Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Abstract

Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.

The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales

“…Parinari campestris was the most basal species in this family and this position is consistent with the findings of Bardon et al (2013), based on six chloroplast markers and one nuclear marker. Moreover, the placement of the eight Chrysobalanaceae species with strong support is consistent with the phylogenetic hypothesis proposed by Malé et al (2014) analyzing the complete plastid DNAs of eight species of this tropical family.…”

“…In conclusion, the complete chloroplast genome of P. edulis differs from the others because of three rearrangement events that resulted in inversions of gene block order ( Figure 3 ). Otherwise, chloroplast genomes tend to be conserved and perfectly collinear, especially in the same plant family, as occurs in Salicaceae (Wu, 2015) and Chrysobalanaceae (Malé et al, 2014), also members of the Malpighiales order. The existence of rearrangements in segments of cp genomes may be useful as phylogenetic markers within genera or even within families, becoming a potential tool for understanding the evolution of plant species.…”

Chloroplast Genome Evolution in Actinidiaceae: clpP Loss, Heterogenous Divergence and Phylogenomic Practice

“…Genome skimming technique is so far one of the simplest and the most economical methodologies to obtain high-copy sequences [22–23], for instance plastome sequences, and to conduct intergeneric or family-wide phylogenomic analyses [24–26]. It is now convenient to obtain complete cp genome sequences and mine markers for plant systematics via genome skimming [27–28].…”

Forest tree genomics: 10 achievements from the past 10 years and future prospects

“…HTS technologies hold great promise for disentangling evolutionary relationships in complex groups, especially in tropical tree taxa in which botanical knowledge remains limited and cryptic species are common Turchetto-Zolet et al 2013). The first HTS studies reconstructed the complete organellar genomes of tree taxa, which resulted in a higher resolution in phylogeography (McPherson et al 2013;van der Merwe et al 2014), taxonomy, and phylogenetics, particularly for tropical taxa (in Chrysobalanacae, Malé et al 2014;in Malpighiales, Xi et al 2012). HTS studies of the nuclear genome are still rare in phylogenetics and phylogeography of trees (but see Carstens et al 2013;Stölting et al 2013).…”