Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes

Abstract

Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well-resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well-supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae

“…S1) is congruent with previous family-level studies [10,12], although there is some incongruence in the position of some genera between plastid-based studies and nuclear gene-based phylogenies [26]. This is the largest phylogeny of Annonaceae to date, and the subfamilies and tribes are all well supported, although the backbone of tribe Miliuseae is not resolved as similarly reported in previous studies [10,12,26]. The dating results (Supplementary Fig.…”

Unravelling the Phylogenomic Relationships of the Most Diverse African Palm GenusRaphia(Calamoideae, Arecaceae)

“…Differences in phylogenetic relationships between the concatenated and coalescent approaches have been increasingly reported in the genomic era [28]. Our results were similar to those in Couvreur et al [19] where higher bootstrap support were obtained when using the concatenation approach, despite the coalescent approach highlighting considerable gene tree conflict. Here, we favour the phylogenetic hypothesis recovered when using the coalescent approach (Figure 1) because these methods allow gene history to be taken into account [Some theoretical paper + [29]] and provide an arguably more realistic reconstruction of phylogenetic relationships when using a large number of independently evolving nuclear markers as used here.…”

“…We sampled a total of 56 individuals (see A1 for details) representing 18 out of the 21 species accepted to date [7,19] and representing all sections described by Otedoh [21]. In order to collect proper material for sequencing, several field trips were undertaken across several African countries including Ivory Coast, Ghana, Gabon, Cameroon, Angola and the Demographic Republic of the Congo between 2012 and 2017.…”

“…We used HybPiper (v1.2) [49] to process our cleaned reads (following [19]) to obtain sequences corresponding to the target exons plus associated intronic sequence data (referred to as supercontigs). We aligned each set of supercontigs using MAFFT (v7.305) [50] with the –auto option and cleaned these alignments with GBLOCKS (v0.91b) [51] using the default parameters and all allowed gap positions.…”

Species delimitation in the genus Greenwayodendron based on morphological and genetic markers reveals new species

“…usambaricum at the rank of species. This is in fact also supported by plastid and nuclear DNA sequences indicating that Usambaricum does not fall within the clade including all Suaveolens (Couvreur & al., ; Migliore & al., ).…”