Gene gain and loss from the Asian corn borer W chromosome

BACKGROUND

Sex-limited chromosomes Y and W share some characteristics, including the degeneration of protein-coding genes, enrichment of repetitive elements, and heterochromatin. However, although many studies have suggested that Y chromosomes retain genes related to male function, far less is known about W chromosomes and whether they retain genes related to female-specific function.

RESULTS

Here, we built a chromosome-level genome assembly of the Asian corn borer, Ostrinia furnacalis Guenée (Lepidoptera: Crambidae, Pyraloidea), an economically important pest in corn, from a female, including both the Z and W chromosome. Despite deep conservation of the Z chromosome across Lepidoptera, our chromosome-level W assembly reveals little conservation with available W chromosome sequence in related species or with the Z chromosome, consistent with a non-canonical origin of the W chromosome. The W chromosome has accumulated significant repetitive elements and experienced rapid gene gain from the remainder of the genome, with most genes exhibiting pseudogenization after duplication to the W. The genes that retain significant expression are largely enriched for functions in DNA recombination, the nucleosome, chromatin, and DNA binding, likely related to meiotic and mitotic processes within the female gonad.

CONCLUSIONS

Overall, our chromosome-level genome assembly supports the non-canonical origin of the W chromosome in O. furnacalis, which experienced rapid gene gain and loss, with the retention of genes related to female-specific function.

Both host and diet shape bacterial communities of predatory mites

Microbial communities, derived from food, ambient, and inner, can affect host ecological adaption and evolution. Comparing with most phytophagous arthropods, predators may have more opportunities to develop specific microbiota depending on the level of prey specialization. To explore how diet sources affect host microbial communities and vary across predator species, we considered 3 types of predators from Phytoseiidae (Acari: Mesostigmata): polyphagous (Amblyseius orientalis Ehara, Neoseiulus barkeri Hughes, and Amblyseius swirskii Athias-Henrio), oligophagous (Neoseiulus californicus McGregor), and monophagous (Phytoseiulus persimilis Athias-Henriot) predatory mites. The polyphagous species were fed on 2 types of diets, natural prey and alternative prey. By using 16S rRNA sequencing, we found that diet was the main source of microbiota in predatory mites, while there was no clear pattern affected by prey specialization. Among 3 polyphagous predators, host species had a larger impact than prey on microbial composition. Unlike A. orientalis or N. barkeri which showed consistency in their microbiota, prey switching significantly affected β-diversity of bacterial composition in A. swirskii, with 56% of the microbial alteration. In short, our results confirmed the substantial influence of diet on host microbial construction in predatory species, and highlighted species differences in shaping the microbiota which are not necessarily related to prey specialization.

Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus)

BACKGROUND

Chicken is one of the most numerous and widely distributed species around the world, and many studies support the multiple ancestral origins of domestic chickens. The research regarding the yellow skin phenotype in domestic chickens (regulated by BCO2) likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens. However, beyond the BCO2 gene region, much remains unknown about the introgression from the grey junglefowl into domestic chickens. Therefore, in this study, based on whole-genome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds, we explored the introgression events from the grey junglefowl to domestic chickens.

RESULTS

We successfully detected introgression regions besides BCO2, including two associated with growth trait (IGFBP2 and TKT), one associated with angiogenesis (TIMP3) and two members of the heat shock protein family (HSPB2 and CRYAB). Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens. Furthermore, we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds, indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained. Additionally, our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens, possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens.

CONCLUSIONS

In summary, our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens, laying the foundation for a deeper understanding of the genetic composition within domestic chickens, and offering new perspectives on the impact of introgression on domestic chickens.

Effects of Supplementing Drinking Water of Parental Pigeons with Enterococcus faecium and Bacillus subtilis on Antibody Levels and Microbiomes in Squabs

Enterococcus faecium (E. faecium) and Bacillus subtilis (B. subtilis) are widely used as probiotics to improve performance in animal production, but there have been few reports of their impacts on pigeon milk. In this study, twenty-four pairs of parental pigeons were randomly divided into four groups, with six replicates, and each pair feeding three squabs. The control group drank normal water. The E. faecium group, B. subtilis group, and mixed group drank water supplemented with 3 × 106 CFU/mL E. faecium, 2 × 107 CFU/mL B. subtilis, and a mixture of these two probiotics, respectively. The experiment lasted 19 days. The results demonstrated that the IgA and IgG levels were significantly higher in the milk of Group D pigeons than in the other groups. At the phylum level, Fimicutes, Actinobacteria, and Bacteroidetes were the three main phyla identified. At the genus level, Lactobacillus, Bifidobacterium, Veillonella, and Enterococcus were the four main genera identified. In conclusion, drinking water supplemented with E. faecium and B. subtilis could improve immunoglobulin levels in pigeon milk, and this could increase the ability of squabs to resist disease. E. faecium and B. subtilis could be used as probiotics in the pigeon industry.

Identification of miRNA Associated with Trichomonas gallinae Resistance in Pigeon (Columba livia)

Trichomonas gallinae (T. gallinae) has a great influence on the pigeon industry. Pigeons display different resistance abilities to T. gallinae, so the study of the molecular mechanism of resistance is necessary in breeding disease resistant lines. MiRNA plays important roles in the immune response, but there are still no reports of miRNA regulating trichomonosis resistance. We used small RNA sequencing technology to characterize miRNA profiles in different groups. T. gallinae was nasally inoculated in one day old squabs, and according to the infection status, the groups were divided into control (C), susceptible (S) and tolerant (T) groups. We identified 2429 miRNAs in total, including 1162 known miRNAs and 1267 new miRNAs. In a comparison among the C, S and T groups, the target genes of differentially expressed miRNAs were analyzed via GO and KEGG annotation. The results showed that the target genes were enriched in immune-response-related pathways. This indicated that the differentially expressed miRNAs had a critical influence on T. gallinae infection. Novel_miR_741, which could inhibit the expression of PRKCQ, was down-regulated in the T group compared to the C group. It was proven that a decreased novel_miR_741 expression would increase the expression of PRKCQ and increase the immune response. This study brings new insights into understanding the mechanism of trichomonosis resistance.

A high adhesion co-assembly based on myclobutanil and tannic acid for sustainable plant disease management

BACKGROUND

Pesticides are irreplaceable inputs for protecting crops from pests and improving crop yield and quality. Self-assembly nanotechnology is a promising strategy by which to develop novel nano-formulations for pesticides. Nano-formulations improve the effective utilization of pesticides and reduce risks to the environment because of their eco-friendly preparation, high drug loading, and desirable physicochemical properties. Here, to enhance the utilization efficiency of myclobutanil (MYC) and develop a novel nano-formulation, carrier-free co-assembled nanoparticles (MT NPs) based on MYC and tannic acid (TA) were prepared by noncovalent molecular interactions using a green preparation process without any additives.

RESULTS

The results showed that the prepared spherical nanoparticles had good stability in neutral and acidic aqueous solutions, low surface tension (40.53 mN m-1 ), high rainfastness, and good maximum retention values on plant leaves. Release of active ingredients from MT NPs could be regulated by altering the molar ratio of subassemblies in the co-assembly and the pH of the environment. Antifungal experiments demonstrated that MT NPs had better activities against Alternaria alternata and Fusarium graminearum [half-maximal effective concentration (EC50 ) = 6.40 and 77.08 mg/L] compared with free MYC (EC50  = 11.46 and 124.82 mg/L), TA (EC50  = 251.19 and 503.81 mg/L), and an MYC + TA mixture (EC50  = 9.62 and 136.21 mg/L). These results suggested that MYC and TA incorporated in the co-assembled nanoparticles had a synergistic antifungal activity. The results of a genotoxicity assessment indicated that MT NPs could reduce the genotoxicity of MYC to plant cells.

CONCLUSION

Co-assembled MT NPs with synergistic antifungal activity have outstanding potential for the management of plant diseases. © 2023 Society of Chemical Industry.

Predatory mite Amblyseius orientalis prefers egg stage and low density of Carpoglyphus lactis prey

Amblyseius orientalis (Ehara) (Acari: Phytoseiidae) is an effective predatory mite for spider mite control on fruit trees in China. In recent decades, it has been produced massively at a commercial natural enemy producer, feeding on the storage mite Carpoglyphus lactis (L.). In the predator production process, the ratio of predatory mites to their prey was found to be critical for the population increase of A. orientalis in large-scale rearings. In this study, we investigated the predatory capacity of A. orientalis on various developmental stages of the prey C. lactis, and the effect of prey numbers on predator reproduction. The maximum predation rate of A. orientalis adults on C. lactis adults was 2.21 per day at the lowest density of five prey adults, and on C. lactis eggs it was 45.07 at the highest density of 60 prey eggs. The preference index C_i of A. orientalis on C. lactis eggs and adults was 0.4312 and - 0.9249, respectively, suggesting that A. orientalis preferred eggs to adults. Amblyseius orientalis could reproduce when it preyed on either eggs or deutonymphs of C. lactis. However, the fecundity of the predatory mites is not always proportional to the provided prey number. Higher density of prey deutonymphs resulted in lower fecundity, whereas more prey eggs resulted in higher fecundity of A. orientalis. Therefore, our study indicated that the choice of suitable density and developmental stage of prey can significantly improve A. orientalis production on a large scale.

Insights into the Global Transcriptome Response of Lentinula edodes Mycelia during Aging

The spawn of Lentinula edodes and other basidiomycete fungi tend to age with long-term culture. This causes heavy yield losses if aging spawn is used for propagation. In this study, we cultivated dikaryotic L. edodes mycelia in plates for 60 days to produce intrinsic aging phenotypes. We found that intracellular reactive oxygen species levels increased in contrast to mitochondrial depolarization and also observed greater DNA fragmentation with longer culture time. Transcriptome analysis of mycelia at different growth stages revealed pronounced expression differences between short- and long-term cultures. In particular, "phenylalanine, tyrosine, and tryptophan biosynthesis", "mitophagy and autophagy", "MAPK signaling pathway", and "ABC transporter" were among the enriched terms in the mycelial aging process. Weighted correlation network analysis identified LeAtg8, LeHog1, LePbs2, and LemTOR as key genes during aging. Western blotting confirmed that LeATG8 and phosphorylated LeHOG1 protein levels were significantly upregulated in aging mycelia. Our combined analytical approach provides insights into the mechanisms that regulate mycelial aging, indicating that autophagy/mitophagy plays a major role in counteracting the effects of age on mycelial growth development.

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

BACKGROUND

Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.

RESULTS

In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86-99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting.

CONCLUSIONS

Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.

Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits

How raffinose (Raf) family oligosaccharides, the major translocated sugars in the vascular bundle in cucurbits, are hydrolyzed and subsequently partitioned has not been fully elucidated. By performing reciprocal grafting of watermelon (Citrullus lanatus) fruits to branch stems, we observed that Raf was hydrolyzed in the fruit of cultivar watermelons but was backlogged in the fruit of wild ancestor species. Through a genome-wide association study, the alkaline alpha-galactosidase ClAGA2 was identified as the key factor controlling stachyose and Raf hydrolysis, and it was determined to be specifically expressed in the vascular bundle. Analysis of transgenic plants confirmed that ClAGA2 controls fruit Raf hydrolysis and reduces sugar content in fruits. Two single-nucleotide polymorphisms (SNPs) within the ClAGA2 promoter affect the recruitment of the transcription factor ClNF-YC2 (nuclear transcription factor Y subunit C) to regulate ClAGA2 expression. Moreover, this study demonstrates that C. lanatus Sugars Will Eventually Be Exported Transporter 3 (ClSWEET3) and Tonoplast Sugar Transporter (ClTST2) participate in plasma membrane sugar transport and sugar storage in fruit cell vacuoles, respectively. Knocking out ClAGA2, ClSWEET3, and ClTST2 affected fruit sugar accumulation. Genomic signatures indicate that the selection of ClAGA2, ClSWEET3, and ClTST2 for carbohydrate partitioning led to the derivation of modern sweet watermelon from non-sweet ancestors during domestication.

Sulfamethoxazole affects the microbial composition and antibiotic resistance gene abundance in soil and accumulates in lettuce

Pot experiments were set up to simulate the soil contamination by three initial concentrations of sulfamethoxazole (SMX) (S1, 100 mg/kg; S2, 200 mg/kg; S3, 300 mg/kg). The content of SMX in soil and its accumulation in lettuce were analysed. Additionally, the effects of SMX on soil microorganisms and antibiotic resistance genes were studied by Illumina high-throughput sequencing and droplet digital polymerase chain reaction (ddPCR). The results demonstrated that the SMX content in soil reduced by 97%, 86% and 75% in the S1, S2 and S3 treatment groups after 120 days, respectively. The accumulated SMX in lettuce was positively correlated with the initial concentration of SMX in soil. SMX contamination significantly reduced the bacterial diversity and altered the composition of bacterial and fungal communities in soil. The dominant bacterial and fungal genera in the SMX-contaminated soil were obviously different from those in the control soil. The relative abundance of sul1 (sulfonamide resistance gene) remarkably increased in the SMX-contaminated soil, while that of other ARGs, such as sul2 and tetracycline and quinolone resistance genes, showed no significant change.

Dimethyl disulfide (DMDS) as an effective soil fumigant against nematodes in China

Root-knot nematode is an important soil pest in horticulture crops and constrains the protected cultivation development after methyl bromide (MB) was phased out in China. Dimethyl disulfide (DMDS) exhibits excellent efficacy against nematodes. Laboratory experiments and field trials were set up to clarify DMDS dose, efficacy, and yield. A dose-response experiment using three methods showed that DMDS presented high efficacy against the nematode Meloidogyne incongnita. The LC50 values of direct fumigation activity in the dessicator method were 0.086 and 0.070 mg L-1 for DMDS and 1,3-D, 29.865 and 18.851 mg L-1 for DMDS and 1,3-D of direct contact activity in the small tube method, 6.438 and 3.061 mg L-1 for DMDS and 1,3-D of soil fumigation activity in the soil fumigation method, respectively. The field trials indicated that DMDS showed an excellent efficacy of 80%-94% on root-knot nematode applied at 10-100 g m-2 on tomato in Tongzhou, Beijing. The crop yields showed no significant difference after applying 10-80 g m-2 DMDS. Results indicate that DMDS applied at 10 g m-2 for controlling root-knot nematode in Beijing is cost effective. In conclusion, DMDS is an excellent soil fumigant that can be used for controlling root-knot nematode and can be an potential novel alternative to MB in China.