Abstract Detail

Species delimitation in polyploid complexes

Cangren, Patrik [1], Jafari, Farzaneh [2], Moila, Ntwae [1], Quatela, Anne-Sophie [1], Bacon, Christine [1], Oxelman, Bengt [1].

How long reads sequencing technologies enable reaching a double challenge in polyploid complexes: species delimitation by Target capture from old herbarium specimens.

The development of long read sequencing technologies such as PacBio SMRT and Oxford Nanopore has revolutionized genomics, with notable consequences for bioinformatics and phylogenomics. These technologies are particularly promising to improve the understanding of polyploid genomics. Indeed, polyploid organisms represent a major challenge for genome assembly, increasing with the ploidy level. Short reads obtained from sequencing platforms such as Illumina make assembly of the correct homoelogues and alleles challenging and in many cases impossible, if overlapping SNPs are missing from the short reads. For long read sequencing, it is essential that the DNA is available in fragment lengths that are long enough. However, for many plants, herbarium specimens sometimes represent the only available source of DNA. Although these specimens may not provide large quantities of “long enough” fragments, there may be enough of them to provide information from targeted low-copy number regions, if short fragments can be successfully removed from the sequencing libraries. This study is aimed at investigating whether long read sequencing will enable sampling data needed for species delimitation in polyploid complexes; it is aimed at investigating as well whether 2 kb-5kb fragments might be sequenced, depending on the age and the preservation state of the herbarium specimens. Our study group is the Arctic and subarctic representatives of Silene sect. Physolychnis, a complex where the most recent taxonomic treatment recognizes 13 taxonomic species and subspecies.

1 - University of Gothenburg, Department of biological and environmental sciences, Box 115, Gothenburg, Västra Götaland, 405 30, Sweden
2 - University of Tehran, Department of Plant Sciences, Tehran, Iran

Keywords:
Polyploid
species delimitation
long read sequencing
Silene sect. Physolychnis
Herbarium Specimens.

Presentation Type: Colloquium Presentations
Session: CO01, Species delimitation in polyploid complexes
Location: Tucson J/Starr Pass
Date: Monday, July 29th, 2019
Time: 10:45 AM
Number: CO01008
Abstract ID:649
Candidate for Awards:None