Sequencing Of Fragments Research Articles

Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA.

Grain number per spike, a pivotal agronomic trait dictating wheat yield, lacks a comprehensive understanding of its underlying mechanism in Pubing3228, despite the identification of certain pertinent genes. Thus, our investigation sought to ascertain molecular markers and candidate regions associated with grain number per spike through a high-density genetic mapping approach that amalgamates site-specific amplified fragment sequencing (SLAF-seq) and bulked segregation analysis (BSA). To facilitate this, we conducted a comparative analysis of two wheat germplasms, Pubing3228 and Jing4839, known to exhibit marked discrepancies in spike shape. By leveraging this methodology, we successfully procured 2,810,474 SLAF tags, subsequently resulting in the identification of 187,489 single nucleotide polymorphisms (SNPs) between the parental strains. We subsequently employed the SNP-index association algorithm alongside the extended distribution (ED) association algorithm to detect regions associated with the trait. The former algorithm identified 24 trait-associated regions, whereas the latter yielded 70. Remarkably, the intersection of these two algorithms led to the identification of 25 trait-associated regions. Amongst these regions, we identified 399 annotated genes, including three genes harboring non-synonymous mutant SNP loci. Notably, the APETALA2 (AP2) transcription factor families, which exhibited a strong correlation with spike type, were also annotated. Given these findings, it is plausible to hypothesize that these genes play a critical role in determining spike shape. In summation, our study contributes significant insights into the genetic foundation of grain number per spike. The molecular markers and candidate regions we have identified can be readily employed for marker-assisted breeding endeavors, ultimately leading to the development of novel wheat cultivars possessing enhanced yield potential. Furthermore, conducting further functional analyses on the identified genes will undoubtedly facilitate a comprehensive elucidation of the underlying mechanisms governing spike development in wheat.

Development and application of a geothermal bio-tracer resistant to extreme environments

Tracers are key to acquiring data on fluid transport behavior and hydrological parameters. In particular, in the harnessing of geothermal energy, it is used to determine the connections between production and injection wells, the hydrological parameters of geothermal reservoirs, and the efficiency of thermal recovery. Traditional tracers are expensive and may pollute the environment. In response to these challenges, we developed a composite bio-tracer that is thermally stable, environmentally friendly, easy to detect, inexpensive to produce, and suitable for environments with temperatures more than 120 °C.The composition of our composite bio-tracer includes a specific artificial DNA (Synthetic hybrid-DNA sequence fragments are implanted into the plasmid) that serves as the tracer label, a label-immobilized carrier and is encapsulation in a protective shell. The overall particle size can be controlled average of about 52 nm, enabling migration along the main channels of the reservoir through fluid flow. Laboratory verification indicated that the bio-tracer remains detectable for more than 30 days in extreme environments (geothermal water environments with temperatures of 120 °C and pH ranging from 1.5 to 13.0). The developed composite bio-tracer has been put into actual geothermal site testing and verification, and after 28 days of on-site testing, the tracer recovery reached 83.1 %.

First Report of Erysiphe astragali Causing Powdery Mildew on Astragalus mongholicus in China.

Astragalus mongholicus Bge. [A. membranaceus Bge. var. mongholicus (Bge.) Hsiao] is a highly valuable perennial medicinal plant mainly distributed in China, whose dry roots are known as Huangqi in traditional Chinese medicine for reinforcing vital energy, strengthening superficial resistance, and promoting tissue regeneration (Lin et al. 2000). A. mongholicus roots of high quality are produced in Northwest and North China. Since July 2021, powdery mildew outbreaks happened annually on the leaves of A. mongholicus in a plantation (123° 56' 40'' E, 47° 22' 20'' N) in Qiqihar city, Heilongjiang Province, China. Disease incidence reached 100% by October (Fig. 1A-C), causing severe impairment of growth. Powdery mildew spots of circular or irregular shapes emerged on upper surface of leaf, resulting in plentiful lesion specks. Dense white hyphae appeared chaotically intertwined. Hyphae were hyaline and highly flexuous, 5.3 - 10.7 μm in diameter (n = 20). Chasmothecia were globose or slightly ovoid-shaped and turned dark brown when matured. Chasmothecia (diameter: 135.2 - 222.9 μm, n = 20) existed abundantly on the diseased leaves in the fields. Conidiophores were 89.0 - 129.9 μm in length (n = 20) and composed of one cylindrical, straight foot cell, followed by two cells and one to three conidia. Conidia were slim ellipsoid-shaped, occasionally ovoid-shaped, measuring 14.6 - 24.7 μm by 6.4 to10.4 μm, length/width ratio was 1.8 - 3.0 (n = 30). Hyphal appressoria were nipple-shaped and appeared in singular, occasionally in pairs. Unbranched germ tube emerged reaching out of the germinating conidia while forming an acute angle with the long axis. Comprehensively, the pathogen exhibited micro-morphology of the genus Erysiphe. For molecular identification, pathogen was carefully scraped off diseased leaves for DNA extraction. We used the DNA samples of three biological replicates for the sequencing of the ITS rDNA fragment (primers by (White et al. 1990). All the samples resulted in an identical ITS sequence (deposited in GenBank as OQ390098.1). It displayed 99.83% identity with OP806835.1 of an E. astragali voucher collected in Iran (Fig. 1D-M, O). Hence, our pathogen was identified as an E. astragali stain. Additionally, we amplified the Mcm7 sequence (using primers by (Ellingham et al. 2019), deposited as OQ397582.1). We propagated 40-day-old A. mongholicus plants via germinating seeds in pot soil and performed pathogenicity tests. Firstly, we incubated detached healthy leaves of propagated plants with severely symptomatic leaves collected from the fields in petri dishes under saturated moisture content and room temperature. Powdery mildew symptoms emerged on each healthy leaf (n = 5) after two weeks. Further, we infected healthy plants (n = 5) by gently pressing and rubbing symptomatic leaves on each healthy leaf, and kept them in a greenhouse (24 ℃, 80% humidity, 16/8-hour light/dark cycle). After a month, symptoms emerged on a number of leaves of each infected plant. We performed micromorphology observation (Fig. 1N-P) and ITS sequencing to confirm that the results fulfilled Koch's postulates. Powdery mildew caused by E. astragali on A. strictus in Tibet (Wang and Jiang 2023) and on A. scaberrimus in Inner Mongolia (Sun et al. 2023) have been reported. Here we report powdery mildew caused by E. astragali on Astragalus mongholicus for the first time. These Astragalus spp. are all acknowledged to have medicinal values in China but their usages are quite different.

Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities.

The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.

Structural insights into a functional unit from an immunogenic mollusk hemocyanin

Mollusk hemocyanins, among the largest known proteins, are used as immunostimulants in biomedical and clinical applications. The hemocyanin of the Chilean gastropod Concholepas concholepas (CCH) exhibits unique properties, which makes it safe and effective for human immunotherapy, as observed in animal models of bladder cancer and melanoma, and dendritical cell vaccine trials. Despite its potential, the structure and amino acid sequence of CCH remain unknown. This study reports two sequence fragments of CCH, representing three complete functional units (FUs). We also determined the high-resolution (1.5Å) X-ray crystal structure of an "FU-g type" from the CCHB subunit. This structure enables in-depth analysis of chemical interactions at the copper-binding center and unveils an unusual, truncated N-glycosylation pattern. These features are linked to eliciting more robust immunological responses in animals, offering insights into CCH's enhanced immunostimulatory properties and opening new avenues for its potential applications in biomedical research and therapies.

First Report of Dickeya dadantii Causing Soft Rot in Cariru in Brazil.

Cariru (Talinum fruticosum) is a non-conventional food plant and a source of vitamins A, B2, B5, and C, calcium, phosphorus, and iron. It is an important crop for producers of the Amazon region and it is used as a leafy green vegetable, similar to spinach, as well as for medicinal purposes. It is cultivated by producers in the states of Pará and Amazonas (Amorim et al. 2014). In February 2020, in gardens of approximately 1.0 and 0.18 ha in the municipality of Ananindeua (01° 34' 12" S - 48° 38' 11" W), Pará, Brazil, we observed approximately 10% of the plants exhibited soft rot symptoms, bacterial oozing, and stem pith disintegration. From cariru infected leaves, the bacteria were selectively isolated using healthy pepper fruit, as described by Moraes et al. (2017). Two strain (UFRADD17 and UFRADD18) were obtained and both showed white, small, "broken glass" colonies on CPG (peptone-casamino acid-glucose) medium when observed in a stereoscope under oblique lighting. Pathogenicity tests were performed on 20-day-old cariru seedlings by depositing 10 ul of the bacterial suspension (106 CFU/ml) onto a wound made on the leaf blade with an entomological pin. After inoculation, seedlings were incubated in a greenhouse for 48 h at 30 ± 2°C and 90 ± 2% RH. Plants treated similarly with sterile distilled water were used as a negative control. Symptoms of soft rot were observed between 12 and 24 h after inoculation. Seedlings used as negative control remained symptomless. Forty-eight hours after inoculation, we reisolated the pathogen and performed rep-PCR (REP, ERIC, and BOX-PCR) analyses (Gama et al. 2018) with the strains used for inoculation and those reisolated from the pathogenicity test to confirm the identity of the strains and to fulfill Koch's postulates. The two re-isolated strains showed the same REP, ERIC, and BOX-PCR profiles as the strains used for inoculation. In addition, there were no differences between the rep-PCR profiles of the isolates UFRADD17 and UFRADD18. These isolates were Gram-negative, grew at 37°C, and were positive for maceration in pepper fruit and potato tubers. Molecular identification of the isolate UFRADD18 was performed from sequencing fragments from the 16S rDNA region and dnaX, fusA, gyrA, and mdH housekeeping genes as previously described (Van der Wolf et al. 2014; Ma et al. 2007). Sequences were deposited in Genbank under accessions OP142347, OP191704, OP191705, OP191706, and OP191707. Blastn analysis showed 96.15% identity with the 16S rDNA region of accession KY231142.1 (400/416 bp), 99.5% identity with dnaX of accession KC844490.1 (396/398 bp), 99.86% identity with fusA of accession CP023467.1 (714/715 bp), 99.74% identity with gyrA of accession KC844598 (387/388 bp), and 99.10% identity with mdH of accession GQ891979.1 (563/560 bp) from the type strain of Dickeya dadantii. A phylogenetic analysis performed by Bayesian inference with the dnaX, fusA, gyrA, and mdH genes grouped the isolate UFRADD18 along with NCPPB898T, with a 1.00 posterior probability. To our knowledge, this is the first report of D. dadantii causing soft rot in cariru in the Brazilian territory. In addition, this report increases understanding of the host range of this bacterium, which is important for adopting management strategies based on the control of alternative hosts.

Soil Microbiome of Abandoned Plaggic Podzol of Different-Aged Fallow Lands and Native Podzol in South Taiga (Leningrad Region)

The soil microbiome is composed of various communities that play an important role in the existence of ecosystem services and the sustainable functioning of ecosystems under high anthropogenic loads. The transition of soils to a fallow state and their subsequent transformation lead to a notable alteration in the taxonomic composition of the soil microbiome, impacting the biochemical processes within the soil and its fertility levels. The object of this study comprised different-aged fallow soils of the southern taiga in the vicinity of Ban’kovo village, Leningrad region. The method comprising the high-throughput sequencing of 16S rRNA gene fragments using an Illumina MiSEQ sequencer was used to analyze the microbial community. The general processing of sequences was carried out with the dada2 (v1.14.1) package. It was found that the morphological organization of fallow soils has significant differences from the native podzol. In fallow soils, there are signs of leaching expressed in the accumulation of leached mineral particles, which indicates the degradation of the fallow–arable horizon. At the same time, there is a decrease in the content of P2O5 and K2O and an increase in the content of N-NH4 and N-NO3 in fallow soil. The analysis of alpha diversity index values showed that the highest level of alpha diversity in the microbial community is characteristic of 40-year-old soil, the alpha diversity index decreased with the increasing time of the fallow state, and the lowest alpha diversity index was observed in the native podzol. According to the values of the beta diversity index, a high correlation between the soil microbiome and the physicochemical characteristics of the soil was revealed, which indicates the formation of functional specialization in the studied microbial communities. As a result of the study of the taxonomic composition of microbial communities in fallow soils, it was found that the most represented microbial communities in fallow soils belong to Nitrosomonadaceae (Pseudomonadota), Mycobacterium (Actinobacteria), Nitrospira (Nitrospirota), and Luteolibacter (Verrucomicrobiota). The duration of post-agrogenic transformation is the leading factor influencing the changes in microbial communities; so, with an increase in the time that soils were in a fallow state, an increase in the oligotrophic microbial community was observed.

Genomic structure analysis and construction of DNA fingerprint for four sheep populations

The Yongdeng Qishan sheep (QS) is a sheep population found locally in China. To gain in-depth knowledge of its population characteristics, three control groups were chosen, comprising the Lanzhou fat-tailed sheep (LFT), TAN sheep (TAN), and Minxian black fur sheep (MBF), inhabiting the nearby environments. This study genotyped a total of 120 individuals from four sheep populations: QS, LFT, TAN, and MBF. Using Specific-Locus Amplified Fragment Sequencing, we conducted genetic diversity, population structure, and selective sweep analysis, and constructed the fingerprint of each population. In total, there were 782 535 single nucleotide polymorphism (SNP) variations identified, with most being situated within regions that are intergenic or intronic. The genetic diversity analysis revealed that the QS population exhibited lower genetic diversity compared to the other three populations. Consistent results were obtained from the principal component, phylogenetic tree, and population structure analysis, indicating significant genetic differences between QS and the other three populations. However, a certain degree of differentiation was observed within the QS population. The linkage disequilibrium (LD) patterns among the four populations showed clear distinctions, with the QS group demonstrating the most rapid LD decline. Kinship analysis supported the findings of population structure, dividing the 90 QS individuals into two subgroups consisting of 23 and 67 individuals. Selective sweep analysis identified a range of genes associated with reproduction, immunity, and adaptation to high-altitude hypoxia. These genes hold potential as candidate genes for marker-assisted selection breeding. Additionally, a total of 86 523 runs of homozygosity (ROHs) were detected, showing non-uniform distribution across chromosomes, with chromosome 1 having the highest coverage percentage and chromosome 26 the lowest. In the high-frequency ROH islands, 79 candidate genes were associated with biological processes such as reproduction and fat digestion and absorption. Furthermore, a DNA fingerprint was constructed for the four populations using 349 highly polymorphic SNPs. In summary, our research delves into the genetic diversity and population structure of QS population. The construction of DNA fingerprint profiles for each population can provide valuable references for the identification of sheep breeds both domestically and internationally.

Endophytic Alternaria and Fusarium species associated to potato plants (Solanum tuberosum L.) in Iran and their capability to produce regulated and emerging mycotoxins

Endophytic fungi live inside virtually every plant species, without causing any apparent disease or damage to the host. Nevertheless, under particular conditions, mutualistic lifestyle of endophytes may change to pathogenic. In this study, the biodiversity of Alternaria and Fusarium species, the two most abundant endophytic fungi isolated from healthy potato plants in two climatically different regions of Iran, Ardebil in the north-west and Kerman in the south-east, was investigated. Seventy-five Fusarium strains and 83 Alternaria strains were molecularly characterized by multi-locus gene sequencing. Alternaria strains were characterized by the sequences of gpd and caM gene fragments and the phylogenetic tree was resolved in 3 well-separated clades. Seventy-three strains were included in the clade A, referred as Alternaria section, 6 strains were included in clade B, referred as Ulocladioides section, and 4 strains were included in clade C, referred as Infectoriae section. Fusarium strains, identified by sequencing the translation elongation factor 1α (tef1), β-tubulin (tub2) and internal transcribed spacer (ITS) genomic regions, were assigned to 13 species, viz. F. brachygibosum, F. clavum, F. equiseti, F. flocciferum, F. incarnatum, F. nirenbergiae, F. nygamai, F. oxysporum, F. proliferatum, F. redolens, F. sambucinum, F. solani and F. thapsinum. Twenty-six selected strains, representative of F. equiseti, F. nirenbergiae, F. oxysporum, F. nygamai, F. proliferatum, and F. sambucinum, were also tested for production of the mycotoxins deoxynivalenol (DON), nivalenol (NIV), diacetoxyscirpenol (DAS), T-2 toxin (T-2), beauvericin (BEA), enniatins (ENNs), fumonisins (FBs), fusaric acid (FA) and moniliformin (MON). None of the tested strains produced trichothecene toxins (DON, NIV, DAS and T-2). Two out of 2 F. equiseti isolates, 1/6 F. oxysporum, 1/3 F. proliferatum, and 1/9 F. nygamai did not produce any of the tested toxins; the rest of strains produced one or more BEA, ENNs, FBs, FA and MON toxins. The most toxigenic strain, F. nygamai ITEM-19012, produced the highest quantities of FBs (7946, 4693 and 4333 μg/g of B1, B2, and B3 respectively), along with the highest quantities of both BEA (4190 μg/g) and MON (538 μg/g). These findings suggest that contamination of potato tubers with mycotoxins in the field or at post-harvest, due to a change in lifestyle of endophytic microflora, should be carefully considered and furtherly investigated.

Validation and Analysis of COIL, a Gene Associated with Multiple Lambing Traits in Sheep.

In a past study, the team used specific-locus amplified fragment sequencing (SLAF sequencing) to detect single-nucleotide polymorphisms (SNPs) contributing to the differences in lambing numbers in Xinjiang sheep. This study verified the correlation between the COIL gene and lambing number characters in sheep and explored its possible mechanism of action. In this study, three SNPs in the COIL gene, namely COILSNP1 (rs7321466), COILSNP2 (rs7314134), and COILSNP3 (rs7321563), were explored in terms of their possible mechanism of action. A tissue expression profiling analysis revealed that the COIL gene was significantly more expressed in the uterus and ovaries than in other tissues (p < 0.05), whereas an association analysis revealed that the number of lambs born was significantly different among individuals with different genotypes of this COILSNP1 (p < 0.05). The Cell Counting Kit-8(CCK-8) revealed that the overexpression of the COIL gene significantly increased the proliferation of mouse ovarian fibroblasts and sheep fibroblasts (p < 0.05). The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) revealed that the overexpression of the COIL gene significantly increased the activity of sheep fibroblasts (p < 0.01) and mouse ovarian fibroblasts (p < 0.05). The overexpression of the COIL gene affected the biogenesis pathway of spliceosomal U snRNPs by validating protein network connections. This activity affects ovulation, embryonic development, and changes in lambing size in sheep.

The perfect storm: Cutaneous leishmaniasis in troops deployed in the Atlantic forest of Argentina.

American cutaneous leishmaniasis (ACL) is the most prevalent form of leishmaniasis, associated with an ulcerative and stigmatizing mucocutaneous pathology. This study assessed the incidence of Leishmania (Viannia) braziliensis in members of the Argentine Army who were exposed to sandfly bites in Iguazú National Park (INP), northeastern Argentina, during an outbreak of ACL in 2019, and the presence of Leishmania in rodents, opossums and phlebotomine sandflies collected in the area of exposure. Samples from military personnel, wild animals and phlebotomine sandflies were analysed. A total of 20 (40%) patients among the Army personnel and two Akodon montensis rodents (11%) were positive for the presence of Leishmania sp. genes by PCR, while Nyssomyia whitmani and Migonemyia migonei, competent vectors of Leishmania, were also found at the same site. Sequences of hsp70 DNA fragments obtained from human samples confirmed the identity of L. (V.) braziliensis. The risk to which military personnel carrying out activities in the forest are exposed is highlighted, and this risk extends to any worker and visitor who circulates without protection in the INP, coming into contact with transmission "hot spots" due to the concentration of vectors, reservoirs and/or parasites.

Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing.

Biofoundries are automated high-throughput facilities specializing in the design, construction, and testing of engineered/synthetic DNA constructs (plasmids), often from genetic parts. A critical step of this process is assessing the fidelity of the assembled DNA construct to the desired design. Current methods utilized for this purpose are restriction digest or PCR followed by fragment analysis and sequencing. The Edinburgh Genome Foundry (EGF) has recently established a single-molecule sequencing quality control step using the Oxford Nanopore sequencing technology, along with a companion Nextflow pipeline and a Python package, to perform in-depth analysis and generate a detailed report. Our software enables researchers working with plasmids, including biofoundry scientists, to rapidly analyze and interpret sequencing data. In conclusion, we have created a laboratory and software protocol that validates assembled, cloned, or edited plasmids, using Nanopore long-reads, which can serve as a useful resource for the genetics, synthetic biology, and sequencing communities.

A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize (Zea mays L.).

The leaf scorching trait at flowering is a crucial thermosensitive phenotype in maize under high temperature stress (HS), yet the genetic basis of this trait remains poorly understood. In this study, we genotyped a 254 RIL-F2:8 population, derived from the leaf scorch-free parental inbred line Abe2 and the leaf scorching maternal inbred line B73, using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 10,112 polymorphic SLAF markers were developed, and a high-density genetic map with a total length of 1,475.88 cM was constructed. The average sequencing depth of the parents was 55.23X, and that of the progeny was 12.53X. Then, we identified a total of 16 QTLs associated with thermotolerant traits at flowering, of which four QTLs of leaf scorching damage (LS) were distributed on chromosomes 1 (qLS1), 2 (qLS2.1, qLS2.2) and 3 (qLS3), which could explain 19.73% of phenotypic variation. Combining one qLS1 locus with QTL-seq results led to the identification of 6 candidate genes. Expression experiments and sequence variation indicated that Zm00001d033328, encoding N-acetyl-gamma-glutamyl-phosphate reductase, was the most likely candidate gene controlling thermotolerant traits at flowering. In summary, the high-density genetic map and genetic basis of thermotolerant traits lay a critical foundation for mapping other complex traits and identifying the genes associated with thermotolerant traits in maize.

Detailed investigation of the binding abilities of the heterodomain of a multiHis cyclopeptide toward Cu(II) ions.

Cyclopeptides hold significant relevance in various fields of science and medicine, due to their unique structural properties and diverse biological activities. Cyclic peptides, characterized by intrinsically higher conformational order, exhibit remarkable stability and resistance to proteolytic degradation, making them attractive candidates for developing targeted drug delivery systems. The aim of this work is to elucidate the unique coordination properties of the multi-His cyclic peptide with c(HDHKHPHHKHHP) sequence (HDCP - heterodomain cyclopeptide). This peptide, indeed, is able to form homo- and hetero-dinuclear complexes in a wide pH range, being thus a good chelator for Cu(II) ions. Herein, we present the results of a combined study, involving potentiometric, spectroscopic (UV-Vis, CD, and EPR), and computational investigations, on its coordination properties. To better understand the interaction pattern with Cu(II) metal ions, two other peptides, each one bearing only one of the two binding domains of HDCP are also considered in this study: c(HDHKHPGGKGGP) = CP1, c(GKGGKPHHKHHP) = CP2, which share sequence fragments of HDCP and allow separate investigations of its coordination domains.

Mitochondrial DNA D-Loop Polymorphisms among the Galla Goats Reveals Multiple Maternal Origins with Implication on the Functional Diversity of the HSP70 Gene.

Despite much attention given to the history of goat evolution in Kenya, information on the origin, demographic history, dispersal route, and genetic diversity of Galla goats remains unclear. Here, we examined the genetic background, diversity, demographic history, and population genetic variation of Galla goats using mtDNA D-loop and HSP70 single-nucleotide polymorphism markers. The results revealed 90 segregating sites and 68 haplotypes in a 600-bp mtDNA D-loop sequence. The overall mean mitochondrial haplotype diversity was 0.993. The haplotype diversities ranged between 0.8939 ± 0.0777 and 1.0000 ± 0.0221 in all populations supporting high genetic diversity. Mitochondrial phylogenetic analysis revealed three Galla goat haplogroups (A, G, and D), supporting multiple maternal ancestries, of which haplogroup A was the most predominant. Analysis of molecular variance (AMOVA) showed considerable variation within populations at 94.39%, evidence of high genetic diversity. Bimodal mismatch distribution patterns were observed while most populations recorded negative results for Tajima and Fu's Fs neutrality tests supporting population expansion. Genetic variation among populations was also confirmed using HSP70 gene fragment sequences, where six polymorphic sites which defined 21 haplotypes were discovered. Analysis of molecular variance revealed a significant FST index value of 0.134 and a high FIS index value of 0.746, an indication of inbreeding. This information will pave the way for conservation strategies and informed breeding to improve Galla or other goat breeds for climate-smart agriculture.

The novel C268A variant of BMP2 is linked to the reproductive performance of Awassi and Hamdani sheep.

Prolificacy-associated genetic markers can be utilized to enhance litter size in the sheep breeding industry. Sheep reproduction is influenced by a multitude of genes, including bone morphogenetic protein 2 (BMP2). This study aimed to explore the potential relationship between variability in the BMP2 gene and reproductive performance in Awassi and Hamdani ewes. The genomic DNA was extracted from 99 single-progeny ewes and 101 twin ewes. Polymerase chain reaction (PCR) was employed to produce an amplicon consisting of four sequence fragments: 277bp, 251bp, 331bp, and 340bp, from exons 1, 2, 3, and 4 of the BMP2 gene, respectively. Three genotypes were identified for amplicons in exon 4 with 340-bp lengths: CC, CA, and AA. Upon analyzing the sequence of the CA genotype 382C > A, a novel mutation was discovered in this genotype. A robust association was identified between the single nucleotide polymorphisms (SNP) 382C > A and reproductive performance through statistical analysis. An important distinction was discovered between ewes carrying SNP 382C > A and those carrying CC in terms of litter sizes, twinning rates, lambing rates, and days to lambing. An analysis of logistic regression revealed a significant association between litter size and the 382C > A SNP. There was a decrease in lamb production among ewes with the CC genotype compared to those with the CA and AA genotypes. These results indicate that the SNP variant 382C > A has a positive influence on the reproductive performance of Awassi and Hamdani sheep. Sheep carrying the 382C > A SNP exhibit increased litter size and overall productivity compared to those without the SNP.

Insights into the multi-chromosomal mitochondrial genome structure of the xero-halophytic plant Haloxylon Ammodendron (C.A.Mey.) Bunge ex Fenzl

BackgroundHaloxylon ammodendron holds significance as an ecological plant, showcasing remarkable adaptability to desert conditions, halophytic environments, and sand fixation. With its potential for carbon sequestration, it emerges as a promising candidate for environmental sustainability. Furthermore, it serves as a valuable C4 plant model, offering insights into the genetic foundations of extreme drought tolerance. Despite the availability of plastid and nuclear genomes, the absence of a mitochondrial genome (mitogenome or mtDNA) hinders a comprehensive understanding of its its mtDNA structure, organization, and phylogenetic implications.ResultsIn the present study, the mitochondrial genome of H. ammodendron was assembled and annotated, resulting in a multi-chromosomal configuration with two circular chromosomes. The mtDNA measured 210,149 bp in length and contained 31 protein-coding genes, 18 tRNA and three rRNA. Our analysis identified a total of 66 simple sequence repeats along with 27 tandem repeats, 312 forward repeats, and 303 palindromic repeats were found. Notably, 17 sequence fragments displayed homology between the mtDNA and chloroplast genome (cpDNA), spanning 5233 bp, accounting for 2.49% of the total mitogenome size. Additionally, we predicted 337 RNA editing sites, all of the C-to-U conversion type. Phylogenetic inference confidently placed H. ammodendron in the Amaranthacea family and its close relative, Suaeda glacum.ConclusionsH. ammodendron mtDNA showed a multi-chromosomal structure with two fully circularized molecules. This newly characterized mtDNA represents a valuable resource for gaining insights into the basis of mtDNA structure variation within Caryophyllales and the evolution of land plants, contributing to their identification, and classification.

Evolution of the MGMT gene in primates: from structure to mobile genetic elements

The article collects data on the evolution of the reparative MGMT gene in primates and traces the evolutionary fate of a number of mobile genetic elements (MGEs). It was concluded that the evolution of the MGMT gene in primates underwent various changes from acquisition to loss of exon/intron sequences. As for primate-specific MGEs, they have a different evolutionary history and path - from the formation of species/genus-specific sequences to deletional degradation and can be components not only of intronic or exonic sequences, but also components of exons in the form of fragmented sequences and not be identified as MGEs.

Functional and structural responses of a halophilic consortium to oily sludge during biodegradation.

Biotreatment of oily sludge and the involved microbial communities, particularly in saline environments, have been rarely investigated. We enriched a halophilic bacterial consortium (OS-100) from petroleum refining oily sludge, which degraded almost 86% of the aliphatic hydrocarbon (C10-C30) fraction of the oily sludge within 7 days in the presence of 100g/L NaCl. Two halophilic hydrocarbon-degrading bacteria related to the genera Chromohalobacter and Halomonas were isolated from the OS-100 consortium. Hydrocarbon degradation by the OS-100 consortium was relatively higher compared to the isolated bacteria, indicating potential synergistic interactions among the OS-100 community members. Exclusion of FeCl2, MgCl2, CaCl2, trace elements, and vitamins from the culture medium did not significantly affect the hydrocarbon degradation efficiency of the OS-100 consortium. To the contrary, hydrocarbon biodegradation dropped from 94.1 to 54.4% and 5% when the OS-100 consortium was deprived from phosphate and nitrogen sources in the culture medium, respectively. Quantitative PCR revealed that alkB gene expression increased up to the 3rd day of incubation with 11.277-fold, consistent with the observed increments in hydrocarbon degradation. Illumina-MiSeq sequencing of 16S rRNA gene fragments revealed that the OS-100 consortium was mainly composed of the genera Halomonas, Idiomarina, Alcanivorax and Chromohalobacter. This community structure changed depending on the culturing conditions. However, remarkable changes in the community structure were not always associated with remarkable shifts in the hydrocarbonoclastic activity and vice versa. The results show that probably synergistic interactions between community members and different subpopulations of the OS-100 consortium contributed to salinity tolerance and hydrocarbon degradation.

The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time.

Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts. We reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study who experienced HIV seroconversion, and used these data to characterize the diversity, lineage origins, and ages of proviral env-gp120 sequences sampled longitudinally up to 12 years on ART. We also studied HIV sequences emerging from the reservoir in two participants. We observed that proviral clonality generally increased over time on ART, with clones frequently persisting long term. While on-ART proviral integration dates generally spanned the duration of untreated infection, HIV emerging in plasma was exclusively younger (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of the gag region in three participants corroborated our env-gp120-based observations, indicating that our observations are not influenced by the HIV region studied. Our results underscore the remarkable genetic stability of the distinct proviral sequences that persist in blood during ART. Our results also suggest that the replication-competent HIV reservoir is a genetically restricted, younger subset of this overall proviral pool.IMPORTANCECharacterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool.