Genome size evolution of the extant lycophytes and ferns

Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.

[Methods on construction of core germplasm collection of Scutellaria baicalensis by ISSR marker]

OBJECTIVE

To build up primary core germplasm of Scutellaria baicalensis.

METHODS

The genetic diversity of 40 germplasm resources of Scutellaria baicalensis in different province were analyzed by ISSR, and the primary core germplasm were constructed with progressive sampling method of smallest genetic distance.

RESULTS

15 primers, which showed good repetitive, special bands and distinct polymorphism, were selected from 51 random ISSR primers. Then the total 248 loci were amplified by these selected 15 primers, with a 97.17% polymorphic loci. The average of Shannon information index (I), Nei's genetic diversity (H), number of alleles and effective number of alleles (NE) by POPGENE 32 analysis were 0.4353, 0.2819, 1.9640 and 1.4617, respectively. It showed there was highly genetic diversity in the 40 germplasm resources. The result of analysis by NTSYS-PC software shows the genetic similarity (Gs) were among 0.64 and 0.80, and there was upper coherence between the clustering result and source core germplasm collection except individual germplasms. The result showed the percentage of polymorphic loci was obviously reduced and the Shannon's information index and Nei's genetic diversity were increased a little, but the index change of germplasm genetic diversity was less than that before sampling. The core germplasms from No. 3 sampling were most representative, whose sampling number was about 30% of the initial sampling, and the percentage of polymorphic loci was that of before sampling 96.8%.

CONCLUSIONS

It was practicable that the methods would be used to construct core germplasm collection of Scutellaria baicalensis by ISSR marker.