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FIGURES 9–12 in A novel multiple sex chromosome system in Orthoptera, found in the tree cricket Oecanthus rubromaculatus Zefa, 2022 (Grylloidea, Oecanthidae)
FIGURES 9–12. Chromosomes of Oecanthus rubromaculatus from Pelotas. 9, Male karyotype with 2n = 12, X 1 X 2 X 3 Y 1 Y 2 Y 3. 10, Initial Diplotene stage highlighting the heteropycnotic X chromosome, distanced from the other sex chromosomes by a chromatin thread (arrow); 11, Diplotene stage with emphasis on the sex chromosome chain; 12, Sister Metaphases II.
FIGURES 1–8 in A novel multiple sex chromosome system in Orthoptera, found in the tree cricket Oecanthus rubromaculatus Zefa, 2022 (Grylloidea, Oecanthidae)
FIGURES 1–8. Chromosomes of Oecanthus rubromaculatus from São Francisco de Paula. 1, karyotype of the female with 2n = 12, X1X1X2X2 (Best mitotic Metaphase found, but missing one of the bivalents from pair 4); 2, complete female mitotic Metaphase; 3–5, Male's Diplotene stages highlighting the heteropycnotic X chromosome, distanced from the other sexchromosomes by a chromatin thread (arrow); 6, Metaphase I; 7, Anaphase I; 8, Sister Metaphases II.
The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications
<div> <div> <p><a href="https://onlinelibrary.wiley.com/doi/10.1111/age.13181">https://onlinelibrary.wiley.com/doi/10.1111/age.13181</a></p> <h1>The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications</h1> <div> </div> <div> <div> <div> <div><a href="https://onlinelibrary.wiley.com/authored-by/Chen/Jianhai">Jianhai Chen</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Zhong/Jie">Jie Zhong</a>, <a href="https://onlinelibrary.wiley.com/authored-by/He/Xuefei">Xuefei He</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Li/Xiaoyu">Xiaoyu Li</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Ni/Pan">Pan Ni</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Safner/Toni">Toni Safner</a>, <a href="https://onlinelibrary.wiley.com/authored-by/%C5%A0prem/Nikica">Nikica Šprem</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Han/Jianlin">Jianlin Han</a></div> </div> </div> </div> <p>The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long-range information provided by 10× Linked-Reads sequencing. We achieved a high-quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference-assistant scaffolding method. Using the ‘assembly-to-assembly’ approach, we identified intra-chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (<em>R</em><sup>2</sup> > 0.64, <em>p</em> < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large-scale inter-chromosomal evolution, by resolving parental-derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (<em>p</em> < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (<em>p</em> < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter-chromosomal interaction between the sex chromosome and autosomes.</p> </div> </div> <div>The work has been pulished here: https://onlinelibrary.wiley.com/doi/full/10.1111/age.13181</div> <div> </div> <div>The current dataset include the genome annotation files.</div> <div> </div> <div>For the whole-genomic assembly, please check NCBI: </div> <div>https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_021656055.1/</div> <div> <table> <tbody> <tr> <th> </th> <th>GenBank</th> </tr> </tbody> <tbody> <tr> <td>Genome size</td> <td>2.5 Gb</td> </tr> <tr> <td>Total ungapped length</td> <td>2.4 Gb</td> </tr> <tr> <td>Number of scaffolds</td> <td>12,642</td> </tr> <tr> <td>Scaffold N50</td> <td>28.3 Mb</td> </tr> <tr> <td>Scaffold L50</td> <td>25</td> </tr> <tr> <td>Number of contigs</td> <td>41,323</td> </tr> <tr> <td>Contig N50</td> <td>157.9 kb</td> </tr> <tr> <td>Contig L50</td> <td>4,562</td> </tr> <tr> <td>GC percent</td> <td>42</td> </tr> <tr> <td>Genome coverage</td> <td>56.0x</td> </tr> <tr> <td>Assembly level</td> <td>Scaffold</td> </tr> </tbody> </table> <p> </p> <h2>Assembly methods</h2> <div>Sequencing technology 10xgenomics Assembly method Supernova v. 2.1.1 <p> </p> <p>part_** are genome fasta for the GCA_021656055.1</p> <p>You could use the following to combine and uncompress.</p> </div> </div> <div> <div> <div><code><span>cat</span> part_* > archive_combined.zip </code></div> </div> <div> <div> </div> <div><code>unzip archive_combined.zip</code></div> </div> </div> <div> </div> <div> </div>
Karyotype diversification and evolution in Silene (Caryophyllaceae) representatives with sex chromosomes: taxonomic and biogeographical implications
Open the record for dataset details and reuse information.
Figure 4 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 4. Fluorescence in situ hybridization of the (TTAGG)n telomere probe (red signals) in meiotic chromosomes of five Ommexechinae species, counterstained with DAPI (blue). Rearranged chromosomes with are indicated for Ca. maculosa (A), O. macropterum (B), O. virens (C), Cl. bimaculata (D), P. signata (E). Bar = 10µm.
Figure 3 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 3. Fluorescence in situ hybridization of multigene families in mitotic and meiotic chromosomes of five Ommexechinae species, counterstained with DAPI (blue). Chromosomes with positive signals for 18S rDNA (A–E), 5S rDNA (F–J), U2 snDNA (K–O) and H3 (P–T) probes are indicated in white for Ca. maculosa (A, F, K, P), O. macropterum (B, G, L, Q), O. virens (C, H, M, R), Cl. bimaculata (D, I, N, S) and P. signata (E, J, O T). Meiotic cells are presented in most species, except for O. macropterum (B, G, L) and O. virens (H), in which mitotic cells are presented. H3 FISH experiment was unsuccessful in O. macropterum, due to lack of material (Q). Bar = 10µm.
Figure 6 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 6. Schematic representation of two pathways in Ommexechinae L1 autosome evolution. To explain the variable L1 morphology and the distal U2 snDNA location, at least two different inversions must be considered. In the first hypothesis (A), two pericentric inversions are considered, the first one (A1–2) modifying L1 morphology (from acrocentric to submetacentric) and U2 snDNA location (from interstitial to distal), and the second one (A2–3) restoring the acrocentric morphology in P. signata and Cl. bimaculata. The alternative hypothesis involves two different kinds of inversions (B). First, a paracentric inversion changes U2 location without affecting morphology (B1–2) and, then, a pericentric one only changes L1 morphology (B2–3). Both hypotheses are further explained in the paragraph.
Figure 1 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 1. Conventional analysis of mitotic and meiotic chromosomes of five Ommexechinae species. The karyotypes (A–E) and metaphase I of males (F–J) are shown for Ca. maculosa (A, F), O. macropterum (B, G), O. virens (C, H), Cl. bimaculata (D, I) and P. signata (E, J). Male karyotypes were obtained from spermatogonial cells (A–C, E) or from cells in anaphase I (D). Chromosomes are arranged in decreasing order size, and bi-armed autosomes are indicated in red. Male metaphase I shows (F–J) the first pair of autosomes indicated with arrows and the sex chromosomes with dotted lines. The structure of P. signata neo-X chromosome is indicated with light-blue colour and the neo-Y with orange (E, J). Inset (J) highlight P. signata neo-XY. Bar = 10µm.
Figure 2 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 2. Distribution of heterochromatin and chromatin base-richness in five Ommexechinae species. C banding (A–E), CMA3 (F–J) and DAPI (K–O) staining were performed in Ca. maculosa (A, F, K), O. macropterum (B, G, L), O. virens (C, H, M), Cl. bimaculata (D, I, N) and P. signata (E, J, O). Pictures were obtained from female somatic mitosis, in exception to CMA3 and DAPI for P. signata (J, O), in which spermatogonial mitosis is presented, and also in (E, inset), in which C-banding pattern is shown for neo-sex bivalent at metaphase I. Autosomes with positive signals for each technique are indicated with black and white arrows and dotted lines. Yellow arrowheads exemplify the centromeric positive pattern for different banding techniques: C-positive (D), CMA3 positive (I), and DAPI positive (L). The red arrowhead exemplifies additional interstitial C positive blocks (C). Neo-sex chromosomes and their positive signals are indicated green (neo-X) and orange (neo-Y). Insets show in detail the banding patterns of chromosomes of S group in O. macropterum (B) and O. virens (C), and P. signata neo-XY (E, J, O). C = centromere, bar = 10µm except indicated otherwise.
Figure 5 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 5. Schematic representation of multigene families chromosomal locations. Species names, probes and chromosome numbers are indicated in each figure. Coloured arrowheads show chromosomes that shared probe locations for at least three species and, therefore, homeology is suggested, as follows: L1 chromosomes of all species (U2 snDNA), L2 (5S rDNA location plus H3 in some cases) of P. signata, Cl. bimaculata, O. virens and Ca. maculosa, M3 of Cl. bimaculata, Ca. maculosa, O. virens and O. macropterum (5S rDNA) and X chromosomes of Cl. bimaculata, Ca. maculosa together with XR of P. signata (18S rDNA).
Data: Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon
<p>Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.</p>
FIGURE 6. Eligmodontia dunaris MNHN 1546 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 6. Eligmodontia dunaris MNHN 1546 (holotype): dorsal (A), ventral (B) and lateral (C) views of skull. Occlusal view of upper (F) and lower molars (I) of paratype LCM 3377. Similar views of E. puerulus LCM 1993 (D and G) and E. hirtipes LCM 1748 (E and H) are included for comparisons.
FIGURE 4. Phylogenetic tree for 56 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 4. Phylogenetic tree for 56 Eligmodontia sequences and two outgroups resulting from the maximum-likelihood analysis of 1140 bp of the cytochrome b gene. Model of sequence evolution was HKY+G+I. Numbers above branches show the percentage values from 500 bootstrap iterations, and Bayesian posterior probabilities (>50 values).
FIGURE 3 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 3. Correspondence of G-band patterns between diploid chromosomes from Eligmodontia sp. 2N = 50 (left pair within each trio, large numbers below, male LCM 3374 from Playa Los Choros) and a representative haploid set from Eligmodontia hirtipes 2N = 50 (right, small numbers below, from male LCM 1283).
FIGURE 2 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 2. Chromosomes of Eligmodontia sp. ordered according size, 2N = 50 (male LCM 3374 from Playa Los Choros). From bone marrow spreads stained with standard Giemsa.
FIGURE 1 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 1. Map of southern South America showing localities for previously (numbered) and presently studied Eligmodontia specimens (modified from Mares et al. 2008). Below species names are modal diploid chromosome numbers/FN. New northcentral Chile Eligmodontia sites are marked with an X. Map of the infertile Atacama Desert in dark gray (from Latorre 2002).
FIGURE 5 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 5. Morphological multivariate relationships of Eligmodontia individuals from north-Central Chile and Argentina, and southern Peru. Projections of scores into Principal Component axes I and II were extracted from correlations of four body and eight skull measurements.
FIGURE 7 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 7. (A) Eligmodontia dunaris MNHN 1547, paratype (Photo A. Spotorno). (B) Habitat at Playa Los Choros dunes, type locality (Photo C. Zuleta); intensive trapping at the plain belt (top, below sea border) failed to capture any Eligmodontia. (C) Eligmodontia dunaris captured and released alive at Caldera, Atacama, showing bipedal posture (Photo E. Valenzuela by permission).
GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads
<p>C.elegans, O.sativa and Human assemblies produced by GALA software</p>
Orca: Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale (Part1)
<p>This dataset (Part 1) provide the core resource files required for using the code of Orca, including models and the hg38 reference genome (resources_core.tar.gz), and the micro-C mcool files required for extracting the experimental observations (resources_mcools.tar.gz). Orca is a sequence-based deep learning modeling framework for multiscale genome 3D architecture.</p>
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