Siekkinen 2015b (Conference Paper) Hechtia

Phylogenetic Study of the Genus Hechtia Utilizing Next Generation Sequencing Genome Skimming

Author(s):—Andy Siekkinen & Michael Simpson in Benko-Iseppon, A.M.; Alves, M. & Louzada, R. (2015) An overview and abstracts of the First World Congress on Bromeliaceae Evolution. Rodriguésia 66(2): A1-A66.

Publication:— (2015).

Abstract:—Next generation sequencing (NGS) technology is transforming the field of plant systematics in its study of lower level taxonomic relationships and investigations of introgression and reticulation. The genus Hechtia (Bromeliaceae), with ~70 described species has generally been a poorly studied genus which has yet to be given a comprehensive taxonomic treatment. This project utilizes next generation sequencing (NGS) genome skimming to create a phylogenetic tree of the genus with species level resolution with the ultimate goal of proposing the first subgeneric classification. Genome skimming entails sequencing nuclear DNA at very shallow depth while recovering high copy genetic material: the plastome, nrDNA cistron, and the mitochondrial genome. This first stage analysis includes over 40% of the genus, with samples from 31 Hechtia speciescovering most of the geographic range and the natural morphological groups within the genus. Two Tillandsia species were included in the analysis as outgroups. The 33 samples were multiplex bar coded and accounted for ~1/3 of a shared Illumina lane. A range of 0.7?2.9 million 101bp single end reads were recovered per sample. De novo and reference-guided assembly methods were used to assemble a 90+kbp partial plastome, the nrDNA cistron, and several mitochondrial genes for all samples. The first diverging lineage contains the Central American species, the second group contains the ?spineless? species followed by a third clade with the lateral blooming species. The more recently diverging lineages will need more exhaustive sampling but look to fall into the following four groups: H. zamudioi group, H. podantha, the majority of Oaxaca/Puebla/Veracruz species, and lastly the species on the Pacific slope. The last two groups represent the largest centers of biodiversity in the genus. Using NGS genome skimming, this project successfully produced trees with the three types of genomic data showing phylogenetic relationships within the genus Hechtia and the large data set generated can be mined for designing primers for low-copy nuclear genes and transcriptomes for future projects.

Keywords:—Hechtia; Next Generation Sequencing; Genome Skimming.