Haploid Genome Length Research Articles

Targeted sequencing of the Panicum miliaceum gene space and genotyping of variant sites from population genetics studies, combined in a single assay, as a tool for broomcorn millet assisted breeding

Broomcorn millet (Panicum miliaceum L.) is a prehistorical cereal, today cultivated as a minor crop with low yields but with a renewed interest for its high water use efficiency and gluten-free grains. To reverse the downward trend in broomcorn millet cultivation, the crop needs genetic improvement and creation of novel genetic variation to increase productivity. In order to facilitate genomics-assisted breeding, we designed a reduced representation genome-sequencing assay that investigates 1.8% of the nuclear DNA in a targeted and reproducible way, with an intensity of genomic sampling that is a direct function of local recombination rate. We used this tool and set up bioinformatics analyses tailored to the polyploid genome of P. miliaceum for maternity and paternity testing, quantification and genomic distribution of homozygous regions and estimation of parental genome contribution for individual seedlings in advanced inbred lines from a breeding program and compared their genomic composition with registered varieties. We found several clues that suggest that the genetic purification process to ensure genetic uniformity is incomplete in varieties of this species. Residual heterozygosity was detected in the genome of three registered varieties ranging from 4.4 to 6.25% of their haploid genome length. Other registered varieties show genome-wide homozygosity. We found, however, evidence of intravarietal genetic variation in three cases that suggest that the breeder seed or commercial seed production had fixed by self-pollination multiple inbred lines with very similar, though not identical, genotypes within each variety.

Little known Curculigo brevifolia deserves a species rank: evidences from morphological, cytological and molecular data

The Curculigo brevifolia resurrected here based on morphological, cytological, and molecular phylogenetic analyses. Curculigo brevifolia morphologically resembles C. orchioides but differs in having bulbils at the tip of leaves for vegetative reproduction, leaves elongated falcately shaped, beaked fruits. Cytological parameters, karyotype formula, total haploid genome length (THL), values of CV CL , M CA also supported the distinctness of C. brevifolia and C. orchioide s. Phylogenetic analysis based on cpDNA data resulted in the recognition of three clades and strongly supported the revised systematics of Hypoxidaceae. The resurrected species nests within the Curculigo clade of Hypoxidaceae and display a close phylogenetic affinity with newly added Curculigo species and C. orchioides .

New chromosome characteristics of the monozoic tapeworm Caryophyllaeus laticeps (Cestoda, Caryophyllidea)

Summary The karyotype of a caryophyllidean tapeworm Caryophyllaeus laticeps (Pallas, 1781) from the freshwater bream Abramis brama (L.) caught in the Slovak part of the River Tisa, was described and originally inspected for amount of heterochromatin and its chromosome localization. The chromosome set comprised nine metacentric and one submetacentric (No. 3) pairs (2n = 20). The chromosomes were up to 12.0 ± 2.5 μm long and the mean total length of haploid genome (TLC) reached 80.6 μm that represents one of the highest yet recorded values among tapeworms. C-banding and staining with fl uorescent dyes DAPI and YOYO1 revealed a distinct banding pattern explicitly on chromosomes with centromeric bright heterochromatin bands present on all 10 chromosome pairs; no pair showed any interstitial heterochromatin. A complete course of spermatocyte meiosis and dynamics of nucleolus formation and degradation during meiotic division was described.

Cytotaxonomical studies on Drimia nagarjunae and a review on the taxonomy of Indian species of Drimia

The genus Drimia (Asparagaceae) is a group of tunicated bulbous plants. Eight species are found in India. However, their circumscription has always been controversial. The species, namely Drimia coromandeliana, D. govindappae and D. nagarjunae have been reduced to a cosmopolitan species D. indica. The species Drimia nagarjunae earlier described from Nellore District, Andhra Pradesh was never collected after the type collection. The present study reports the karyomorphological details of Drimia nagarjunae for the first time, since this species could now be collected from Chinnar wildlife sanctuary, Idukki district, Kerala. Amongst the Indian species of Drimia, D. nagarjunae (2n = 20) is the most robust species, with the mean chromosome length measuring 6.09 ± 2.40 μm, total haploid genome length 60.87 ± 2.40 μm. The longest chromosome pair measures 10.48 ± 1.28 μm while the shortest is 3.83 ± 0.39 μm long, and the pair number 6 had a satellite exhibiting the karyotype formula: 7st + 3t. Taxonomic notes on doubtful taxa (Drimia coromandeliana, D. govindappae and D. nagarjunae) have also been provided to elucidate the current status of the genus Drimia in India.

Karyotype, Heterochromatin, and Physical Mapping of 5S and 18-5.8-26S rDNA Genes in Setiechinopsis (Cactaceae), an Argentine Endemic Genus

Abstract Setiechinopsis is a monotypic Argentine endemic genus (S. mirabilis) of the tribe Trichocereeae. It is one of the most difficult cacti to find and grows in lowlands and brackish soils. Our aim was to analyze for the first time its cytogenetic features in two populations. It presented 2n = 22 with small chromosomes (mean chromosome length = 2.87 μm; mean haploid genome length = 31.60 μm). The karyotype was symmetrical: 10m + 1sm. The first m pair (No. 1) had nucleolar organizing regions and terminal microsatellites on the short arms. The ratio of the length of the largest m chromosome pair (No. 1) to that of the smallest m chromosome pair (No. 10) was 1.55. Banding patterns showed CMA+/DAPI− constitutive NOR-associated heterochromatin in m chromosome pair No. 1, comprising the distal satellite and a small proximal band. Additionally, four m chromosome pairs showed CMA+/DAPI− pericentromeric bands. The percentage of CMA+/DAPI− heterochromatin was 11.22% of the total karyotype length. No CMA−/DAPI+ ...

Karyotypes and fluorescent chromosome banding patterns in southern AfricanLycium(Solanaceae)

Abstract Chromosomal analyses of several southern African Lycium species resulted in diploid (2n = 24: L. amoenum, L. bosciifolium, L. ferocissimum, L. oxycarpum, L. tenue), tetraploid (2n = 48: L. gariepense, L. strandveldense, L. hantamense), and hexaploid (2n = 72: L. tetrandrum) counts. Chromosomes in all species were short (mean length = 2.00 μm; mean haploid genome length = 23.77 μm). Further, all species shared a highly symmetrical karyotype formula with 10 m pairs and 2 sm pairs, except L. bosciifolium with only one sm pair. The first m pair had a terminal microsatellite on the short arms. Fluorescent chromosome banding patterns with CMA/ DAPI staining in the diploid species showed NOR-associated heterochromatin in the first satellited pair. The tetraploids L. gariepense and L. hantamense had two chromosome pairs with a CMA+/DAPI−terminal band. Phylogenetic studies have shown that the southern African species are included in a monophyletic group including all Old World Lycium; these species are like...

Identifying Allelic Loss and Homozygous Deletions in Pancreatic Cancer without Matched Normals Using High-Density Single-Nucleotide Polymorphism Arrays

Recent advances in oligonucleotide arrays and whole-genome complexity reduction data analysis now permit the evaluation of tens of thousands of single-nucleotide polymorphisms simultaneously for a genome-wide analysis of allelic status. Using these arrays, we created high-resolution allelotype maps of 26 pancreatic cancer cell lines. The areas of heterozygosity implicitly served to reveal regions of allelic loss. The array-derived maps were verified by a panel of 317 microsatellite markers used in a subset of seven samples, showing a 97.1% concordance between heterozygous calls. Three matched tumor/normal pairs were used to estimate the false-negative and potential false-positive rates for identifying loss of heterozygosity: 3.6 regions (average minimal region of loss, 720,228 bp) and 2.3 regions (average heterozygous gap distance, 4,434,994 bp) per genome, respectively. Genomic fractional allelic loss calculations showed that cumulative levels of allelic loss ranged widely from 17.1% to 79.9% of the haploid genome length. Regional increases in "NoCall" frequencies combined with copy number loss estimates were used to identify 41 homozygous deletions (19 first reports), implicating an additional 13 regions disrupted in pancreatic cancer. Unexpectedly, 23 of these occurred in just two lines (BxPc3 and MiaPaCa2), suggesting the existence of at least two subclasses of chromosomal instability (CIN) patterns, distinguished here by allelic loss and copy number changes (original CIN) and those also highly enriched in the genomic "holes" of homozygous deletions (holey CIN). This study provides previously unavailable high-resolution allelotype and deletion breakpoint maps in widely shared pancreatic cancer cell lines and effectively eliminates the need for matched normal tissue to define informative loci.

A Comparative Study of Chromosome Morphology among Some Genotypes of Cicer arietinum L.

Karyotypic analysis was performed for 11 genotypes of chickpea (Cicer arietinum L.) in order to determine their potential genetic relationships. Pretreatment of root tips in 8-hydroxyquinoline, followed by fixation in Lewitsky solution and hydrolysis in 1N NaOH at 60°C, then staining in aceto-iron-hematoxylin for 15-20 h, confirmed a somatic chromosome number of 2n = 16 in all genotypes. This karyotype consisted of: a pair with the longest satellited submetacentric chromosome, a pair with the shortest metacentric chromosome and six pairs of metacentric to submetacentric chromosomes. Intraspecific variabilities were observed for haploid chromosome length, primary constriction position and karyotypic formula. But all of the studied genotypes showed the same karyotype asymmetry, 1B. Haploid genome length ranged from 24.88 μm±0.50 in G6 (Bieanij cv) to 18.48±0.60 μm in G10 (Flip93-93c cv). Cluster analysis classified the 11 genotypes in three groups, having different sizes of chromosomes and arms.

Chromosome banding patterns in the annual species of Cicer

Somatic karyotypes of the nine annual species of Cicer (2n = 16) were analyzed using C-banding. Highly significant differences in haploid genome length and C-band positive heterochromatin content were observed. The haploid genome length ranged from 20.0 μm in the wild species C. judaicum to 28.7 μm in the cultivated species C. arietinum, and significant differences for this character were observed between accessions within several species. Based on their heterochromatin content, the species were divided into two groups: low heterochromatin content (average of 41.7%), which included C. arietinum, C. chorassanicum, C. echinospermum, C. judaicum, C. pinnatifidum, C. reticulatum, and C. yamashitae, and high heterochromatin content (average of 59.5%), which included C. bijugum and C. cuneatum. Within-group variation for heterochromatin content was insignificant, while differences between groups were highly significant. There seemed to be a trend for reduction in C-heterochromatin content in the course of evolution in Cicer. In all species studied, C-bands were located proximally around the centromere with occasional bands in intercalary and distal positions. C-banding patterns allowed for chromosome identification and matching pairs of homologues in all species analyzed.

Evidence for Dependence of Resonant Frequency of Millimeter Wave Interaction withEscherichia coliK12 Cells on Haploid Genome Length

The method of anomalous viscosity time dependence (AVTD) was used to study the influence of millimeter electromagnetic radiation (EMR) on the genome conformational state (GCS) of Escherichiu coli K12 cells. Strain N99 of wild-type, lysogenic strains N99(A) and N99(λ,λimm434bio10) were used. In the 41.28-41.37 GHz and 51.73-51.79 GHz ranges the resonance effect of low-intensity EMR (10-10 W/cm2) on the GCS of N99 cells was shown. The resonance frequencies were 41.324 ± 0.001 GHz and 51.765 ± 0.002 GHz, respectively. The insertion in bacterial chromosome of prophage λ [strain N99(λ)] and prophage λimm434bio10 [strain N99(λ, λimm434bio10)] reduced both resonance frequencies considerably. The decrease of both resonance frequencies was proportionate to the increase of the haploid genome length. Shifts of the resonance frequency were not accompanied by change in the sign of effective circular EMR polarization. The results indicate that the frequencies of resonance interaction of E. coli cells with low-intensity...

The Gyratrix hermaphroditus Species Complex (Platyhelminthes: Kalyptorhynchia) in the Darwin Area (Northern Territory, Australia)

Abstract. A karyological and morphological analysis of 71 specimens representing the Gyratrix hermaphroditus species complex (Kalyptorhynchia: Polycystididae) from various habitats (marine, brackish, freshwater) around Darwin (N.T., Australia) was conducted. Different karyotypes were found, distinct for chromosome numbers (2n = 4; 2n = 6), centromere position of corresponding chromosomes, and haploid genome length. Differences in the morphology of male sclerotized organs were found to be consistent with differences in karyology, thus revealing the existence of numerous sibling species of the complex in the Darwin area. Most species encountered were karyologically and morphologically distinguishable from previously known species of the complex. One Australian species was not significantly different from a European species, suggesting the possibility of extensive distribution. Evolution of karyotypes in the Australian species generally follows the pathways envisaged for the European species; however, the ecological distinction by which limnal species in Europe have 2n = 4 and marine species 2n = 6 did not hold among Australian species. This situation is ascribed to the peculiar environment of the Darwin

Karyological Observations on Monocelididae (Turbellaria, Proseriata): Karyometrical Analysis of Four Species Pertaining to the Subfamily Minoninae

SUMMARYFour species of Minoninae (Turbellaria, Proseriata) have been examined (Minona n. sp., Duplominona paucispina, D. corsicana, Duploperaclistus circocirrus). All show n = 3, 2n = 6 and they have remarkably similar karyotypes. The basic diploid set is made up of one pair of large metacentric chromosomes, one pair of medium-sized chromosomes (metacentric in three species and submetacentric in the fourth) and a third pair of small acrocentric chromosomes. Absolute haploid genome length is similar in three of the species but differs significantly in Duplominona corsicana where it is much higher. The chromosome number n = 3, found not only in these species but also in others of the family Monocelididae, can be considered as the basic number of the family and a plesiomorphic condition for all the Proseriata.