Phylogenetic relationships within Lactuca L. (Asteraceae), including African species, based on chloroplast DNA sequence comparisons

Abstract

Lettuce (Lactuca sativa L.) belongs to the genus Lactuca L. and is an important vegetable worldwide. Over the past decades, there have been many controversies about the phylogeny of Lactuca species due to their complex and diverse morphological characters and insufficient molecular sampling. In this study we provide the most extensive molecular phylogenetic reconstruction of Lactuca, including African wild species, using two chloroplast genes (ndhF and trnL-F). The sampling covers nearly 40 % of the total endemic African Lactuca species and 34 % of the total Lactuca species. DNA sequences from all the subfamilies of Asteraceae in Genebank and those generated from Lactuca herbarium samples were used to establish the affiliation of Lactuca within Asteracaeae. Based on the subfamily tree, we selected 33 ndhF sequences from 30 species and 79 trnL-F sequences from 48 species to infer relationships within the genus Lactuca using randomized axelerated maximum likelihood and Bayesian inference analyses. Biogeographical, chromosomal and morphological character states were reconstructed over the Bayesian tree topology. We conclude that Lactuca contains two distinct phylogenetic clades-the crop clade and the Pterocypsela clade. Other North American, Asian and widespread species either form smaller clades or mix with the Melanoseris species. The newly sampled African endemic species probably should be treated as a new genus.

Sub‐Paratethyan origin and Middle to Late Miocene principal diversification of the Lactucinae (Compositae: Cichorieae) inferred from molecular phylogenetics, divergence‐dating and biogeographic analysis

“…The topology of clade J1 is fully in line with the recent findings by Wei & al. (2016Wei & al. ( , 2017 based on plastid DNA.…”

“…The latter were recently also addressed in a molecular phylogenetic investigation of Lactuca by Wei & al. (2016Wei & al. ( , 2017, but with rather limited sampling.…”

Herbarium genomics: skimming and plastomics from archival specimens

“…In a sense, genome skimming may be compared with Sanger sequencing, in which 'rare variants' are marginalized against a main, average signal peak in the Sanger trace files. Genome skimming has become a fairly standard approach in the cost-effective generation of, for instance, plastome DNA sequence data in angiosperms (Straub et al 2012;Bock et al 2014;Bakker et al 2016;Wei et al 2017). Where it is intuitively attractive to assemble and publish entire plastomes, this may not be necessary when phylogenetic reconstruction is the main objective.…”

The complete chloroplast genome sequence and phylogenetic analysis of Flaveria bidentis (L.) Kuntze, an invasive alien plant species in China

“…The DNA isolation was sequenced using the Illumina HiSeq X Ten platform at Novogene Biotech Co. (Beijing, China). The obtained raw data (6.2 G) was processed and assembled as described by Bakker et al (2016) and Wei et al (2017). The assembly was mapped to the reference Galinsoga quadriradiata cp genome sequence (Accession number NC_031853) using Geneious v10.1.3 software (Ma et al 2013).…”