Genome size determination of Scirpus mariqueter and its related species

Abstract

Genome size is an important feature of a species’ genome and is usually measured by the DNA C-value, which can be used for quickly testing genome ploidy and provide an important basis for taxonomy and evolutionary biology. Scirpus mariqueter is a species with important ecological effects in the Yangtze River estuary and Hangzhou Bay, China. It is considered as a hybrid of S. planiculmis and S. triqueter, and it is difficult to accurately determine ploidy due to its small chromosomes. However, in recent years, some researchers, based on molecular markers, have raised doubts about the classification and nomenclature of S. mariqueter. Therefore, more experimental evidence on the taxonomic attributes, genomic characteristics and possible ploidy variation of S. mariqueter and its related species is needed. In this study, the genomic characteristics of S. mariqueter sample CJ1 were determined by genome survey analysis with a sequencing depth of approximately 120×. The DNA C-value and relative ploidy of 13 samples of S. mariqueter and its sympatric, related species (S. triqueter and S. planiculmis) were estimated by flow cytometry with Vigna radiata as a reference. The results were as follows: (1) Genome Survey analysis showed that the genome size of CJ1 was 244.12 Mbp, with a 0.68% heterozygosity rate, 42.38% sequence repeat, and 37.25% GC content. (2) The flow cytometry results showed that the ploidy of S. mariqueter samples from different regions was the same, with 1C values ranging from 234.87 Mbp to 242.5 Mbp, and the genome size of CJ1 was highly consistent with the genome Survey results. (3) The 1C value of S. planiculmis was between 251.77 Mbp and 264.13 Mbp, and the 1C value of S. triqueter was 537.33 Mbp. Because the genome size of hybrids is usually between or larger than those of their parents, it is unlikely that S. mariqueter is a hybrid of the two species based on the abovementioned genome size. This study provides genomic characteristics of S. mariqueter and its related species and lays a foundation for its whole-genome sequencing. At the same time, it also rejects the hypothesis that S. mariqueter originated from hybridization between S. planiculmis and S. triqueter.

Keywords

• flow cytometry
• genome size
• genome survey analysis
• scirpus mariqueter
• scirpus