group markers.…”

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

“…[Heyduk et al., ]). Such a lineage‐specific design may also work at higher taxonomic levels (e.g., families Annonaceae [Couvreur et al., ], Arecaceae [de La Harpe et al., ], and Fabaceae [Vatanparast et al., ] and order Zingiberales [Carlsen et al., ]) and even at lower taxonomic levels (e.g., at the population‐level in Euphorbia balsamifera Aiton using a genus‐level probe set for Euphorbia L. [Villaverde et al., ]). In contrast to lineage‐specific probe sets, a universal angiosperm‐wide set for anchored hybrid enrichment of ~400 loci has been developed (Buddenhagen et al., ) that has been successfully applied to a number of studies, for example for Aristolochia L. (Wanke et al., ) and Protea L. (Mitchell et al., ).…”