Tools for Drawing Informative Idiograms

S, Mahmoudi; Mirzaghaderi, Ghader

doi:10.1101/2021.09.29.459870

Cited by 6 publications

(3 citation statements)

References 29 publications

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“…Chromosomal and karyotypic indices for numerical characterization of mitotic metaphase chromosomes of the Nigella species were measured using IdeoKar software ( Mahmoudi and Mirzaghaderi, 2021 ). The calculated indices include total chromosome length of the haploid complement (HCL); mean chromosome length (CL), and mean centromeric index (CI).…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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Nigella 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 N. sativa, N. damascena and N. bucharica was performed using low-pass Illumina genomic reads followed by karyotyping and FISH mapping of seven Nigella species using the in silico identified repeats and ribosomal DNA (rDNA) probes. High- and moderate-copy repeat sequences occupy 57.52, 59.01, and 64.73% of N. sativa, N. damascena and N. bucharica 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 Nigella species possess large genomes of about 7.4 to 12.4 Gbp/1C. Only two satellite repeats in N. sativa, one in N. damascena and four in N. bucharica 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 Nigella species. Interestingly, in N. hispanica, 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 2n = 2x = 12 and a karyotype formula of 10m + 2t (including N. sativa, N. arvensis, N. hispanica as the first group and N. damascena and N. orientalis as the second group) and a more distant group with 2n = 2x = 14 and a karyotype formula of 8m + 2st + 4t (including N. integrifolia and N. bucharica). These karyotype groups agreed with the phylogenetic analysis using ITS and rbcL 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 Nigella.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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“…Suitable plates from freshly prepared slides were photographed with Leica DM 750 microscope with attached camera at 1000X magnification. Five cells with well-spread metaphase chromosomes were selected for karyotype analysis by using KaryoMeasure software (Mahmoudi and Mirzaghaderi 2021). Karyological parameters, viz.…”

Section: Taxonomymentioning

confidence: 99%

A new Senecio (Asteraceae) from the Anjaneri Hills of Nashik, India

Jeswani,

Yadav,

Lekhak

2024

Preprint

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A new species of Senecio L. (Asteraceae, Senecioneae), Senecio anjanericus is described and illustrated from the Anjaneri Hills of Nashik district, Maharashtra, India based on morphological and cytogenetical studies. The species resembles Senecio bombayensis but differs from it in small size of the ligules, presence of conspicuous foliose supplementary bracts and dense indumentum on stem. The somatic chromosome count was observed to be 2n=2x=20, with all the chromosomes exhibiting median region centromeres. Detailed morphology, illustration and karyotypic features of the new species are provided.

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“…Ten cells at mitotic metaphase stage were photographed for measurement of arm length and gray value in each E. dahuricus chromosomes. The ideogram of St, Y, H chromosomes was conducted by software KaryoMeasure [54]. Software ImageJ was used to process fluorescence in image and to measure the average gray value.…”

Section: Drawing Karyotype Ideogrammentioning

confidence: 99%

Chromosome Rearrangement in Elymus dahuricus Revealed by ND-FISH and Oligo-FISH Painting

Jiang,

Liu,

Yang

et al. 2023

Plants

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As a perennial herb in Triticeae, Elymus dahuricus is widely distributed in Qinghai–Tibetan Plateau and Central Asia. It has been used as high-quality fodders for improving degraded grassland. The genomic constitution of E. dahuricus (2n = 6x = 42) has been revealed as StStHHYY by cytological approaches. However, the universal karyotyping nomenclature system of E. dahuricus is not fully established by traditional fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). In this study, the non-denaturing fluorescent in situ hybridization (ND-FISH) using 14 tandem-repeat oligos could effectively distinguish the entire E. dahuricus chromosomes pairs, while Oligo-FISH painting by bulked oligo pools based on wheat-barley collinear regions combined with GISH analysis, is able to precisely determine the linkage group and sub-genomes of the individual E. dahuricus chromosomes. We subsequently established the 42-chromosome karyotype of E. dahuricus with distinctive chromosomal FISH signals, and characterized a new type of intergenomic rearrangement between 2H and 5Y. Furthermore, the comparative chromosomal localization of the centromeric tandem repeats and immunostaining by anti-CENH3 between cultivated barley (Hordeum vulgare L.) and E. dahuricus suggests that centromere-associated sequences in H subgenomes were continuously changing during the process of polyploidization. The precise karyotyping system based on ND-FISH and Oligo-FISH painting methods will be efficient for describing chromosomal rearrangements and evolutionary networks for polyploid Elymus and their related species.

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Tools for Drawing Informative Idiograms

Cited by 6 publications

References 29 publications

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

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

A new Senecio (Asteraceae) from the Anjaneri Hills of Nashik, India

Chromosome Rearrangement in Elymus dahuricus Revealed by ND-FISH and Oligo-FISH Painting

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