Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling

Genome size and the position of 18S ribosomal DNA (rDNA) were analysed in two Himacerus, eight Nabis and two Prostemma species from the family Nabidae using flow cytometry and fluorescence in situ hybrization techniques. The karyotypes of Nabis biformis and Nabis maoricus, each with 2n = 16 + XY, and Prostemma aeneicolle, with 2n = 26 + XY, were recorded for the first time. All the species displayed one or two 18S rDNA signals on the X chromosome and up to two signals on the Y chromosome. Several females exhibited two different types of X chromosome breakage, namely within or outside of the 18S rDNA region. Measurements of nuclear DNA content revealed significant differences between all three genera under study. Most notably, the nuclear DNA content of Himacerus species, with 2n = 32/36 + XY (2C = 9–10 pg), was double that of Nabis species, with 2n = 16 + XY (2C = 4–6 pg). Therefore, the previously rejected theory of an autosomal polyploidy event in the evolution of the genus Himacerus is strongly supported by the results of the present study and is now being resurrected.

Performance of gene expression analyses using de novo assembled transcripts in polyploid species

MotivationQuality of gene expression analyses using de novo assembled transcripts in species experienced recent polyploidization is yet unexplored.ResultsFive plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or better than Corset and Grouper in precision, but lower in sensitivity. In species that lack polyploidy event in the past few million years, DGE analyses using de novo assembled transcriptome identified 50–76% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species with more recent polyploidy event, the percentage decreased to 7–30%. In addition, 7–89% of differentially expressed genes from de novo assembly are contaminations. Gene co-expression network analyses using de novo assemblies vs. mapping to the reference genes recovered the same module that significantly correlated with treatment in one of the five species tested.Availability and ImplementationCommands and scripts used in this study are available at https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/; Analysis files are available at Dryad doi: [email protected] informationSupplementary data are available at Bioinformatics online