scholarly journals Descending Dysploidy and Bidirectional Changes in Genome Size Accompanied Crepis (Asteraceae) Evolution

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1436
Author(s):  
Magdalena Senderowicz ◽  
Teresa Nowak ◽  
Magdalena Rojek-Jelonek ◽  
Maciej Bisaga ◽  
Laszlo Papp ◽  
...  
Keyword(s):  
Genome Size ◽  
Dna Sequences ◽  
Chromosome Numbers ◽  
Karyotype Evolution ◽  
Base Number ◽  
Ancestral State ◽  
Ancestral Genome ◽  
Independent Events ◽  
Karyotype Asymmetry ◽  
Major Direction

The evolution of the karyotype and genome size was examined in species of Crepis sensu lato. The phylogenetic relationships, inferred from the plastid and nrITS DNA sequences, were used as a framework to infer the patterns of karyotype evolution. Five different base chromosome numbers (x = 3, 4, 5, 6, and 11) were observed. A phylogenetic analysis of the evolution of the chromosome numbers allowed the inference of x = 6 as the ancestral state and the descending dysploidy as the major direction of the chromosome base number evolution. The derived base chromosome numbers (x = 5, 4, and 3) were found to have originated independently and recurrently in the different lineages of the genus. A few independent events of increases in karyotype asymmetry were inferred to have accompanied the karyotype evolution in Crepis. The genome sizes of 33 Crepis species differed seven-fold and the ancestral genome size was reconstructed to be 1 C = 3.44 pg. Both decreases and increases in the genome size were inferred to have occurred within and between the lineages. The data suggest that, in addition to dysploidy, the amplification/elimination of various repetitive DNAs was likely involved in the genome and taxa differentiation in the genus.

scholarly journals Karyotype asymmetry shapes diversity within the physaloids (Physalidinae, Physalideae, Solanaceae)

2020 ◽  
Author(s):  
Julieta Rodríguez ◽  
Rocío Deanna ◽  
Franco Chiarini
Keyword(s):  
Chromosome Number ◽  
Karyotype Evolution ◽  
Phylogenetic Signal ◽  
Monotypic Genus ◽  
Independent Events ◽  
Phylogenetic Methods ◽  
Karyotype Asymmetry ◽  
Chromosome Arm ◽  
Cytogenetic Analyses ◽  
Diploid Ancestor

AbstractWithin the cosmopolitan family Solanaceae, Physalideae is the tribe with the highest generic diversity (30 genera and more than 200 species). This tribe embraces subtribe Physalidinae, in which positions of some genera are not entirely resolved. Chromosomes may help on this goal, by providing information on the processes underlying speciation. Thus, cytogenetic analyses were carried out in the subtribe in order to establish its chromosome number and morphology. Physalidinae is characterized by x = 12 and most species shows a highly asymmetric karyotype. These karyotype traits were mapped onto a molecular phylogeny to test the congruence between karyotype evolution and clade differentiation. A diploid ancestor was reconstructed for the subtribe, and five to six polyploidy independent events were estimated, plus one aneuploidy event (X = 11 in the monotypic genus Quincula). Comparative phylogenetic methods showed that asymmetry indices and chromosome arm ratio (r) have a high phylogenetic signal, whereas the number of telocentric and submetacentric chromosomes presented a conspicuous amount of changes. Karyotype asymmetry allow us to differentiate genera within the subtribe. Overall, our study suggests that Physalidineae diversification has been accompanied by karyotype changes, which can be applied to delimit genera within the group.

Cytotaxonomy of Allium (Amaryllidaceae) subgenera Cyathophora and Amerallium sect. Bromatorrhiza

Phytotaxa ◽  
2017 ◽  
Vol 331 (2) ◽  
pp. 185 ◽  
Author(s):  
MIN-JIE LI ◽  
XIAN-LIN GUO ◽  
JUAN LI ◽  
SONG-DONG ZHOU ◽  
QING LIU ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Karyotype Evolution ◽  
Diploid Species ◽  
Basic Chromosome Number ◽  
Molecular Evidence ◽  
Basic Chromosome ◽  
Karyotype Asymmetry

In the present study, we examined the karyotype data of subg. Cyathophora and sect. Bromatorrhiza, to determine some disputed karyotypes (e.g., A. spicatum and A. fasciculatum), and further to estimate the karyotype evolution along their phylogenetic frameworks. Our results revealed a fairly stable basic chromosome number (x = 8) in subg. Cyathophora, and we therefore revised x = 8 as the basic chromosome number of A. spicatum, rather than x = 10 mostly due to misidentifications concerning A. fasciculatum. The karyotype asymmetry analyses for subg. Cyathophora indicated that, the karyotype evolution for diploid species showing a high karyotype similarity was mainly due to intrachromosomal changes, while the interchromosomal changes were linked to the evolution of tetraploid populations. However, indeed different dysploid basic chromosome numbers (x = 7, 10, 11) and greatly different karyotype patterns occurred in sect. Bromatorrhiza, corresponding to the subsections revealed by molecular evidence. The combined evidence suggested that species with x = 11 compose a segmental allotriploid complex. It was also indicated that karyotype pattern of polyploids usually is closely related with  their diploid progenitors.

Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

2019 ◽  
Vol 104 (1) ◽  
pp. 33-48 ◽  
Author(s):  
Alejandro Zuluaga ◽  
Martin Llano ◽  
Ken Cameron
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
R Package ◽  
Morphological Characters ◽  
Ancestral State ◽  
Seed Shape ◽  
Long Distance ◽  
The Pacific ◽  
And Migration ◽  
The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

Karyotype evolution and chromosome numbers in Chrysopsis (Nutt.) Ell. sensu Semple (Compositae–Astereae)

1980 ◽  
Vol 58 (2) ◽  
pp. 164-171 ◽  
Author(s):  
J. C. Semple ◽  
C. C. Chinnappa
Keyword(s):  
Chromosome Numbers ◽  
Karyotype Evolution ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Acrocentric Chromosomes

The karyotypes of all species of Chrysopsis were analysed and four basic complements were recognised. The X = 5 karyotype was possessed by all seven n = 5 species and consisted of three submetacentric and two acrocentric chromosomes, one bearing the nucleolar organizer region medially on its short arm. Each X = 4 species had a distinct karyotype. The n = 4 karyotype of C. mariana had diverged less from the X = 5 karyotype than that of C. pilosa. The X2 = 9 karyotype shared by three n = 9 taxa was found to be little more than a combination of the X = 5 karyotype and the X = 4 mariana karyotype and was therefore of allopolyploid origin. Some shifting in the location of the nucleolar organizer region has occurred in each group.

scholarly journals Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae)

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 517 ◽  
Author(s):  
Daniel García-Souto ◽  
Sandra Alonso-Rubido ◽  
Diana Costa ◽  
José Eirín-López ◽  
Emilio Rolán-Álvarez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Chromosome Numbers ◽  
Gene Clusters ◽  
Chromosomal Mapping ◽  
Closely Related Species ◽  
Submetacentric Chromosome ◽  
The Family ◽  
Littorina Arcana

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Littorina arcana, L. saxatilis, and L. compressa, the flat periwinkles L. obtusata and L. fabalis, the common periwinkle L. littorea, the mangrove periwinkle Littoraria angulifera, the beaded periwinkle Cenchritis muricatus, and the small periwinkle Melarhaphe neritoides was performed. All species showed diploid chromosome numbers of 2n = 34, and karyotypes were mostly composed of metacentric and submetacentric chromosome pairs. None of the periwinkle species showed chromosomal differences between male and female specimens. The chromosomal mapping of major and minor rDNA and H3 histone gene clusters by fluorescent in situ hybridization demonstrated that the patterns of distribution of these DNA sequences were conserved among closely related species and differed among less related ones. All signals occupied separated loci on different chromosome pairs without any evidence of co-localization in any of the species.

CYTOTAXONOMY, PHYLOGENY, AND CANADIAN DISTRIBUTION OF CIRSIUM UNDULATUM AND CIRSIUM FLODMANII

1961 ◽  
Vol 39 (1) ◽  
pp. 21-33 ◽  
Author(s):  
C. Frankton ◽  
R. J. Moore
Keyword(s):  
North American ◽  
Chromosome Numbers ◽  
World Wide ◽  
North American Species ◽  
Base Number ◽  
Total Length ◽  
The World ◽  
Cirsium Undulatum

The morphology and specific differences of Cirsium undulatum (Nutt.) Spreng. and of C. flodmanii (Rydb.) Arthur are described and their Canadian distributions are reported in detail. The chromosome numbers are C. undulatum f. undulatum and f. album Farwell, 2n = 26; C. flodmanii f. flodmanii and f. albiflorum D. Löve, 2n = 22. The origin of four North American species of Cirsium that do not follow the world-wide base number 17 is discussed; it is postulated that reduction in number has occurred by translocations. The chromosomes of species with reduced numbers are larger than those of the unreduced species but the total length of the chromosomes of both groups is approximately the same.

scholarly journals Cytogenetics and Genome Size Evolution in Illicium L.

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 620-623
Author(s):  
Thomas G. Ranney ◽  
Connor F. Ryan ◽  
Lauren E. Deans ◽  
Nathan P. Lynch
Keyword(s):  
North America ◽  
Plant Breeding ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Phylogenetic Analyses ◽  
Basal Angiosperm ◽  
Ploidy Levels ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Improvement Programs

Illicium is an ancient genus and member of the earliest diverging angiosperms known as the Amborellales, Nymphaeales, and Austrobaileyales (ANA) grade. These adaptable, broadleaf evergreen shrubs, including ≈40 species distributed throughout Asia and North America, are valued for diverse culinary, medicinal, and ornamental applications. The study of cytogenetics of Illicium can clarify various discrepancies and further elucidate chromosome numbers, ploidy, and chromosome and genome size evolution in this basal angiosperm lineage and provide basic information to guide plant breeding and improvement programs. The objectives of this study were to use flow cytometry and traditional cytology to determine chromosome numbers, ploidy levels, and relative genome sizes of cultivated Illicium. Of the 29 taxa sampled, including ≈11 species and one hybrid, 2C DNA contents ranged from 24.5 pg for Illicium lanceolatum to 27.9 pg for Illicium aff. majus. The genome sizes of Illicium species are considerably higher than other ANA grade lineages indicating that Illicium went through considerable genome expansion compared with sister lineages. The New World sect. Cymbostemon had a slightly lower mean 2C genome size of 25.1 pg compared with the Old World sect. Illicium at 25.9 pg, providing further support for recognizing these taxonomic sections. All taxa appeared to be diploid and 2n = 2x = 28, except for Illicium floridanum and Illicium mexicanum which were found to be 2n = 2x = 26, most likely resulting from dysploid reduction after divergence into North America. The base chromosome number of x = 14 for most Illicium species suggests that Illicium are ancient paleotetraploids that underwent a whole genome duplication derived from an ancestral base of x = 7. Information on cytogenetics, coupled with phylogenetic analyses, identifies some limitations, but also considerable potential for the development of plant breeding and improvement programs with this genus.

Selection intensity for codon bias.

Genetics ◽  
1994 ◽  
Vol 138 (1) ◽  
pp. 227-234 ◽  
Author(s):  
D L Hartl ◽  
E N Moriyama ◽  
S A Sawyer
Keyword(s):  
Amino Acids ◽  
Dna Sequences ◽  
Codon Bias ◽  
Enteric Bacteria ◽  
Average Intensity ◽  
Ancestral State ◽  
Selection Intensity ◽  
Coding Region ◽  
Effective Population ◽  
Synonymous Codons

Abstract The patterns of nonrandom usage of synonymous codons (codon bias) in enteric bacteria were analyzed. Poisson random field (PRF) theory was used to derive the expected distribution of frequencies of nucleotides differing from the ancestral state at aligned sites in a set of DNA sequences. This distribution was applied to synonymous nucleotide polymorphisms and amino acid polymorphisms in the gnd and putP genes of Escherichia coli. For the gnd gene, the average intensity of selection against disfavored synonymous codons was estimated as approximately 7.3 x 10(-9); this value is significantly smaller than the estimated selection intensity against selectively disfavored amino acids in observed polymorphisms (2.0 x 10(-8)), but it is approximately of the same order of magnitude. The selection coefficients for optimal synonymous codons estimated from PRF theory were consistent with independent estimates based on codon usage for threonine and glycine. Across 118 genes in E. coli and Salmonella typhimurium, the distribution of estimated selection coefficients, expressed as multiples of the effective population size, has a mean and standard deviation of 0.5 +/- 0.4. No significant differences were found in the degree of codon bias between conserved positions and replacement positions, suggesting that translational misincorporation is not an important selective constraint among synonymous polymorphic codons in enteric bacteria. However, across the first 100 codons of the genes, conserved amino acids with identical codons have significantly greater codon bias than that of either synonymous or nonidentical codons, suggesting that there are unique selective constraints, perhaps including mRNA secondary structures, in this part of the coding region.

scholarly journals Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Gabriela Vuletin Selak ◽  
Marina Raboteg ◽  
Audrey Dubost ◽  
Danis Abrouk ◽  
Katja Žanić ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Whole Genome ◽  
Ribosomal Operon ◽  
Adriatic Coast ◽  
Olive Trees

Here, we present the total genome sequence of Pantoea sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of Pantoea sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of Pantoea spp.

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