AUTHOR=Orooji Fatemeh , Mirzaghaderi Ghader , Kuo Yi-Tzu , Fuchs Jörg 

TITLE=Variation in the Number and Position of rDNA Loci Contributes to the Diversification and Speciation in Nigella (Ranunculaceae)

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.917310

DOI=10.3389/fpls.2022.917310

ISSN=1664-462X

ABSTRACT=<p><italic>Nigella</italic> is a small genus belonging to the Ranunculaceae family which is presumably originated and distributed in Aegean and the adjacent Western-Irano-Turanian region. Comparative repeat analysis of <italic>N. sativa</italic>, <italic>N. damascena</italic> and <italic>N. bucharica</italic> was performed using low-pass Illumina genomic reads followed by karyotyping and FISH mapping of seven <italic>Nigella</italic> species using the <italic>in silico</italic> identified repeats and ribosomal DNA (rDNA) probes. High- and moderate-copy repeat sequences occupy 57.52, 59.01, and 64.73% of <italic>N. sativa</italic>, <italic>N. damascena</italic> and <italic>N. bucharica</italic> genomes, respectively. Roughly, half of the genomes are retrotransposons (class I transposons), while DNA transposons (class II transposons) contributed to only about 2% of the genomes. The analyzed <italic>Nigella</italic> species possess large genomes of about 7.4 to 12.4 Gbp/1C. Only two satellite repeats in <italic>N. sativa</italic>, one in <italic>N. damascena</italic> and four in <italic>N. bucharica</italic> were identified, which were mostly (peri)centromeric and represented about 1% of each genome. A high variation in number and position of 45S rDNA loci were found among <italic>Nigella</italic> species. Interestingly, in <italic>N. hispanica</italic>, each chromosome revealed at least one 45S rDNA site and one of them occurs in hemizygous condition. Based on the chromosome numbers, genome size and (peri)centromeric satellites, three karyotype groups were observed: Two with 2<italic>n</italic> = 2<italic>x</italic> = 12 and a karyotype formula of 10m + 2t (including <italic>N. sativa</italic>, <italic>N. arvensis</italic>, <italic>N. hispanica</italic> as the first group and <italic>N. damascena</italic> and <italic>N. orientalis</italic> as the second group) and a more distant group with 2<italic>n</italic> = 2<italic>x</italic> = 14 and a karyotype formula of 8m + 2st + 4t (including <italic>N. integrifolia</italic> and <italic>N. bucharica</italic>). These karyotype groups agreed with the phylogenetic analysis using ITS and <italic>rbc</italic>L sequences. We conclude that variation in (peri)centromeric sequences, number and localization of rDNA sites as well as chromosome number (dysploidy) are involved in the diversification of the genus <italic>Nigella</italic>.</p>