Short Chromosome Research Articles

Length-sensitive partitioning of Caenorhabditis elegans meiotic chromosomes responds to proximity and number of crossover sites

Sensing and control of size are critical for cellular function and survival. A striking example of size sensing occurs during meiosis in the nematode Caenorhabditis elegans. C.elegans chromosomes compare the lengths of the two chromosome "arms" demarcated by the position of their single off-center crossover, and they differentially modify these arms to ensure that sister chromatid cohesion is lost specifically on the shorter arm in the first meiotic division, while the longer arm maintains cohesion until the second division. While many of the downstream steps leading to cohesion loss have been characterized, the length-sensing process itself remains poorly understood. Here, we have used cytological visualization of short and long chromosome arms, combined with quantitative microscopy, live imaging, and simulations, to investigate the principles underlying length-sensitive chromosome partitioning. By quantitatively analyzing short-arm designation patterns on fusion chromosomes carrying multiple crossovers, we develop a model in which a short-arm-determining factor originates at crossover designation sites, diffuses within the synaptonemal complex, and accumulates within crossover-bounded chromosome segments. We demonstrate experimental support for a critical assumption of this model: that crossovers act as boundaries to diffusion within the synaptonemal complex. Further, we develop a discrete simulation based on our results that recapitulates a wide variety of observed partitioning outcomes in both wild-type and previously reported mutants. Our results suggest that the concentration of a diffusible factor is used as a proxy for chromosome length, enabling the correct designation of short and long arms and proper segregation of chromosomes.

RCC1 depletion drives protein transport defects and rupture in micronuclei.

Micronuclei (MN) are a commonly used marker of chromosome instability that form when missegregated chromatin recruits its own nuclear envelope (NE) after mitosis. MN frequently rupture, which results in genome instability, upregulation of metastatic genes, and increased immune signaling. MN rupture is linked to NE defects, but the cause of these defects is poorly understood. Previous work from our lab found that chromosome identity correlates with rupture timing for small MN, i.e. MN containing a short chromosome, with more euchromatic chromosomes forming more stable MN with fewer nuclear lamina gaps. Here we demonstrate that histone methylation promotes rupture and nuclear lamina defects in small MN. This correlates with increased MN size, and we go on to find that all MN have a constitutive nuclear export defect that drives MN growth and nuclear lamina gap expansion, making the MN susceptible to rupture. We demonstrate that these export defects arise from decreased RCC1 levels in MN and that additional loss of RCC1 caused by low histone methylation in small euchromatic MN results in additional import defects that suppress nuclear lamina gaps and MN rupture. Through analysis of mutational signatures associated with early and late rupturing chromosomes in the Pan-Cancer Analysis of Whole Genomes (PCAWG) dataset, we identify an enrichment of APOBEC and DNA polymerase E hypermutation signatures in chromothripsis events on early and mid rupturing chromosomes, respectively, suggesting that MN rupture timing could determine the landscape of structural variation in chromothripsis. Our study defines a new model of MN rupture where increased MN growth, caused by defects in protein export, drives gaps in nuclear lamina organization that make the MN susceptible to membrane rupture with long-lasting effects on genome architecture.

Rye-durum wheat 1BL.1RS translocation: implications for drought tolerance and nutritional status.

The translocation of the short chromosome arm 1RS of rye onto the 1B chromosome of common wheat has been shown to improve resistance to stress and yield. Here, translocation was operated in durum wheat and its effects on drought tolerance were evaluated. Both the 1BL.1RS translocation line (Svevo 1BL.1RS) and the corresponding Svevo control were exposed to drought for 7 days. Significant differences were found in root morphology between Svevo and Svevo 1BL.1RS under control and drought conditions. Although Svevo 1BL.1RS experienced more severe growth inhibition due to drought than Svevo, it exhibited greater resilience to oxidative stress. Furthermore, several drought-responsive genes were upregulated in both shoots and roots only in the translocation line. Notably, in roots of Svevo 1BL.1RS, the expression of these genes was also higher in the control condition compared to Svevo, suggesting that these genes could be constitutively expressed at higher levels in the translocation line. Moreover, the 1BL.1RS translocation had a significant impact on the plant's ability to accumulate nutrients under drought. Overall, the impact on sulfate accumulation and the expression of genes associated with its assimilation pathways are particularly noteworthy, highlighting the involvement of sulfur in the plant response to water stress. Additionally, the genetic characterization of Svevo 1BL.1RS revealed variants extending beyond the translocation, located in drought stress-responsive genes.

Chromosome size-dependent polar ejection force impairs mammalian mitotic error correction.

Accurate chromosome segregation requires sister kinetochores to biorient, attaching to opposite spindle poles. To this end, the mammalian kinetochore destabilizes incorrect attachments and stabilizes correct ones, but how it discriminates between these is not yet clear. Here, we test the model that kinetochore tension is the stabilizing cue and ask how chromosome size impacts that model. We live image PtK2 cells, with just 14 chromosomes, widely ranging in size, and find that long chromosomes align at the metaphase plate later than short chromosomes. Enriching for errors and imaging error correction live, we show that long chromosomes exhibit a specific delay in correcting attachments. Using chromokinesin overexpression and laser ablation to perturb polar ejection forces, we find that chromosome size and force on arms determine alignment order. Thus, we propose a model where increased force on long chromosomes can falsely stabilize incorrect attachments, delaying their biorientation. As such, long chromosomes may require compensatory mechanisms for correcting errors to avoid chromosomal instability.

Genetic analysis and prenatal diagnosis for a Chinese pedigree affected with co-morbid Ornithine carbamoyl transferase deficiency and MECP2 duplication syndrome

To explore the genetic basis for a Chinese pedigree affected with co-morbid Ornithine carbamoyl transferase deficiency (OTCD) and MECP2 duplication syndrome. A proband who was admitted to the Neonatal Intensive Care Unit of Gansu Provincial Maternal and Child Health Care Hospital on December 19, 2017 was selected as the study subject. High-throughput sequencing and multiplex ligation-dependent probe amplification (MLPA) were carried out for her pedigree, and short tandem repeat-based linkage analysis and chromosome copy number variation sequencing (CNV-seq) were used for the prenatal diagnosis. The proband, a 3-day-old female, was found to harbor heterozygous deletion of exons 7-9 of the OTC gene. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the variant was classified as likely pathogenic (PVS1+PM2_Supporting+PP4). The proband was diagnosed with OTCD , which was in keeping with her acute encephalopathy and metabolic abnormalities (manifesting as hyperammonemia, decreased blood citrulline, and increased urine orotic acid). Prenatal diagnosis was carried out for the subsequent pregnancy. The fetus did not harbor the exons 7-9 deletion of the OTC gene, but was found to carry a duplication in Xq28 region (which encompassed the whole region of MECP2 duplication syndrome) and was positive for the SRY sequence. The same duplication was also found in the proband and her mother. Considering the possible existence of X-chromosome inactivation, the proband was diagnosed with two X-linked recessive disorders including OTCD and MECP2 duplication syndrome, and the fetus was determined as a male affected with the MECP2 duplication syndrome. Discoveries of the pathogenic variants underlying the OTCD and MECP2 duplication syndrome have enabled clinical intervention, treatment, genetic counseling and prenatal diagnosis for this pedigree.

Can ploidy levels explain the variation of Herbertia lahue (Iridaceae)?

Polyploidy is often related with phenotypic variation, as observed in Herbertia lahue, a geophyte species. This study examined the H. lahue polyploid series and departure in cytogenetic, morphometric, and pollen data. Diploids (2n=2x=14) present bimodal karyotype with two long and five short chromosome pairs, while hexaploids (2n=6x=42) and octoploids (2n=8x=56) present a gradual decrease in chromosome size. All cytotypes have CMA+/DAPI- bands co-localized with 18S rDNA sites in the satellite region (no DAPI+ bands in any cytotype). Unlike diploids and octoploids, 5S rDNA interstitial sites in hexaploids are not in a syntenic position with 18S rDNA sites. Genome size is effective as an indirect predictor of the cytotypes since 2C-values increased according to ploidy level. The reduction in the number of the rDNA sites in polyploids associated with their lower 1Cx-values compared to diploids may suggest a genome downsizing process. Morphometric analysis revealed significant differences among cytotypes, and discriminant analysis identified three morphometric groupings corresponding to the cytotypes. The phenotypic variation observed in pollen grains, bulbs, and ovary characters suggested the gigas effect. Concluding, remarkable differentiation was observed at both genomic and phenotypic characters in all the cytotypes analyzed, suggesting a possible ongoing speciation process in H. lahue.

Cytogenetical studies of some Convolvulaceae members from the Western Ghats, India reveal uniformity in karyotypes

Karyotypes of six Ipomoea and one Merremia species were studied. Chromosome counts of 2n = 30 for I. corymbosa, I. kotschyana, I. marginata f. candida and M. rhyncorhiza) and 2n = 60 for I. ochracea were observed for the first time. Meiotic course of five Ipomoea species was also examined for the first time and two counts, i.e. n = 15 and n = 30 were recorded. Meiosis was found normal. Karyotypes of the studied species exhibited uniformity. All the species had chromosomes with median region centromeres and karyotypes were symmetrical (Stebbins’ 4A category). I. marginata f. candida had the shortest chromosomes with mean length of 0.99 ± 0.02 µm. I. ochracea and I. corymbosa had the longest chromosomes with mean length of 1.22 ± 0.05 µm and 1.22 ± 0.01 µm, respectively. As chromosomes were small and exhibited uniform morphology, fluorescent banding or fluorescent in-situ hybridization can be useful to differentiate the karyotypes and understand species interrelationships.

Mitotic metaphase karyotype of the mosquito Anopheles arabiensis Patton (Diptera: Culicidae) from Kassala State, eastern Sudan

The mosquito Anopheles arabiensis Patton is the most important malaria vector in Sudan. The study was conducted for the first time to describe numerically the karyotype of An. arabiensis from Kassala State, eastern Sudan. Adults An. arabiensis were caught from human dwellings during the rainy season of 2022. We examined for the first time the utility of brain ganglia tissues of adult mosquitoes for mitotic chromosomal preparations using Giemsa stain - spreading technique. High-quality chromosomal preparations were examined and photographed. Chromosome measurements were carried out using computer software and analyzed statistically using SPSS® software. The diploid mitotic chromosome complement of An. arabiensis consists of three pairs of chromosomes, two pairs of metacentric autosomes (chromosome II and chromosome III) and one acrocentric dot-shaped pair, sex chromosome, which is homomorphic in females (XX) and heteromorphic in males (XY). Chromosome II was described as the longest (2.61±0.07) of the complement and constitute 44.39% of the total length (5.88 μm) of the haploid chromosomes set, while chromosome I (X=1.39 ±0.04; Y=1.04±0.04) as the shortest chromosome. Chromosome X appears in the males significantly larger than chromosome Y (P = 0.00). Chromosome III has an intermediate length (1.88±0.06) compared with the other chromosomes. Comparison of the average lengths of the three chromosome pairs by ANOVA test revealed highly statistical significant differences between them (P < 0.00). The study establishes a strong cytogentic data, which can contribute to accurate identification of the mosquito An. arabiensis and to planning human malaria vector control programs in Kassala State, eastern Sudan.

Oligonucleotide skews enable comprehensive and insightful characterization of GC- and TA-skew properties observed throughout the human genome with support of unsupervised AI with reference to gene- and Alu-polarity skews

GC and TA skew are fundamental genomic features observed widely from bacteria to humans. They have been described as replication- and transcription-coupled skews because they are mainly caused by differences in mutation and repair biases between complementary DNA strands in replication and transcription processes. The skews are clearly observed in bacteria, plants and birds, but are more difficult to accurately identify in mammals, including humans. The main reason for this difficulty is that the correlation between GC and TA skew is not high for their variation in the mammalian genomes. In this study, we focused not only on these mononucleotide skews but also on di- and trinucleotide skews, first in 100-kb sequences of two short human chromosomes (chr21 and 22), and by using the conventional distribution map analysis, we clearly observed these skews over these chromosomes, except for centromeric heterochromatin regions where diverse repetitive sequences are densely clustered. Then, by using a batch learning self-organizing map (BLSOM), which can display large amounts of sequence data at once, we detected the oligonucleotide skews across nearly the entire human genome. Next, to understand skews within centromeric heterochromatin regions, we focused on Alu sequences ubiquitously distributed in the human genome and analyzed mono-, di-, and trinucleotide skews by referring to the polarity of Alu sequences. Since this polarity is unevenly distributed in the human genome, a clear TA skew was observed by reflecting the evident A-richness to T of Alu elements. However, due to some degree of their G-richness to C, TA and GC skews showed inversely correlated variations, when analyzing Alu sequences alone. Notably, when we analyzed genome sequences after excluding Alu sequences, the concordant correlation between GC- and TA-skew variations increased, indicating that a large amount of Alu sequences has made the detection of these mononucleotide skews in the human genome more difficult than in other organisms. Analysis of oligonucleotide skews using BLSOM is thought to be suitable for characterizing sequence features in skew transition regions.

Major histocompatibility complex complement (MHC) Bf alleles show trans species evolution between man and chimpanzee

HLA and disease studies by using single allele statistics have been fruitless during the last 40 years for explaining association pathogenesis of the associated diseases.Other approaches are necessary to untangle this puzzle. We aim to revisit complement alleleism in humans and primates for both studying MHC and disease association to complotypes and extended MHC haplotypes in order to also explain the positive directional selection of maintaining immune response genes (complement, MHC adaptive and MHC non-specific genes) that keeps these three type of genes together in a short chromosome stretch (MHC) for million years. These genes may be linked to conjointly avoid microbes attack and autoimmunity. In the present paper, it is obtained a new Bf chimpanzee allele, provisionaly named Patr-Bf*A:01,that differs from other Bf alleles by having CTG at eleventh codon of exon 2 in order to start the newly suggested methodology and explain functional and evolutionary MHC obscure aspects. Exons 1 to 6 of Ba fragment of Bf gene were obtained from chimpanzee. This new chimpanzee Factor B allele (Patr-Bf*A:01) is to be identical to a infrequent human Bf allele (SNP rs641153); it stresses the strong evolutive pressure upon certain alleles that are trans specific. It also may apply to MHC extended haplotipes which may conjointly act to start an adequate immune response. It is the first time that a complement MHC class III allele is described to undergo trans species evolution,in contrast to class I and class II alleles which had already been reported . Allelism of complement factors are again proposed for studying MHC complement genes, complotypes, and extended MHC haplotypes which may be more informative that single MHC marker studies.

Incidence and frequency of desynapsis in Eremurus persicus (Jaub. & Spach) Boiss.(Asphodelaceae) – A native and important medicinal plant species of Western Himalaya

Eremurus persicus (Jaub. & Spach) Boiss. (Asphodelaceae); a little known species of genus Eremurus grows in arid and semi-arid regions, on rocky mountains in Central Asia and Middle East. The species is native and an important medicinal plant used to treat various diseases. In the current study, we examined male meiosis, karyotypic variability, pollen viability and reproductive output of three populations of the target species. All the studied populations have diploid chromosome count of 2n = 2x =14. Meiotic course in majority of the pollen mother cells (PMCs) in all the three populations is not normal due to the presence of desynapsis at diplotene and metaphase-I. Instead of 7IIs most of the PMCs examined reveal varying number of bivalents and univalents. Anaphasic segregation is also affected in few PMCs. Present study also revealed that the species has asymmetric karyotype of 10 long and 4 short chromosomes. Species exhibits fruit abortion that results in extremely low fruit/seed set. The meiotic abnormalities and low fruit/seed set may be attributed to restricted distribution of this important plant species. Present study may prove helpful in devising the conservation and management strategies for this prized plant species.

Karyomorphological Study in <i>Ledebouria botryoides</i> (Asparagaceae)

Cytogenetical studies were conducted on Ledebouria botryoides. We reported 2n=60 (15m+10sm+5st) chromosomes. The karyotype was asymmetrical and fell into the 4B category of Stebbins’ asymmetry classes. Two groups of chromosomes were observed, i.e. 15 pairs of long chromosomes (2.82–6.65 µm) and 15 pairs of short chromosomes (1.67–2.80 µm). Two chromosome pairs had a satellite on the short arms. The meiotic course was found to be normal with n=30 bivalents.

Whole-genome doubling drives oncogenic loss of chromatin segregation

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies1–8. However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here we show that in p53-deficient cells, WGD induces loss of chromatin segregation (LCS). This event is characterized by reduced segregation between short and long chromosomes, A and B subcompartments and adjacent chromatin domains. LCS is driven by the downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primes genomic regions for subcompartment repositioning in WGD cells. This results in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Notably, subcompartment repositioning events were largely independent of chromosomal alterations, which indicates that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, which suggests that chromatin evolution is a hallmark of WGD-driven cancer.

Interrelated effects of chromosome size, mechanics, number, location-orientation and polar ejection force on the spindle accuracy: a 3D computational study.

The search-and-capture model of spindle assembly has been a guiding principle for understanding prometaphase for decades. The computational model presented allows one to address two questions: how rapidly the microtubule-kinetochore connections are made, and how accurate these connections are. In most previous numerical simulations, the model geometry was drastically simplified. Using the CellDynaMo computational platform, we previously introduced a geometrically and mechanically realistic 3D model of the prometaphase mitotic spindle, and used it to evaluate thermal noise and microtubule kinetics effects on the capture of a single chromosome. Here, we systematically investigate how geometry and mechanics affect a spindle assembly's speed and accuracy, including nuanced distinctions between merotelic, mero-amphitelic, and mero-syntelic chromosomes. We find that softening of the centromere spring improves accuracy for short chromosome arms, but accuracy disappears for long chromosome arms. Initial proximity of chromosomes to one spindle pole makes assembly accuracy worse, while initial chromosome orientation matters less. Chromokinesins, added onto flexible chromosome arms, allow modeling of the polar ejection force, improving a spindle assembly's accuracy for a single chromosome. However, spindle space crowding by multiple chromosomes worsens assembly accuracy. Our simulations suggest that the complex microtubule network of the early spindle is key to rapid and accurate assembly.

Chromosome size affects alignment efficiency in mammalian mitosis.

The kinetochore connects chromosomes to spindle microtubules during cell division. Accurate chromosome segregation requires sister kinetochores to biorient, attaching to opposite spindle poles. To achieve biorientation, the kinetochore destabilizes incorrect attachments and stabilizes correct ones. How it discriminates correct from incorrect attachments is not clear. Here, we test the model that tension serves as the stabilizing cue at correct attachments and how that model affects chromosomes of different sizes. Live imaging of mitotic PtK2 cells reveals long chromosomes align at the metaphase plate more slowly than short chromosomes. Using laser ablation to shorten long chromosome arms—reducing polar ejection forces on them—we show that chromosomes align faster after ablation, indicating chromosome size affects alignment efficiency. Finally, artificially enriching for incorrect attachments using STLC washouts and imaging error correction live, we show that long chromosomes exhibit a delay in correcting errors, rather than simply in attachment formation. We propose a model where increased polar ejection forces on long chromosomes stabilize not only correct but also incorrect attachments, delaying their biorientation and alignment. As such, long chromosomes may experience more challenges correcting errors and, as a result, higher missegregation rates.

Apomixis for no bacteria-induced thelytoky in Diglyphus wani (Hymenoptera: Eulophidae).

In Hymenoptera species, the reproductive mode is usually arrhenotoky, where haploid males arise from unfertilized eggs and diploid females from fertilized eggs. In addition, a few species reproduce by thelytoky, where diploid females arise from unfertilized eggs. Diploid females can be derived through various cytological mechanisms in thelytokous Hymenoptera species. Hitherto, these mechanisms were revealed mainly in endosymbiont-induced thelytokous Hymenoptera species. In contrast, thelytokous Hymenoptera species in which a reproductive manipulator has not been verified or several common endosymbionts have been excluded were paid less attention in their cytological mechanisms, for instance, Diglyphus wani (Hymenoptera: Eulophidae). Here, we investigated the cytological mechanism of D. wani using cytological methods and genetic markers. Our observations indicated that the diploid karyotypes of two strains of D. wani consist of four pairs of relatively large metacentric chromosomes and one pair of short submetacentric chromosomes (2n = 10). The arrhenotokous strains could complete normal meiosis, whereas the thelytokous strain lacked meiosis and did not expulse any polar bodies. This reproductive type of lacking meiosis is classified as apomictic thelytoky. Moreover, a total of 636 microsatellite sequences were obtained from thelytokous D. wani, dominated by dinucleotide repeats. Genetic markers results showed all three generations of offspring from thelytokous strain maintained the same genotype as their parents. Our results revealed that D. wani is the first eulophid parasitoid wasp in Hymenoptera whose thelytoky was not induced by bacteria to form an apomictic thelytoky. These findings provide a baseline for future inner molecular genetic studies of ameiotic thelytoky.

EDEM2 is a diagnostic and prognostic biomarker and associated with immune infiltration in glioma: A comprehensive analysis.

Glioma is a highly common pathological brain tumor. Misfolded protein response, which is strongly associated with the growth of cancerous tumors, is mediated by the gene, endoplasmic reticulum degradation-enhancing alpha-mannosidase-like protein 2. However, this gene has not been linked to glioma. To assess the same, we used The Cancer Genome Atlas, Chinese Glioma Genome Atlas, and Genotype-Tissue Expression datasets. The gene was overexpressed in gliomas. This overexpression was linked to unfavorable clinical characteristics, such as the World Health Organization grade, isocitrate dehydrogenase mutation, and the combined loss of the short arm chromosome 1 and the long arm of chromosome 19. Quantitative polymerase chain reaction experiments and immunohistochemistry on clinical samples from our institution verified the gene's expression and clinical importance. The Human Protein Atlas website verified the messenger ribonucleic acid expression of the gene in glioma cell lines, and immunohistochemistry verified the presence of its protein. A previous survival study indicated that its high expression is substantially related to a bad prognosis. It was identified as an independent predictor of primary glioma prognosis using multivariate Cox regression analysis. To forecast individual survival, we created a nomogram based on this (concordance-index = 0.847). Additionally, functional annotation demonstrated its major role in the control of the extracellular matrix and immune system. The scratch assay and transwell migration assay confirmed the decreased invasive ability of U251 glioma cells with the gene knockdown. Its increased expression was found to be related to the extent of macrophage infiltration using the CIBERSORT, ESTIMATE, Single-sample Gene Set Enrichment Analysis, and Tumor Immune Single-Cell Hub (TISCH) algorithms. The Tumor Immune Dysfunction and Exclusion algorithm revealed that the gene can accurately predict the response of immunotherapy (area under the receiver operating characteristic curve = 0.857). Further, isocitrate dehydrogenase 1 mutation is typically more frequent when the gene expression is high. Finally, five medicines targeting this gene were discovered utilizing the molecular docking program and drug sensitivity analysis of the RNAactDrug website. Low expression of the gene inhibited glioma cell invasion. Therefore, the gene is helpful for the diagnosis, prognosis, and case-specific immunotherapy of glioma.

Capture Hi-C reveals the influence on dynamic three-dimensional chromosome organization perturbed by genetic variation or vanillin stress in Saccharomyces cerevisiae.

Studying the mechanisms of resistance to vanillin in microorganisms, which is derived from lignin and blocks a major pathway of DNA double-strand break repair in yeast, will benefit the design of robust cell factories that produce biofuels and chemicals using lignocellulosic materials. A high vanillin-tolerant Saccharomyces cerevisiae strain EMV-8 carrying site mutations compared to its parent strain NAN-27 was selected for the analyses. The dynamics of the chromatin structure of eukaryotic cells play a critical role in transcription and the regulation of gene expression and thus the phenotype. Consequently, Hi-C and transcriptome analyses were conducted in EMV-8 and NAN-27 in the log phase with or without vanillin stress to determine the effects of mutations and vanillin disturbance on the dynamics of three-dimensional chromosome organization and the influence of the organization on the transcriptome. The outcomes indicated that the chromosome interaction pattern disturbed by vanillin stress or genetic mutations in the log phase was similar to that in mouse cells. The short chromosomes contact the short chromosomes, and the long chromosomes contact the long chromosomes. In response to vanillin stress, the boundaries of the topologically associating domain (TAD) in the vanillin-tolerant strain EMV-8 were more stable than those in its parent strain NAN-27. The motifs of SFL1, STB3, and NHP6A/B were enriched at TAD boundaries in both EMV-8 and NAN-27 with or without vanillin, indicating that these four genes were probably related to TAD formation. The Indel mutation of YRR1, whose absence was confirmed to benefit vanillin tolerance in EMV-8, caused two new interaction sites that contained three genes, WTM2, PUP1, and ALE1, whose overexpression did not affect vanillin resistance in yeast. Overall, our results revealed that in the log phase, genetic mutations and vanillin disturbance have a negligible effect on three-dimensional chromosome organization, and the reformation or disappearance of TAD boundaries did not show an association with gene expression, which provides an example for studying yeast chromatin structure during stress tolerance using Hi-C technology.

Cytogenetics and Crop Improvement Studies in Pigeonpea [Cajanus cajan (L.) Millsp.]: A Review

Pigeonpea has 2n= 2x= 22 chromosomes with length ranging from 5.73±1.15 μm to 10.92±2.69 μm. The largest long arm of chromosome pair (q) was 6.22±1.05 μm, while the shortest measured 3.37±0.83 μm. The longest short arm chromosome pair was 4.70±1.65 μm, while the shortest measured 2.37±0.43 μm. Metacentric and submetacentric chromosomal shapes exist in pigeonpea, but metacentric dominating. Pigeonpea’s karyotypic formula is 2n= 2x= 9m+2 sm. In pigeonpea, regardless of maturity groups, the main and foremost goal is to breed for higher yield/area/time. Resistance to diseases including wilt, sterility mosaic, phytophthora and alternaria blights, as well as insect pests like pod borers and pod flies, is being bred for. Resistance to abiotic stresses like drought tolerance can be achieved by osmotic adjustment (OA), dehydration tolerance and relative water content (RWC). Reduced Na and Cl translocation from root to stem, osmoprotectants and the optimal leaf area index (LAI) for salinity tolerance. Many outstanding varieties has been developed in pigeonpea through germplasm selection, pedigree breeding, mutation breeding and Heterosis breeding.

The genome sequence of the scarce swallowtail, Iphiclides podalirius.

The scarce swallowtail, Iphiclides podalirius (Linnaeus, 1758), is a species of butterfly in the family Papilionidae. Here, we present a chromosome-level genome assembly for Iphiclides podalirius as well as gene and transposable element annotations. We investigate how the density of genomic features differs between the 30 Iphiclides podalirius chromosomes. We find that shorter chromosomes have higher heterozygosity at four-fold-degenerate sites and a greater density of transposable elements. While the first result is an expected consequence of differences in recombination rate, the second suggests a counter-intuitive relationship between recombination and transposable element evolution. This high-quality genome assembly, the first for any species in the tribe Leptocircini, will be a valuable resource for population genomics in the genus Iphiclides and comparative genomics more generally.