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Figure 1 from: Astuti G, Bartolucci F, Conti F, Cera B, Giacò A, Orsenigo S, Sandroni L, Peruzzi L (2021) Chromosome numbers for the Italian flora: 12. Italian Botanist 12: 123-131. https://doi.org/10.3897/italianbotanist.12.79031
Figure 1 Allium permixtum Guss. from Monte Ocre (Rocca di Cambio, L'Aquila), 2n = 24. Scale bar: 10 μm.
Figure 5 from: Astuti G, Bartolucci F, Conti F, Cera B, Giacò A, Orsenigo S, Sandroni L, Peruzzi L (2021) Chromosome numbers for the Italian flora: 12. Italian Botanist 12: 123-131. https://doi.org/10.3897/italianbotanist.12.79031
Figure 5 Hieracium tenuiflorum Arv.-Touv. from San Romolo (Sanremo, Imperia), 2n = 27. Scale bar: 10 μm.
Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation
<p><i>Pogona vitticeps</i> has female heterogamety (ZZ/ZW) but the master sex determining gene is unknown, as is the case for all reptiles. We show that <i>nr5a1</i>, a gene that is essential in mammalian sex determination, has alleles on the Z and W chromosomes (Z-<i>nr5a1</i> and W-<i>nr5a1</i>), which are both expressed and can recombine. Three transcript isoforms of Z-<i>nr5a1</i> were detected in gonads of adult ZZ males, two of which encode a functional protein. However, ZW females produced sixteen isoforms, most of which contained premature stop codons. The array of transcripts produced by the W-borne allele (W-<i>nr5a1</i>) is likely to produce truncated polypeptides that could act as a competitive inhibitor to the full-length intact protein. We hypothesize that an altered configuration of the W chromosomes affects the conformation of the primary transcript generating inhibitory W-borne isoforms that suppress testis determination. Under this hypothesis, the GSD system of <i>P. vitticeps</i> is a W-borne dominant female-determiner that may be controlled epigenetically.</p>
Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
<p>Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A., Vales M.I., Vining K., Visser R.G.F., Vossen J., Yencho G.C., Anglin N.L., Bachem C.W.B., Endelman J.B., Shannon L.M., Strömvik M.V., Tai H.H., Usadel B., Buell C.R., and Finkers R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2022.01.003.</p> <p>Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The <em>StCDF1</em> locus controls maturity and analysis of six tetraploid genomes revealed 12 allelic variants correlated with maturity in a dosage dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.</p>
A chromosome-level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae)
<p><em>Paracymoriza distinctalis</em> is a semi-aquatic lepidopteran insect, which is of great value for studying the differentiation of the Pyraloidea super family. However, the understanding of heredity, evolution, and functional genomics of <em>P. distinctalis</em> are limited by few genome-wide resources. Here, we applied PacBio sequencing and the chromosome capture technique to assemble the first <em>P. distinctalis</em> genome from a single female individual. The genome size is 1.2 Gb with 32 chromosomes and the N50 is 38.91 Mb. Approximately 576.37 Mb, accounting for 48.93% of the genome, was identified as repeats. The genome comprises 39,003 protein-coding genes, 66.56% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of <em>P. distinctalis</em> and <em>Chilo suppressalis</em> lived ~83.5 million years ago. This chromosome-level genome assembly work is not only conducive to the understanding of <em>P. distinctalis</em>, but also may promote the study of the genomes of other lepidopteran species.</p>
A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii
<p>The fungal plant pathogen <em>Austropuccinia psidii</em> is spreading globally and causing myrtle rust disease symptoms on plants in the family Myrtaceae. <em>A. psidii </em>is dikaryotic, with two nuclei that do not exchange genetic material during the dominant phase of its life-cycle. Phased and scaffolded genome resources for rust fungi are important for understanding heterozygosity, mechanisms of pathogenicity, pathogen population structure and for determining the likelihood of disease spread. We have assembled a chromosome-level phased genome for the pandemic biotype of <em>A. psidii </em>and, for the first time, show that each nucleus contains 18 chromosomes, in line with other distantly related rust fungi. We show synteny between the two haplo-phased genomes and provide a new tool, ChromSyn, that enables efficient comparisons between chromosomes based on conserved genes. Our genome resource includes a fully assembled and circularised mitochondrial sequence for the pandemic biotype. Please cite the following manuscript: https://www.biorxiv.org/content/10.1101/2022.04.22.489119v1</p>
The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication
<p>The distribution of recombination events along large cereal chromosomes is uneven and generally restricted to gene-rich telomeric ends. In order to understand how the lack of recombination affects diversity in the large pericentromeric regions, we assembled and analysed deep exome capture data from a panel of 879 cultivars, landraces, and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared to wild barley. We observed a mixture of completely and partially differentiated SNPs between domesticated and wild genepools, suggesting the former were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. While most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated 2-row and 6-row types associated with different geographical origins. Within the pericentromeric regions we identified 22,387 non-synonymous SNPs, of which 92 were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be ‘highly deleterious’. GO terms associated with the pericentromeric regions revealed housekeeping genes to be over-represented. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools with different evolutionary processes driving domestication and diversification.</p>
Chromosome 19 LD data for simulating summary statistics
<p>This data set contains two files both of which contain R objects.</p> <p>snpdata.RDS : A data frame with snp information</p> <p>evd_list_chr19_hm3.RDS : A list of eigen decomposition of the SNP correlation matrix spanning chromosome 19</p> <p>These data contain only SNPs in both 1k Genomes and HapMap3. Correlation matrices were estimated using LD Shrink. These data were built for use with the causeSims R package found here: https://github.com/jean997/causeSims</p>
Data from: The phylogenetic origins and evolutionary history of holocentric chromosomes
In eukaryotes, we can recognize two kinds of chromosomes, based on the location of the kinetochores. The majority of eukaryotes have monocentric chromosomes, in which kinetochoric activity is concentrated in a single locus. In several unrelated eukaryotic lineages, chromosomes are holocentric, having diffuse centromeric / kinetochoric activity along the length of the chromosome. Whether holocentric chromosomes are derived or ancestral is still under debate. This study uses the phylogenetic tree from Time Tree of Life project, comprising more than 50,000 sampled species, to reconstruct the evolution of holocentry. Asymmetrical two-state Markov (Mk2) models were compared with BiSSE models to assess sensitivity of our conclusions to possible effects of holocentry on lineage diversification rates. Our analyses based on Mk2 and BiSSE models inferred that the rate of transition from holocentric to monocentric chromosomes is two orders of magnitude higher than the reverse direction. The ancestral state of all eukaryotes is ambiguous depending on the model, inferred to be either monocentric (Mk2) or holocentric (BiSSE). Whatever the direction, the multiple transitions and high diversity of centromere organization across the tree of life are what we would expect if there are selective advantages to both chromosome types. Understanding those selective advantages is key to understanding how genetic information is organized and transmitted from one generation to the next, and why these major evolutionary transitions in centromere organization have occurred in the first place.
FIGURE 1 in Low and high elevation Heliosperma species (Caryophyllaceae)-insight based on chromosome number, pollen characters and seed micromorphology
FIGURE 1. Map of sampled Heliosperma species in Albania, North Macedonia and Kosovo.
Supplementary material 1 from: Lin C-X, Xu G-L, Jin Z-F, Liao W-B, Xu K-W (2022) Molecular, chromosomal, and morphological evidence reveals a new allotetraploid fern species of Asplenium (Aspleniaceae) from southern Jiangxi, China. PhytoKeys 199: 113-127. https://doi.org/10.3897/phytokeys.199.81292
Table S1
Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci
<p><span>Repetitive DNA represents an important driver of sex chromosome differentiation. Yet repetitive sequences tend to be misrepresented or overlooked in genomic studies. We analysed repetitive landscape of sex chromosomes in several populations of a turquoise killifish <em>Nothobranchius</em> <em>furzeri</em> and its sister species <em>N</em>. <em>kadleci</em> (Teleostei: Nothobranchiidae), representatives of African annual killifishes with high rate of karyotype and sex chromosome evolution. We combined bioinformatic analyses of repeatome with molecular cytogenetic techniques such as comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, genes for ribosomal RNAs (rDNA) and bacterial artificial chromosomes (BACs) and immunostaining of </span><span>SYCP3 and MLH1 proteins, which marked lateral elements of synaptonemal complexes and recombination sites, respectively</span><span>. We revealed that <em>N</em>. <em>furzeri</em> and <em>N</em>. <em>kadleci</em> share the XY sex chromosome system, which is thus much older than previously assumed. Sex chromosomes are mostly heteromorphic as evidenced by distinct distribution of satellite DNAs and major rDNA. Yet, the heteromorphic X and Y sex chromosomes pair almost exclusively regularly in meiosis, which implies synaptic adjustment. Physical mapping of BACs identified inversions on Y chromosomes of the <em>N</em>. <em>kadleci</em> populations, similar to the pattern previously reported in <em>N</em>. <em>furzeri</em>. Yet, the repetitive DNA landscape of X and Y sex chromosomes either diverged in parallel in populations of both species, or it evolved in their common ancestor and thus predates the inversions. The observed differentiation via repeat repatterning thus cannot be explained by the classical sexual antagonistic model. Rather, we hypothesized that relaxed meiotic drive and recombination reduced by neutral processes could drive changes in repeatome and secondary inversions could be maintained </span><span>by sexually antagonistic regulatory effects resulting from evolution of dosage compensation. </span><span><br></span></p>
Chromosome-level genome of Capitulum mitella reveals an ancient whole-genome duplication event and intertidal adaptation of barnacles
<p><span>Barnacles are the only sessile crustaceans inhabiting intertidal zone, an extremely stressful environment for sessile organisms. Herein, we report the chromosome-level genome of a stalked barnacle, <em>Capitulum</em> <em>mitella</em>, which is a dominant intertidal cirripede of the west Pacific Ocean coast. After comprehensive comparative genomic analyses, it is the first time to find an ancient whole-genome duplication (WGD) event that preceded the divergence of Lepadomorpha and Sessilia approximately </span><span>237 million years ago. </span><span>The retained duplicated genes of WGD are primarily enriched in many environmental information processing pathways, shedding light on its adaptive evolution of intertidal sessile life. In addition, transcriptomic and metabolomic sequencing and analyses of <em>C</em>. <em>mitella</em> indicated that the upregulation of some expanded anti-stress factors and accumulation of acyl-carnitines help barnacles adapt to stressful intertidal conditions. Therefore, this study provides a valuable resource for understanding the unique intertidal adaptation mechanism of sessile crustaceans and reveals novel WGD events in invertebrates.</span></p>
Figure 1 from: Peruzzi L, Astuti G, Bernardo L, Carta A, D'Antraccoli M, Roma-Marzio F, Ruffini Castiglione M (2017) Chromosome numbers for the Italian flora: 3. Italian Botanist 3: 1-6. https://doi.org/10.3897/italianbotanist.3.12257
Figure 1 - Bellevalia webbiana Parl., 2n = 16. Metaphasic plate and haploid idiogram. Scale bar: 10 μm.
Figure 10 from: Peruzzi L, Astuti G, Bartolucci F, Conti F, Roma-Marzio F (2016) Chromosome numbers for the Italian flora: 2. Italian Botanist 2: 29-42. https://doi.org/10.3897/italianbotanist.2.10900
Figure 10 - Anthemis cretica L. subsp. petraea (Ten.) Oberpr. & Greuter, 2n = 36. Scale bar: 10 μm.
Figure 13 from: Peruzzi L, Astuti G, Bartolucci F, Conti F, Roma-Marzio F (2016) Chromosome numbers for the Italian flora: 2. Italian Botanist 2: 29-42. https://doi.org/10.3897/italianbotanist.2.10900
Figure 13 - Helleborus viridis L. subsp. abruzzicus (M.Thomsen, McLewin & B.Mathew) Bartolucci, F.Conti & Peruzzi, 2n = 32. Scale bar: 10 μm.
Figure 6 from: Peruzzi L, Astuti G, Bartolucci F, Conti F, Roma-Marzio F (2016) Chromosome numbers for the Italian flora: 2. Italian Botanist 2: 29-42. https://doi.org/10.3897/italianbotanist.2.10900
Figure 6 - Knautia dinarica (Murb.) Borbás subsp. silana (Grande) Ehrend., 2n = 40. Scale bar: 10 μm.
Figure 7 from: Peruzzi L, Astuti G, Bartolucci F, Conti F, Rizzotto M, Roma-Marzio F (2016) Chromosome numbers for the Italian flora: 1. Italian Botanist 1: 39-53. https://doi.org/10.3897/italianbotanist.1.8818
Figure 7 Thymus striatus Vahl subsp. acicularis (Waldst. & Kit.) Ronniger, 2n = 26. Scale bar: 5 μm.
Figure 4 from: Peruzzi L, Astuti G, Bartolucci F, Conti F, Rizzotto M, Roma-Marzio F (2016) Chromosome numbers for the Italian flora: 1. Italian Botanist 1: 39-53. https://doi.org/10.3897/italianbotanist.1.8818
Figure 4 Colchicum bulbocodium Ker Gawl. subsp. versicolor (Ker Gawl.) K.Perss., 2n = 22. Scale bar: 10 μm.
Supplementary material 1 from: Dhar MK, Kour G, Kaul S (2017) B chromosome in Plantago lagopus Linnaeus, 1753 shows preferential transmission and accumulation through unusual processes. Comparative Cytogenetics 11(2): 375-392. https://doi.org/10.3897/compcytogen.v11i2.11779
Tables S1 and S2 : Explanation note: Table S1: Sequences of primers used for SSR analysis.
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