Intestinal Bacterial Diversity and Functional Analysis of Three Lepidopteran Corn Ear Worm Larvae

Insects, as the most abundant animal group on earth, and their symbionts help their hosts to adapt to various environments. Conogethes punctiferalis, Ostrinia furnacalis and Helicoverpa armigera are three main pests co-occurring in the ear stage of corn, which significantly affect the yield and quality of corn. The purpose of this study was to compare the diversity and function of the intestinal bacteria of the three co-occurring lepidopteran pests, C. punctiferalis, O. furnacalis and H. armigera, and to explore the reason of their prevalence from the microbiota’s view. Our results showed the difference of diversity and abundance of the gut bacteria of three co-occurring lepidopteran pests at the ear stage. Proteobacteria and Firmicutes were the dominant phyla, and the Enterobacteriaceae and Enterococcaceae were the dominant families in the three pests. Compared with the other two pests, Bacteroidetes was found much more in C. punctiferalis. In addition, C. punctiferalis showed more correlation and similarity in bacteria composition with corn endophytic bacteria, as well as had obvious advantages in metabolic, environmental information processing, cellular processes and organic systems function pathways. Our findings may provide insight into the prevalence of corn earworm larvae from the perspective of gut microbiota and function prediction

Novel microsatellite markers reveal low genetic diversity and evidence of heterospecific introgression in the critically endangered Chinese Crested Tern (Thalasseus bernsteini)

The Chinese Crested Tern, Thalasseus bernsteini, is one of the most endangered seabird species in the world, with only small breeding populations of around 100 individuals. To profile the genetic properties of this population, we screened 200 short tandem repeat sequences from a de novo assembled genome of the Great Crested Tern, T. bergii, which is the sister species of T. bernsteini. We designed a panel of 12 novel microsatellites, and genotyped nine and 23 individuals of T. bernsteini and T. bergii, respectively. The results showed that T. bernsteini genetic diversity was lower than that of T. bergii, and no inbreeding was detected. There was no sign of recent bottleneck events in the two species, but T. bernsteini showed signals of a post-bottleneck population expansion. Gene flow analysis indicated introgression between the two species, but the magnitude from T. bernsteini to T. bergii was higher than the opposite. This could be explained by Hubb’s principle, which states that there is a propensity of rarer species to reproduce with abundant congeners. Overall, our efforts provide useful genetic tools for conservation genetic studies of T. bernsteini and potentially other crested terns which face several natural and anthropogenic threats. The findings of this study further highlight that introgression may be a neglected factor in species conservation that needs to be seriously considered for conservation management. Availability of data and materials: The dataset of all microsatellite are available from the corresponding author upon request

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains a significant number of missing segments. Here, we reported a high-quality and almost complete Col-0 genome assembly with two gaps (named Col-XJTU) by combining the Oxford Nanopore Technologies ultra-long reads, Pacific Biosciences high-fidelity long reads, and Hi-C data. The total genome assembly size is 133,725,193 bp, introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome. All five chromosomes of the Col-XJTU assembly are highly accurate with consensus quality (QV) scores > 60 (ranging from 62 to 68), which are higher than those of the TAIR10.1 reference (ranging from 45 to 52). We completely resolved chromosome (Chr) 3 and Chr5 in a telomere-to-telomere manner. Chr4 was completely resolved except the nucleolar organizing regions, which comprise long repetitive DNA fragments. The Chr1 centromere (CEN1), reportedly around 9 Mb in length, is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats. Using the cutting-edge sequencing data and novel computational approaches, we assembled a 3.8-Mb-long CEN1 and a 3.5-Mb-long CEN2. We also investigated the structure and epigenetics of centromeres. Four clusters of CEN180 monomers were detected, and the centromere-specific histone H3-like protein (CENH3) exhibited a strong preference for CEN180 Cluster 3. Moreover, we observed hypomethylation patterns in CENH3-enriched regions. We believe that this high-quality genome assembly, Col-XJTU, would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms, as well as the genetic and epigenetic features in plants

Enhanced C‐To‐T and A‐To‐G Base Editing in Mitochondrial DNA with Engineered DdCBE and TALED

Abstract Mitochondrial base editing with DddA‐derived cytosine base editor (DdCBE) is limited in the accessible target sequences and modest activity. Here, the optimized DdCBE tools is presented with improved editing activity and expanded C‐to‐T targeting scope by fusing DddA11 variant with different cytosine deaminases with single‐strand DNA activity. Compared to previous DdCBE based on DddA11 variant alone, fusion of the activation‐induced cytidine deaminase (AID) from Xenopus laevis not only permits cytosine editing of 5′‐GC‐3′ sequence, but also elevates editing efficiency at 5′‐TC‐3′, 5′‐CC‐3′, and 5′‐GC‐3′ targets by up to 25‐, 10‐, and 6‐fold, respectively. Furthermore, the A‐to‐G editing efficiency is significantly improved by fusing the evolved DddA6 variant with TALE‐linked deoxyadenosine deaminase (TALED). Notably, the authors introduce the reported high‐fidelity mutations in DddA and add nuclear export signal (NES) sequences in DdCBE and TALED to reduce off‐target editing in the nuclear and mitochondrial genome while improving on‐target editing efficiency in mitochondrial DNA (mtDNA). Finally, these engineered mitochondrial base editors are shown to be efficient in installing mtDNA mutations in human cells or mouse embryos for disease modeling. Collectively, the study shows broad implications for the basic study and therapeutic applications of optimized DdCBE and TALED

Abrogation of graft ischemia‐reperfusion injury in ischemia‐free liver transplantation

Abstract Background Ischemia‐reperfusion injury (IRI) is considered an inherent component of organ transplantation that compromises transplant outcomes and organ availability. The ischemia‐free liver transplantation (IFLT) procedure has been developed to avoid interruption of blood supply to liver grafts. It is unknown how IFLT might change the characteristics of graft IRI. Methods Serum and liver biopsy samples were collected from IFLT and conventional liver transplantation (CLT) recipients. Pathological, metabolomics, transcriptomics, and proteomics analyses were performed to identify the characteristic changes in graft IRI in IFLT. Results Peak aspartate aminotransferase (539.59 ± 661.76 U/L versus 2622.28 ± 3291.57 U/L) and alanine aminotransferase (297.64 ± 549.50 U/L versus 1184.16 ± 1502.76 U/L) levels within the first 7 days and total bilirubin levels by day 7 (3.27 ± 2.82 mg/dl versus 8.33 ± 8.76 mg/dl) were lower in the IFLT versus CLT group (all p values < 0.001). The pathological characteristics of IRI were more obvious in CLT grafts. The antioxidant pentose phosphate pathway remained active throughout the procedure in IFLT grafts and was suppressed during preservation and overactivated postrevascularization in CLT grafts. Gene transcriptional reprogramming was almost absent during IFLT but was profound during CLT. Proteomics analysis showed that “metabolism of RNA” was the major differentially expressed process between the two groups. Several proinflammatory pathways were not activated post‐IFLT as they were post‐CLT. The activities of natural killer cells, macrophages, and neutrophils were lower in IFLT grafts than in CLT grafts. The serum levels of 14 cytokines were increased in CLT versus IFLT recipients. Conclusions IFLT can largely avoid the biological consequences of graft IRI, thus has the potential to improve transplant outcome while increasing organ utilization