Development of microsatellite markers using next-generation sequencing for the columnar cactus Echinopsis chiloensis (Cactaceae)

Development of novel SSR molecular markers using a Next-Generation Sequencing approach (ddRADseq) in Stetsonia coryne (Cactaceae)

The Cactaceae family is native to the American continent with several centers of diversity. In South America, one of these centers is the Central Andes and many species are considered to be threatened or vulnerable according to the International Union for Conservation of Nature (IUCN). Stetsonia coryne is an emblematic giant columnar cacti of the Chaco phytogeographic province. It has an extensive geographical distribution in many countries of the continent. However, to date there are no specific molecular markers for this species, neither reports of population genetic variability studies, such as for many cactus species. The lack of information is fundamentally due to the lack of molecular markers that allow these studies. In this work, by applying a Genotyping by Sequencing (GBS) technique, we developed polymorphic SSR markers for the Stetsonia coryne and evaluated their transferability to phylogenetically close species, in order to account for a robust panel of molecular markers for multispecies-studies within Cactaceae.

Cross-amplification of microsatellite loci in the cacti species from Brazilian Chaco

Cactaceae species are an important component of the Brazilian Chaco landscape. Sixteen species are reported to this region, including 13 genera representing three Cactaceae subfamilies. All these species are native and have been locally threatened by the advance of the deforestation, which can negatively impact their genetic diversity. In order to test genetic markers that can potentially be used to screen the population diversity of these species, we checked the cross-amplification performance of 27 nuclear and 23 plastid microsatellite loci in all 16 cacti species from Brazilian Chaco. We tested the cross-amplification of the 50 microsatellite (SSR) loci in one specimen of each cacti species and considered it successful when at least one band of the expected size was generated. Thirteen species (81%) had at least 18 nuclear microsatellite loci amplified, while seven species (43%) had at least 11 chloroplast microsatellite loci amplified. We also reviewed current knowledge of SSR studies with Cactaceae in 50 studies available in the Web of Science^®, and found that only five cacti species that occur in the Brazilian Chaco have representatives of the same genus with described SSR loci. The high cross-amplification rates indicated that these microsatellites markers can be helpful for future population genetic studies with cacti species from the Brazilian Chaco. Since their diversity levels and gene flow patterns are still poorly known, analyses with universal and transferable markers provide important tools to guide conservation efforts on this highly neglected region.

Response of xerophytic plants to glacial cycles in southern South America

BACKGROUND AND AIM

Quaternary glaciations strongly affected the distribution of species from arid and semi-arid environments, as temperature drops were accompanied by strong fluctuations in rainfall. In this study, we examined the response of xerophytic species to glacial cycles, determining the genetic patterns and climatic niche of Echinopsis chiloensis var. chiloensis, an endemic columnar cactus of arid and semi-arid regions of Chile.

METHODS

We analysed 11 polymorphic microsatellites for 130 individuals from 13 populations distributed across the entire distribution of the species. We examined genetic diversity and structure, identified possible patterns of isolation by distance (IBD) and tested two competing population history scenarios using Approximate Bayesian Computation. The first scenario assumes a constant population size while the second includes a bottleneck in the southern population. The latter scenario assumed that the southernmost populations experienced a strong contraction during glaciation, followed by a postglacial expansion; by contrast, the area of the northernmost populations remained as a stable refugium. We also used ecological niche modelling (ENM) to evaluate the location and extension of suitable areas during the Last Glacial Maximum (LGM) and the mid-Holocene.

KEY RESULTS

We found a decline in genetic diversity towards high latitudes and a significant IBD pattern that together with ENM predictions suggest that E. chiloensis var. chiloensis experienced range contraction northwards during wet-cold conditions of the LGM, followed by expansion during aridification of the mid-Holocene. In addition to IBD, we detected the presence of a strong barrier to gene flow at 32°30'S, which according to coalescence analysis occurred 44 kyr BP. The resulting genetic clusters differed in realized climatic niche, particularly in the variables related to precipitation.

CONCLUSIONS

Our results suggest that the cactus E. chiloensis var. chiloensis experienced range contraction and fragmentation during the wet-cold conditions of the LGM, which may have facilitated ecological differentiation between northern and southern populations, promoting incipient speciation.

The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data

Medicinal effects of Crepidiastrum denticulatum have been previously reported. However, the genomic resources of this species and its applications have not been studied. In this study, based on the next generation sequencing method (Miseq sequencing system), we characterize the chloroplast genome of C. denticulatum which contains a large single copy (84,112 bp) and a small single copy (18,519 bp), separated by two inverted repeat regions (25,074 bp). This genome consists of 80 protein-coding gene, 30 tRNAs, and four rRNAs. Notably, the trnT_GGU is pseudogenized because of a small insertion within the coding region. Comparative genomic analysis reveals a high similarity among Asteraceae taxa. However, the junctions between LSC, SSC, and IRs locate in different positions within rps19 and ycf1 among examined species. Also, we describe a newly developed single nucleotide polymorphism (SNP) marker for C. denticulatum based on amplification-refractory mutation system (ARMS) technique. The markers, inferred from SNP in rbcL and matK genes, show effectiveness to recognize C. denticulatum from other related taxa through simple PCR protocol. The chloroplast genome-based molecular markers are effective to distinguish a potentially medicinal species, C. denticulatum, from other related taxa. Additionally, the complete chloroplast genome of C. denticulatum provides initial genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Crepidiastrum as well as other taxa in Asteraceae.