Intragenomic Polymorphism of the ITS 1 Region of 35S rRNA Gene in the Group of Grasses with Two-Chromosome Species: Different Genome Composition in Closely Related Zingeria Species

Abstract

Zingeria (Poaceae) is a small genus that includes Z. biebersteiniana, a diploid species with the lowest chromosome number known in plants (2n = 4) as well as hexaploid Z. kochii and tetraploid Z. pisidica, and/or Z. trichopoda species. The relationship between these species and the other low-chromosomes species Colpodium versicolor are unclear. To explore the intragenomic polymorphism and genome composition of these species we examined the sequences of the internal transcribed spacer 1 of the 35S rRNA gene via NGS approach. Our study revealed six groups of ribotypes in Zingeria species. Their distribution confirmed the allopolyploid nature of Z. kochii, whose probable ancestors were Colpodium versicolor and Z. pisidica. Z. pisidica has 98% of rDNA characteristic only for this species, and about 0.3% of rDNA related to that of Z. biebersteiniana. We assume that hexaploid Z. kochii is either an old allopolyploid or a homodiploid that has lost most of the rRNA genes obtained from Z. biebersteiniana. In Z. trichopoda about 81% of rDNA is related to rDNA of Z. biebersteiniana and 19% of rDNA is derived from Poa diaphora sensu lato. The composition of the ribotypes of the two plants determined by a taxonomy specialist as Z. pisidica and Z. trichopoda is very different. Two singleton species are proposed on this base with ribotypes as discriminative characters. So, in all four studied Zingeria species, even if the morphological difference among the studied species was modest, the genomic constitution was significantly different, which suggests that these are allopolyploids that obtained genomes from different ancestors.

Grasses through space and time: An overview of the biogeographical and macroevolutionary history of Poaceae

“…(9 spp., some annuals, Africa, Southwest Asia, including Zingeria P.A. Smirn., (Gnutikov et al, 2020; Rodionov et al, 2020; Tkach et al, 2020); Hyalopoa (Tzvelev) Tzvelev (6 spp., Southwest Asia); Hyalopodium Röser & Tkach (2 spp., Southwest Asia); Paracolpodium (Tzvelev) Tzvelev (7 spp., Southwest & Central Asia); Phippsia (Trin.) R. Br.…”

“…(9 spp., some annuals, Africa, Southwest Asia, including Zingeria P.A. Smirn., (Gnutikov et al, 2020;Rodionov et al, 2020;Tkach et al, 2020) Miliinae Dumort., with a stem date of 10.87 Ma, contains Milium L. (6 spp., or more, some annuals, Eurasia and northeastern North America; Tzvelev & Probatova, 2019). The genus is mainly restricted to Asia, with one perennial species reaching across northern Eurasia with disjunct populations in eastern North America.…”

Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing

“…The USERCH 45 , and UNOISE 46 algorithms were employed to process Illumina high-throughput sequencing data to identify the unique variants of the ITS1 sequences flanked by 18S rDNA and 5.8S rDNA as well as to calculate their comparative frequency (number of read pairs uniquely mapped to one variant). Obtained denoised sequences are called ZOTUs (zero-radius OTUs) 46 , or ribotypes 21 , 39 , 40 . ZOTUs with a read count of 10 or more were used in the further analysis.…”

“…First-generation interspecific hybrids always have both parents' rDNA in the genome [27][28][29][30] . In the next generations, some species retain rDNA [31][32][33] , while others undergo rDNA homogenization, resulting in the loss of most of the rDNA of one of the parents and only a minor number of 35S rDNA loci remaining in the genome, which can be detected via sequencing cloned PCR products 22,28,[33][34][35] or by using next-generation-sequencing (NGS) 16,21,[36][37][38][39][40][41] . Analysis of the intraindividual polymorphism of 35S rDNA fragments has been successfully used to study hybrids in various groups of plants [29][30][31][32][33] .…”

Licorice Germplasm Resources Identification Using DNA Barcodes Inner-Variants

“…Surprisingly, no haplotype PT-iii in psbA-trnH of G. inflata has been reported [48][49][50][51]. Therefore, it is speculated that the hybridization event occurred in the generation of sample GGY1-1 and ZhaG-1 with a male parent of G. glabra, which is based on the characteristic that the chloroplast DNA of glycyrrhiza interspecific hybridization is mainly inherited by the male parent [8,52]. To obtain stable genetic single glycyrrhiza germplasm resources, the low heterozygosity of the seed population should be ensured, and the low variability of the single seed in the population should be confirmed.…”