The disclosure provides adenosine deaminases that are capable of deaminating adenosine in DNA. The disclosure also provides fusion proteins comprising a Cas9 (e.g., a Cas9 nickase) domain and adenosine deaminases that deaminate adenosine in DNA. In some embodiments, the fusion proteins further comprise a nuclear localization sequence (NLS), and/or an inhibitor of base repair, such as, a nuclease dead inosine specific nuclease (dISN).

Adenosine nucleobase editors and uses thereof

Provided herein are systems, compositions, and methods of introducing protective and/or loss-of-function variants of CCR5 and CCR2. Variants may be introduced using a CRISPR/Cas9-based nucleobase editor or other guide nucleotide sequence-programmable DNA binding protein domain-based fusion protein described herein. Further provided herein are compositions and methods of preventing and treating conditions related to HIV infection and progression as well as to AIDS.

Editing of CCR5 receptor gene to protect against HIV infection

Faba bean (Vicia faba L.), a globally important grain legume providing a stable source of dietary protein, was one of the earliest plant cytogenetic models. However, the lack of draft genome annotations and unclear structural information on mRNA transcripts have impeded its genetic improvement. To address this, we sequenced faba bean leaf transcriptome using the PacBio single-molecule long-read isoform sequencing platform. We identified 28,569 nonredundant unigenes, ranging from 108 to 9669 bp, with a total length of 94.5 Mb. Many unigenes (3597, 12.5%) had 2–20 isoforms, indicating a highly complex transcriptome. Approximately 96.5% of the unigenes matched sequences in public databases. The predicted proteins and transcription factors included NB-ARC, Myb_domain, C3H, bHLH, and heat shock proteins, implying that this genome has an abundance of stress resistance genes. To validate our results, we selected WCOR413-15785, DHN2-12403, DHN2-14197, DHN2-14797, COR15-14478, and HVA22-15 unigenes from the ICE-CBF-COR pathway to analyze their expression patterns in cold-treated samples via qRT-PCR. The expression of dehydrin-related genes was induced by cold stress. The assembled data provide the first insights into the deep sequencing of full-length RNA from faba bean at the single-molecule level. This study provides an important foundation to improve gene modeling and protein prediction.

/pdf/unraveling-the-complexity-of-faba-bean-vicia-faba-l-yuk2abj0ih.pdf

Unraveling the complexity of faba bean (Vicia faba L.) transcriptome to reveal cold-stress-responsive genes using long-read isoform sequencing technology.

Polygenic genome-wide association mapping identified two regions of the cowpea genome associated with different components of resistance to its major post-harvest pest, the seed beetle Callosobruchus maculatus. Cowpea (Vigna unguiculata) is an important grain and fodder crop in arid and semi-arid regions of Africa, Asia, and South America, where the cowpea seed beetle, Callosobruchus maculatus, is a serious post-harvest pest. Development of cultivars resistant to C. maculatus population growth in storage could increase grain yield and quality and reduce reliance on insecticides. Here, we use a MAGIC (multi-parent, advanced-generation intercross) population of cowpea consisting of 305 recombinant inbred lines (RILs) to identify genetic variants associated with resistance to seed beetles. Because inferences regarding the genetic basis of resistance may depend on the source of the pest or the assay protocol, we used two divergent geographic populations of C. maculatus and two complementary assays to measure several aspects of resistance. Using polygenic genome-wide association mapping models, we found that the cowpea RILs harbor substantial additive-genetic variation for most resistance measures. Variation in several components of resistance, including larval development time and survival, was largely explained by one or several linked loci on chromosome 5. A second region on chromosome 8 explained increased seed resistance via the induction of early-exiting larvae. Neither of these regions contained genes previously associated with resistance to insects that infest grain legumes. We found some evidence of gene–gene interactions affecting resistance, but epistasis did not contribute substantially to resistance variation in this mapping population. The combination of mostly high heritabilities and a relatively consistent and simple genetic architecture increases the feasibility of breeding for enhanced resistance to C. maculatus.

/pdf/disparate-genetic-variants-associated-with-distinct-2ex8jjurwb.pdf

Disparate genetic variants associated with distinct components of cowpea resistance to the seed beetle Callosobruchus maculatus.

Chlorophyll is the primary source of color in widespread green plants. It has been investigated in mung bean seed coats and cotyledons. This study aimed to examine chromatic changes in mung beans during heat processing. It observed pigment variation within the cotyledons and seed coats of mung beans. Following thermal treatment from 0 to 50 min, the color of mung bean products changed, primarily from a decrease in chlorophyll content in the seed coat (from 6.57 to 1.28 mg/100 g, with significant differences. p < 0.05), accompanied by the formation of tawny pheophytin. However, the b value of mung bean seed coat showed an increasing trend with significant differences (yellowness, 21.55 increasing to 34.85, p < 0.05). Interestingly, the total flavonoid content in the seed coat tended to increase with thermal time (2.93 to 18.74 µg/mg) with statistical differences (p < 0.05). The condensation reaction of flavonoids with other polyphenolic compounds formed dark-brown polymers, resulting in a significant decrease in brightness (L value) of the cooking solution with thermal processing time (p < 0.05). Thus, the chlorophyll extraction and purification of the mung bean seed coat confirmed the morphological change of chlorophyll combined with the Maillard reaction, resulting in the color change after thermal treatment. It showed that a significant reason for the discoloration of mung beans was pheophytin from chlorophyll in the processing process.

/pdf/effect-of-heat-treatment-on-nutritional-and-chromatic-1imnevly.pdf

Effect of Heat Treatment on Nutritional and Chromatic Properties of Mung Bean (Vigna radiata L.)

Two polygalacturonase-inhibiting proteins (VrPGIP) of Vigna radiata confer resistance to bruchids (Callosobruchus spp.).

Mungbean (Vigna radiata [L.]) is an important economic crop grown in South, and East Asia. The low contiguity of the current assembly of V. radiata genome has limited its application. Here, we report a high-quality chromosome-scale assembled genome of V. radiata to facilitate the investigation of its genome characteristics and evolution. By combination of Nanopore long reads, Illumina short reads and Hi-C data, we generated a high-quality genome assembly of V. radiata, with 473.67 megabases assembled into 11 chromosomes with contig N50 and scaffold N50 of 11.3 and 42.4 megabases, respectively. A total of 52.8% of the genome was annotated as repetitive sequences, among which LTRs (long terminal repeats) were predominant (33.9%). The genome of V. radiata was predicted to contain 33,924 genes, 32,470 (95.7%) of which could be functionally annotated. Evolutionary analysis revealed an estimated divergence time of V. radiata from its close relative V. angularis of ~11.66 million years ago. In addition, 277 V. radiata specific gene families, 18 positively selected genes were detected and functionally annotated. This high-quality mungbean genome will provide valuable resources for further genetic analysis and crop improvement of mungbean and other legume species.

/pdf/high-quality-genome-assembly-annotation-and-evolutionary-wkujtukj64.pdf

High-quality genome assembly, annotation and evolutionary analysis of the mungbean (Vigna radiata) genome

The invention discloses a cowpea salt tolerance related trait closely linked InDel molecular marker, primers and application thereof. The cowpea salt tolerance related trait closely linked InDel molecular marker is a nucleotide sequence shown as SEQ ID NO.2 and obtained by PCR amplification on the genomic DNA of salt-tolerant cowpea variety Suzi 41 with an upstream primer shown as SEQ ID NO.1 anda downstream primer shown as SEQ ID NO.2. The primers for amplification of the InDel molecular marker provided by the invention has the upstream primer shown as SEQ ID NO.1 and the downstream primer shown as SEQ ID NO.2. The marker and the primers are utilized for assistant selection, and can quickly screen salt-tolerant cowpea strains for salt-tolerant breeding of cowpea, improve the breeding accuracy and selection efficiency, and save the cost.

Cowpea salt tolerance related trait closely linked InDel molecular marker, primers and application thereof

Faba bean (Vicia faba L.) is one of the most widely grown cool season legume crops in the world. Winter faba bean normally has a vernalization requirement, which promotes an earlier flowering and pod setting than unvernalized plants. However, the molecular mechanisms of vernalization in faba bean are largely unknown. Discovering vernalization-related candidate genes is of great importance for faba bean breeding. In this study, the whole transcriptome of faba bean buds was profiled by using next-generation sequencing (NGS) and single-molecule, real-time (SMRT) full-length transcriptome sequencing technology. A total of 29,203 high-quality non-redundant transcripts, 21,098 complete coding sequences (CDS), 1,045 long non-coding RNAs (lncRNAs), and 12,939 simple sequence repeats (SSRs) were identified. Furthermore, 4,044 differentially expressed genes (DEGs) were identified through pairwise comparisons. By Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, these differentially expressed transcripts were found to be enriched in binding and transcription factor activity, electron carrier activity, rhythmic process, and receptor activity. Finally, 50 putative vernalization-related genes that played important roles in the vernalization of faba bean were identified; we also found that the levels of vernalization-responsive transcripts showed significantly higher expression levels in cold-treated buds. The expression of VfSOC1, one of the candidate genes, was sensitive to vernalization. Ectopic expression of VfSOC1 in Arabidopsis brought earlier flowering. In conclusion, the abundant vernalization-related transcripts identified in this study will provide a basis for future researches on the vernalization and faba bean breeding and established a reference full-length transcriptome for future studies on faba bean.

/pdf/single-molecule-real-time-and-illumina-based-rna-sequencing-2fwzcpy0to.pdf

Single-Molecule Real-Time and Illumina-Based RNA Sequencing Data Identified Vernalization-Responsive Candidate Genes in Faba Bean (Vicia faba L.)

This study aimed to investigate the proximate and phytochemicals present in seeds of 24 mung bean (Vigna radiate L.) genotypes from four provinces of China for estimating their nutritional and antioxidant properties. Proximate analysis of mung bean genotypes revealed that starch, protein, fat, ash and water-soluble polysaccharide ranged from 39.54–60.66, 17.36–24.89, 4.24–12.18, 2.78–3.53 and 1.99–2.96 g/100 g respectively. The five principal fatty acids detected in mung beans were stearic acid, palmitic acid, linoleic acid, oleic acid, and linolenic acid. The contents of insoluble-bound phenolic compounds, soluble phenolic compounds, and flavonoids ranged from 0.78 to 1.5 mg GAE g− 1, 1.78 to 4.10 mg GAE g− 1, and 1.25 to 3.52 mg RE g− 1, respectively. The black seed coat mung bean genotype M13 (Suheilv 1) exhibited highest flavonoid and phenolic contents which showed strong antioxidant activity. Two flavonoids (vitexin and isovitexin) and four phenolic acids (caffeic, syringic acid, p-coumaric, and ferulic acids) were identified by HPLC. Vitexin and isovitexin were the major phenolic compounds in all mung bean genotypes. The content of soluble phenolic compounds had positive correlation with DPPH (r2 = 0.713) and ABTS (r2 = 0.665) radical scavenging activities. Principal component analysis indicated that the first two principal components could reflect most details on mung bean with a cumulative contribution rate of 66.1%. Twenty-four mung bean genotypes were classified into four groups based on their phenolic compounds contents and antioxidant activities. The present study highlights the importance of these mung bean genotypes as a source of nature antioxidant ingredient for the development of functional foods or a source of health promoting food.

Xue Chenchen

Papers

Two polygalacturonase-inhibiting proteins (VrPGIP) of Vigna radiata confer resistance to bruchids (Callosobruchus spp.).

High-quality genome assembly, annotation and evolutionary analysis of the mungbean (Vigna radiata) genome

Cowpea salt tolerance related trait closely linked InDel molecular marker, primers and application thereof

Single-Molecule Real-Time and Illumina-Based RNA Sequencing Data Identified Vernalization-Responsive Candidate Genes in Faba Bean (Vicia faba L.)

Nutritional, phytochemical and antioxidant properties of 24 mung bean (Vigna radiate L.) genotypes