A syntelog-based pan-genome provides insights into rice domestication and de-domestication.

BACKGROUND: Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate. RESULTS: Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice. CONCLUSIONS: This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.

MoS2/PDA@Cu composite as a peroxidase-mimicking enzyme with high-effect antibacterial and anticancer activity.

Since nanozymes were proposed, their applications have become more and more extensive. As a research hotspot in recent years, MoS2 also shows many enzyme-like properties. However, as a novel peroxidase, MoS2 has the disadvantage of a low maximum reaction rate. In this study, the MoS2/PDA@Cu nanozyme was synthesized by a wet chemical method. The modification of PDA on the surface of MoS2 achieved the uniform growth of small-sized Cu Nps. The obtained MoS2/PDA@Cu nanozyme displayed excellent peroxidase-like activity and antibacterial properties. The minimum inhibitory concentration (MIC) of the MoS2/PDA@Cu nanozyme against S. aureus reached 25 µg mL-1. Furthermore, it showed a more pronounced inhibitory effect on bacterial growth with the addition of H2O2. The maximum reaction rate (Vmax) of the MoS2/PDA@Cu nanozyme is 29.33 × 10-8 M s-1, which is significantly higher as compared to that of HRP. It also exhibited excellent biocompatibility, hemocompatibility and potential anticancer properties. When the concentration of the nanozyme was 160 µg mL-1, the viabilities of 4T1 cells and Hep G2 cells were 45.07% and 32.35%, respectively. This work indicates that surface regulation and electronic transmission control are good strategies for improving peroxidase-like activity.

The complete chloroplast genome of japonica type weedy rice (Oryza sativa f. spontanea).

As a noxious weed, weedy rice (Oryza sativa f. spontanea Roshev. 1931) has threatened global food security and sustainable crop production. On the other hand, weedy rice has a strong tolerance for abiotic stresses and the potential to provide rich resources for rice genetic improvement. Thus, for a more comprehensive understanding of its speciation, we sequenced and assembled the first complete chloroplast genome of Oryza sativa f. spontanea (japonica type). The complete chloroplast genome was 134,555 bp in length and encoded 133 genes, including 83 protein-coding genes, 42 tRNA genes and 8 rRNA genes. Phylogenetic analysis revealed that the indica-japonica differentiation of weedy rice was closely related to cultivated rice, and Oryza sativa f. spontanea (japonica type) was genetically more closely clustered with cultivated rice O. sativa (japonica type) than O. nivara or other wild rice.

Genomic insights into the evolution of Echinochloa species as weed and orphan crop.

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

Population genomic analysis reveals domestication of cultivated rye from weedy rye.

Rye (Secale cereale) is an important crop with multiple uses and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. The geneticist N.I. Vavilov proposed that cultivated rye had been domesticated from weedy rye, rather than directly from wild species like other crops. Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds. To this end, in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild, weedy, and cultivated rye, and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans. We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits, including shattering, grain yield, and disease resistance. Furthermore, we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye. Taken together, our findings unravel the domestication history of cultivated rye, suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale, and provide an important resource for future rye and wheat breeding.

The complete chloroplast genome of weedy rice Oryza sativa f. spontanea.

The emergence of weedy rice (Oryza sativa f. spontanea) has been considered as a serious global agricultural problem in recent decades. To better understand its speciation, here we assembled the complete chloroplast genome of O. sativa f. spontanea with the length of 134,502 bp. The assembly contains a large single-copy (LSC, 80,549 bp), a small single-copy (SSC, 12,347 bp) and a pair of inverted repeats (IRa and IRb, 20,803 bp each). A total of 132 unique genes were annotated, including 82 protein-coding genes, 42 tRNA genes and eight rRNA genes. Phylogenetic analysis showed that O. sativa f. spontanea (indica type) appears closely related to cultivated indica rice rather than wild rice, supporting the hypothesis that weedy rice originated from cultivated rice.

Ewing's Sarcoma/Peripheral Primitive Neuroectodermal Tumors in Bronchus.

Ewing sarcoma/peripheral primitive neuroectodermal tumors (ES/pPNET), a member of the Ewing sarcoma family of tumors, is a malignant soft tissue tumor with small undifferentiated neuroectodermal cells. Primary trachea-bronchial ES/pPNET is very rare. The most common pulmonary ES is due to a metastasis. We describe a case of ES/pPNET which originated in the left basal trunk bronchus. The patient was a 30-year-old male, presenting with irritable cough and fever for 10 days. A tumor of 60 mm in diameter was found in the left basal trunk bronchus, extending to the left lower lobe. No distant metastases were detected. Histopathological examination revealed a malignancy of ES/pPNET with a diffuse proliferation of round cells, a Flexner-Wintersteiner rosette formation and positive staining for CD99. The patient was successfully treated with a combination of left lower lobectomy and adjuvant chemotherapy and has remained disease-free for approximately 18 months at follow-up. This case highlights that ES/pPNET should be considered as a differential diagnosis in cases of trachea-bronchial tumors.