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Phenotype evaluation rawdata of Acinetobacter baumannii harboring chromosomal parallel mutations or an evolved plasmid
<p>OXA-23 is the predominant carbapenemase in carbapenem-resistant <em>Acinetobacter baumannnii</em>. The co-evolutionary dynamics of <em>A. baumannii</em> and OXA-23-encoding plasmids are poorly understood. Here, we transformed <em>A. baumannnii</em> ATCC 17978 with pAZJ221, a <em>bla</em><sub>OXA-23</sub>-containing plasmid from a clinical <em>A. baumannnii</em> isolate A221, and subjected the transformant to experimental evolution in the presence of a sub-inhibitory concentration of imipenem for nearly 400 generations. We used population sequencing to track genetic changes at six time-points and evaluated phenotypic changes. Increased fitness of evolving populations, temporary duplication of <em>bla</em><sub>OXA-23</sub> in pAZJ221, interfering allele dynamics, and chromosomal locus-level parallelism were observed. To characterize genotype-to-phenotype associations, we focused on six mutations in parallel targets predicted to affect small RNAs and a cyclic dimeric (3'→5') GMP-metabolizing protein. Six isogenic mutants with or without pAZJ221 were engineered to test for the causal effects of these mutations on fitness costs and plasmid kinetics, the evolved plasmid containing two copies of <em>bla</em><sub>OXA-23</sub> was transferred to ancestral ATCC 17978. Five of the six mutations contributed to improved fitness in the presence of pAZJ221 under imipenem pressure, and all but one of them impaired plasmid conjugation ability. The duplication of <em>bla</em><sub>OXA-23</sub> contributed to host fitness under carbapenem pressure but imposed a burden on the host in antibiotic-free media relative to the unevolved pAZJ221. Overall, our study provides a framework for the co-evolution of <em>A. baumannii</em> and a clinical blaOXA-23-containing plasmid, involving early <em>bla</em><sub>OXA-23</sub> duplication followed by chromosomal adaptations.</p>
Color and W-chromosome sequence data from study on maternal inheritance of egg mimicry
<div>This dataset supports a study demonstrating that host-specific egg mimicry in the brood-parasitic African cuckoo finch <em>Anomalospiza imberbis</em> is maternally inherited. It includes egg reflectance spectra for the background colour of 188 cuckoo finch eggs from four host species in Zambia, and consensus sequences for 68 W-linked ddRAD-seq loci derived from 80 female cuckoo finches belonging to four different host-specific maternal lineages from three host species in Zambia. These data derive from two partially overlapping samples of eggs: some eggs with genetic data lacked egg spectral data, and vice versa. W-linked genetic data were all of offspring origin as they derived from embryonic or nestling tissue. Additional phenotypic data (host nest species and descriptions of egg phenotype), date and location data associated with each egg spectrum are provided in a separate file. Data on the origin of the individuals contributing to the W-linked loci are provided in Table S1 of the associated publication.</div>
The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding the origin of domestic goat
<p>The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated <i>in silico</i> strategy for identifying and assembling the goat Y-linked scaffolds <span>using existing data</span>. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat Radiation-Hybrid map (RH map). The existing whole-genome re-sequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.</p>
FIGURE 2 in External morphology of larva and polytene chromosomes of Clunio marinus Haliday, 1855 (Diptera, Chironomidae, Orthocladiinae) from two localities of the Atlantic coast
FIGURE 2. Larva of Clunio marinus Holiday, lab.stock, Spain, Vigo. A. Pecten epipharyngis (PE), premandible (Pm); B. Maxilla with maxillary palp (mp) and lacinial chaetae (LCh); C. Clypeus with setae SI and SII and premandible (Pm); D. Caudal part with posterior parapods (pp), anal seta (as), and supra anal setae (ss). Scale bar, 10 µm.
FIGURE 3 in External morphology of larva and polytene chromosomes of Clunio marinus Haliday, 1855 (Diptera, Chironomidae, Orthocladiinae) from two localities of the Atlantic coast
FIGURE 3. Larvae of Clunio marinus Holiday, lab. stock, Spain, Vigo. A. Clypeus and frontal apotome with setae S1 to S5. Scale bar, 10 µm.
FIGURE 6 in External morphology of larva and polytene chromosomes of Clunio marinus Haliday, 1855 (Diptera, Chironomidae, Orthocladiinae) from two localities of the Atlantic coast
FIGURE 6. Larvae of Clunio marinus Holiday, lab. stock, Germany, Helgoland. A. Clypeus and frontal apotome with setae S3 to S5. Scale bar, 10 µm.
FIGURE 1 in External morphology of larva and polytene chromosomes of Clunio marinus Haliday, 1855 (Diptera, Chironomidae, Orthocladiinae) from two localities of the Atlantic coast
FIGURE 1. Larva of Clunio marinus Holiday, lab. stock, Spain, Vigo. A. Mandible; B. Mentum with median and lateral teeth; C. Antenna: blade (bl), style (st); D. Premandible (Pm). Scale bar, 10 µm.
FIGURE 5 in External morphology of larva and polytene chromosomes of Clunio marinus Haliday, 1855 (Diptera, Chironomidae, Orthocladiinae) from two localities of the Atlantic coast
FIGURE 5. Larva of Clunio marinus Holiday, lab. stock, Germany, Helgoland. A. Pecten epipharyngis (PE) and premandible (Pm); B. Maxilla with maxillary palp (mp) and lacinial chaetae (LCh); C. Caudal part with posterior parapods (pp), anal seta (as) and supra anal seta (ss). Scale bar, 10 µm.
FIGURE 4 in External morphology of larva and polytene chromosomes of Clunio marinus Haliday, 1855 (Diptera, Chironomidae, Orthocladiinae) from two localities of the Atlantic coast
FIGURE 4. Larva of Clunio marinus Holiday, lab. stock, Germany, Helgoland. A. Mandible; B. Mentum with median and lateral teeth; C. Antenna: blade (bl), style (st); D. Premandible (Pm). Scale bar, 10 µm.
FIGURE 7. A in External morphology of larva and polytene chromosomes of Clunio marinus Haliday, 1855 (Diptera, Chironomidae, Orthocladiinae) from two localities of the Atlantic coast
FIGURE 7. A. Polytene chromosomes: I, II, III of Clunio marinus Holiday, lab. stock, Spain, Vigo. Heterozygous inversion in chromosome III. Arrows indicate the markers of the chromosomes I and III. NOR—Nucleolar Organizer; BR—Balbiani Ring. B. Heterozygous inversion in chromosome III. Scale bar, 10 µm.
Data from: Whole-genome phylogeography of the Blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome
<p>Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the Blue-faced honeyeater (<em>Entomyzon cyanotis</em>), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within <em>E. cyanotis</em> across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3 – 1.7 MYA). Evidence for introgression between non-sister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and explore its diversity, divergence and introgression landscape. We show that, as in some Sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome, with the ancestral pseudoautosomal region (PAR) appearing to become non-recombinant between Z and W, along with most of the fused chromosome 5 (~37.2 Mbp). The added non-recombinant portion of the neo-Z displays reduced heterozygosity and faster population genetic differentiation compared with the ancestral Z. Yet, the new PAR shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.</p>
FIGURE 2 in Low and high elevation Heliosperma species (Caryophyllaceae)-insight based on chromosome number, pollen characters and seed micromorphology
FIGURE 2. Chromosome number and pollen characters in Heliosperma spp. Somatic chromosome number (2n = 26) in root meristematic cell of H. pusillum subsp. chromodontum (a), pollen size, shape and viability after Alexander staining in H. macranthum (green—non-viable and purple—viable pollen grains inserted) (b).
FIGURE 5 in Low and high elevation Heliosperma species (Caryophyllaceae)-insight based on chromosome number, pollen characters and seed micromorphology
FIGURE 5. Factorial analysis of mixed data (FAMD) of seeds characters and hierarchical clustering on its principal components (HCPC). Distribution of the quantitative variables (a). Distribution of the qualitative variables (b); 2-4rows—number of rows in crest; 1- 2chambers—number of hilum chambers; marginal/middle—hilum location; brown/black—colour of seed; present/lack—waxes in hilum chambers; matt/shiny—surface type. Variation of elevation variable (c). Variation of habitat variable (numbers correspond to NATURA 2000 codes) (d). Five clusters of species identified by Hierarchical Clustering on Principal Components (HCPC) (e). ALP—H. alpestre; MAC—H. macranthum; RET—H. retzdorffianum; NIC—H. nikolicii; OLI—H. oliverae; PUS—H. pusillum subsp. pusillum; ALB—H. pusillum subsp. albanicum; MARK—H. pusillum subsp. markgrafii; MON—H. pusillum subsp. monachorum; CAN—H. pusillum var. candavicum; CHROM—H. pusillum subsp. chromodontum.
FIGURE 4 in Low and high elevation Heliosperma species (Caryophyllaceae)-insight based on chromosome number, pollen characters and seed micromorphology
FIGURE 4. Seed microstructure in Heliosperma spp. a0–a3 and b0–b3 general seed view, c0–c3 view of cells near crest (dorsal view), d0–d3 view of the cells near the hilum (ventral view), e0–e3—view of the hilum. a0–e0—H. macranthum, a1–e1—H. pusillum subsp. chromodontum, a2–e2—H. retzdorffianum, a3–e3—H. pusillum ssp. markgrafii. Bars in a0–a3 = 500 µm, b0–b3 = 250 µm, c0–c3, d0–d3, e0–e3 = 30 µm.
FIGURE 3 in Low and high elevation Heliosperma species (Caryophyllaceae)-insight based on chromosome number, pollen characters and seed micromorphology
FIGURE 3. Capsules of Heliosperma macranthum (a) and H. retzdorffianum (b, c). Note seeds sticked to the pubescent plants (arrows in c).
FIGURE 3. Heliophila verna. A. Plant. B. Mitotic chromosome spread. Scale, 10 in Heliophila verna (Brassicaceae), a new species from the Northern Cape of South Africa
FIGURE 3. Heliophila verna. A. Plant. B. Mitotic chromosome spread. Scale, 10 µm. C and D. Photos of the type locality in Kamieberg of the Northern Cape. Arrows indicates the exact collection site. (Photos by T.M.).
Chromosome variation graphs (Chr22 and Chr1)
<p>Chromosome variation graphs used in the experiments of GraphChainer's experiments (<a href="https://doi.org/10.1101/2022.01.07.475257">https://doi.org/10.1101/2022.01.07.475257</a>).</p> <p>The graphs were built with vg, using (<a href="https://doi.org/10.5281/zenodo.6587237">https://doi.org/10.5281/zenodo.6587237</a>) as the reference and <a>ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5c.20130502.sites.vcf.gz</a> as the variants.</p> <p>The rest of the graphs can be found at <a href="https://doi.org/10.5281/zenodo.6587252">https://doi.org/10.5281/zenodo.6587252</a></p>
Distribution. WC core and SE peninsula of Sulawesi, including Mt Kanino, Mt Nokilalaki, Mt Lehio, Rano Rano, and Mamasa regions, Quarles Range, Mt Rantemario, and Mt Latimojong. Descriptive notes. er 155-242 mm, tail 138-190 mm, ear 23-29 mm, hind-foot 28-45 mm; weight 95-170 g. The Montane Hill Rat is the largest member of the B. fratrorum species group, with broad head, long rostrum, and robust body. Pelage is moderately long, soft, and lustrous, with shortish blackish guard hairs mixed throughout. Dorsum is brownish gray, speckled with buff that is a mix of dark gray underfur and overhairs with brown tips and buffy bands, being dark gray for the most part. Sides are paler grayish brown and fade into ventral pelage. Sides of muzzle are white. Venter is grayish white or dark grayish white, although some are grayish buff, with gray hairs and unpigmented tips or unpigmented altogether, respectively. Juveniles are duller and darker, with more grayish white underparts. Feet are long and slender, with white digits. Ears are large, covered in short unpigmented hair, rubbery, and gray and brown hues. Tail is 88-102% of head-body length and mainly bicolored, brownish gray to blackish gray dorsally and glossy white ventrally, with white tip most of the time. Scrotum is gray. Skull is large, with long and wide rostrum and narrow zygomatic plate. Fleas (e.g. Sigmactenus, Stivalius, Musserella, and Dasypsyllus), ticks (Rhipicephalus) pseudoscorpions (Magachernes and Chiridiochernes), and nematodes (Bunomystrongylus and Sibulura) have been recorded from the Montane Hill Rat. There are two pairs of inguinal mammae. Chromosomal complement is 2n = 42, FN = 60 (females) or FN = 61 (males). in Muridae
Distribution. WC core and SE peninsula of Sulawesi, including Mt Kanino, Mt Nokilalaki, Mt Lehio, Rano Rano, and Mamasa regions, Quarles Range, Mt Rantemario, and Mt Latimojong. Descriptive notes. er 155-242 mm, tail 138-190 mm, ear 23-29 mm, hind-foot 28-45 mm; weight 95-170 g. The Montane Hill Rat is the largest member of the B. fratrorum species group, with broad head, long rostrum, and robust body. Pelage is moderately long, soft, and lustrous, with shortish blackish guard hairs mixed throughout. Dorsum is brownish gray, speckled with buff that is a mix of dark gray underfur and overhairs with brown tips and buffy bands, being dark gray for the most part. Sides are paler grayish brown and fade into ventral pelage. Sides of muzzle are white. Venter is grayish white or dark grayish white, although some are grayish buff, with gray hairs and unpigmented tips or unpigmented altogether, respectively. Juveniles are duller and darker, with more grayish white underparts. Feet are long and slender, with white digits. Ears are large, covered in short unpigmented hair, rubbery, and gray and brown hues. Tail is 88-102% of head-body length and mainly bicolored, brownish gray to blackish gray dorsally and glossy white ventrally, with white tip most of the time. Scrotum is gray. Skull is large, with long and wide rostrum and narrow zygomatic plate. Fleas (e.g. Sigmactenus, Stivalius, Musserella, and Dasypsyllus), ticks (Rhipicephalus) pseudoscorpions (Magachernes and Chiridiochernes), and nematodes (Bunomystrongylus and Sibulura) have been recorded from the Montane Hill Rat. There are two pairs of inguinal mammae. Chromosomal complement is 2n = 42, FN = 60 (females) or FN = 61 (males).
As currently delineated, this is a complex comprising at least two species, as dem- onstrated by the work of J. M. Lamb and colleagues in 2014 and A. Monadjem and colleagues in 2015. Large gray-bellied specimens attributed to M. triton form two highly divergent molecular and chromosomal clades: on the one hand, from Tanzania, Malawi, and Mozambique (with chromosomal complement of 2n = 20-22, FN = 34); and, on the other, from DR Congo (with 2n = 32, FN = 34. Monotypic. Distribution. Extreme S South Sudan, S Ethiopia (Bale Mts), NE DR Congo, and from Uganda and Kenya SW & S to Angola, Zambia, WC Mozambique, and Malawi. in Muridae
As currently delineated, this is a complex comprising at least two species, as dem- onstrated by the work of J. M. Lamb and colleagues in 2014 and A. Monadjem and colleagues in 2015. Large gray-bellied specimens attributed to M. triton form two highly divergent molecular and chromosomal clades: on the one hand, from Tanzania, Malawi, and Mozambique (with chromosomal complement of 2n = 20-22, FN = 34); and, on the other, from DR Congo (with 2n = 32, FN = 34. Monotypic. Distribution. Extreme S South Sudan, S Ethiopia (Bale Mts), NE DR Congo, and from Uganda and Kenya SW & S to Angola, Zambia, WC Mozambique, and Malawi.
Distribution. Although previously thought to be more widespread, on chromosomal and molecular grounds it is restricted to Sudanian savanna belt from Senegal to W Ethiopia. in Muridae
Distribution. Although previously thought to be more widespread, on chromosomal and molecular grounds it is restricted to Sudanian savanna belt from Senegal to W Ethiopia.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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