miR159 Represses a Constitutive Pathogen Defense Response in Tobacco

MicroR159 (miR159) regulation of GAMYB expression is highly conserved in terrestrial plants; however, its functional role remains poorly understood. In Arabidopsis (Arabidopsis thaliana), although GAMYB-like genes are constitutively transcribed during vegetative growth, their effects are suppressed by strong and constitutive silencing by miR159. GAMYB expression occurs only if miR159 function is inhibited, which results in detrimental pleiotropic defects, questioning the purpose of the miR159-GAMYB pathway. Here, miR159 function was inhibited in tobacco (Nicotiana tabacum) and rice (Oryza sativa) using miRNA MIM159 technology. Similar to observations in Arabidopsis, inhibition of miR159 in tobacco and rice resulted in pleiotropic defects including stunted growth, implying functional conservation of the miR159-GAMYB pathway among angiosperms. In MIM159 tobacco, transcriptome profiling revealed that genes associated with defense and programmed cell death were strongly activated, including a suite of 22 PATHOGENESIS-RELATED PROTEIN (PR) genes that were 100- to 1,000-fold upregulated. Constitutive expression of a miR159-resistant GAMYB transgene in tobacco resulted in phenotypes similar to that of MIM159 tobacco and activated PR gene expression, verifying the dependence of the above-mentioned changes on GAMYB expression. Consistent with the broad defense response, MIM159 tobacco appeared immune to Phytophthora infection. These findings suggest that the tobacco miR159-GAMYB pathway functions in the biotic defense response, which becomes activated upon miR159 inhibition. However, PR gene expression was not upregulated in Arabidopsis or rice when miR159 was inhibited, suggesting that miR159-GAMYB pathway functional differences exist between species, or factors in addition to miR159 inhibition are required in Arabidopsis and rice to activate this broad defense response

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed

Brassica napus (AACC, 2n=38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large-scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7 and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double-low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double-low and double-high), accompanied by an increase in genetic load in the double-low group. This study demonstrates distinctive genomic footprints and deleterious SNP (Single Nucleotide Polymorphism) variants for local adaptation by recent intra- and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid cro

GSCtool: A Novel Descriptor that Characterizes the Genome for Applying Machine Learning in Genomics

Machine learning (ML) is one of the core driving forces for the next breeding stage, and Breeding 4.0. Genotype matrix based on single‐nucleotide polymorphisms (SNPs) is often used in ML for genome‐to‐phenotype prediction. Genotype matrix has an inherent defect, as the feature spaces it generates across different individuals or groups are inconsistent, and this hinders the application of ML. To overcome the challenge, a genome descriptor, Genic SNPs Composition Tool (GSCtool) is developed, which counts the number of SNPs in each gene of the genome so the dimension of the feature vectors equals the number of annotated genes in a species. Compared to using the genotype matrix, using GSCtool significantly decreases the model training time and has a higher accuracy of phenotype prediction. GSCtool also achieves good performance in variety identification, which is useful in crop variety protection. In general, GSCtool will help facilitate the application and study of genomic ML. The source code and test data of GSCtool are freely available at https://github.com/SZJhacker/GSCtool and https://gitee.com/shenzijie/GSCtool

The complete chloroplast genome of weedy rye Secale cereale subsp. segetale

Weedy rye (Secale cereale subsp. segetale Zhukov 1928) is a problematic weed species in wheat field. However, it can potentially provide valuable genetics resources to increase the genetic variations and introduce desirable genes for rye and wheat breeding. Here, we assembled the complete chloroplast genome of S. cereale subsp. segetale. The chloroplast genome is 137,051 bp in length, containing a large single copy region (81,090 bp), a small single copy region (12,795 bp) and two separated inverted repeat regions (21,583 bp). A total of 131 unique genes were annotated, consisting of 82 protein-coding genes, 41 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that Secale cereale subsp. segetale (weedy rye) and S. cereale subsp. cereale (rye) clustered together as sisters to other Secale species

Surveillance of Hepatitis E Virus Contamination in Shellfish in China

Background: Hepatitis E virus (HEV) has been confirmed to be a zoonotic virus of worldwide distribution. HEV contamination in the water environment has not been well examined in China. The objective of this study was to evaluate HEV contamination in shellfish in a coastal area of China. Such contamination would be significant for evaluating public health risks. Methods: samples of three species shellfish were collected from thirteen points of estuarine tidal flats around the Bohai Gulf and screened for HEV RNA using an in-house nested RT-PCR assay. The detected HEV-positive samples were further verified by gene cloning and sequencing analysis. Results: the overall HEV-positive detection rate is approximately 17.5% per kilogram of shellfish.  HEV was more common among S. subcrenata (28.2%), followed by A. granosa (14.3%) and R. philippinarum (11.5%). The phylogenetic analysis of the 13 HEV strains detected revealed that gene fragments fell into two known 4 sub-genotypes (4b/4d) groups and another unknown group. Conclusions: 13 different sub-genotype 4 HEVs were found in contaminated shellfish in the Bohai Gulf rim. The findings suggest that a health risk may exist for users of waters in the Bonhai area and to consumers of shellfish.  Further research is needed to assess the sources and infectivity of HEV in these settings, and to evaluate additional shellfish harvesting areas

The complete chloroplast genome of Nicotiana plumbaginifolia

Nicotiana plumbaginifolia Vivianiis 1802 is an annual herb, native to Mexico and South America. It is one of the most widely distributed tobacco species. As a wild tobacco, N. plumbaginifolia has provided several economically important disease-resistance genes to cultivated tobacco. We assembled the complete chloroplast genome of N. plumbaginifolia. The chloroplast genome is 155,945 bp in length, which includes a large single copy region (86,621 bp), a small single copy region (18,528 bp) and two separated inverted repeat regions (25,398 bp). A total of 117 unique genes were annotated, consisting of 84 protein-coding genes, 29 tRNA genes and 4 rRNA genes. Based on chloroplast genomes of 17 Nicotiana species, phylogenetic analyses indicated that N. plumbaginifolia was closely related to N. suaveolens and N. amplexicaulis

The Conservation of Long Intergenic Non-Coding RNAs and Their Response to <i>Verticillium dahliae</i> Infection in Cotton

Long intergenic non-coding RNAs (lincRNAs) have been demonstrated to be vital regulators of diverse biological processes in both animals and plants. While many lincRNAs have been identified in cotton, we still know little about the repositories and conservativeness of lincRNAs in different cotton species or about their role in responding to biotic stresses. Here, by using publicly available RNA-seq datasets from diverse sources, including experiments of Verticillium dahliae (Vd) infection, we identified 24,425 and 17,713 lincRNAs, respectively, in Gossypium hirsutum (Ghr) and G. barbadense (Gba), the two cultivated allotetraploid cotton species, and 6933 and 5911 lincRNAs, respectively, in G. arboreum (Gar) and G. raimondii (Gra), the two extant diploid progenitors of the allotetraploid cotton. While closely related subgenomes, such as Ghr_At and Gba_At, tend to have more conserved lincRNAs, most lincRNAs are species-specific. The majority of the synthetic and transcribed lincRNAs (78.2%) have a one-to-one orthologous relationship between different (sub)genomes, although a few of them (0.7%) are retained in all (sub)genomes of the four species. The Vd responsiveness of lincRNAs seems to be positively associated with their conservation level. The major functionalities of the Vd-responsive lincRNAs seem to be largely conserved amongst Gra, Ghr, and Gba. Many Vd-responsive Ghr-lincRNAs overlap with Vd-responsive QTL, and several lincRNAs were predicted to be endogenous target mimicries of miR482/2118, with a pair being highly conserved between Ghr and Gba. On top of the confirmation of the feature characteristics of the lincRNAs previously reported in cotton and other species, our study provided new insights into the conservativeness and divergence of lincRNAs during cotton evolution and into the relationship between the conservativeness and Vd responsiveness of lincRNAs. The study also identified candidate lincRNAs with a potential role in disease response for functional characterization

Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability

Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater

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

Abstract 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

Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus

Abstract Background Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an important seed oil crop worldwide and the target of many genetic improvement activities. To understand better the function of lncRNAs in regulating plant metabolic activities, we carried out a genome-wide lncRNA identification of lncRNAs in Brassica napus with a focus on lncRNAs involved in lipid metabolism. Twenty ribosomal RNA depleted strand specific RNA-seq (ssRNA-seq) datasets were generatred using RNAs isolated from B. napus seeds at four developmental stages. For comparison we also included 30 publically available RNA-seq datasets generated from poly(A) enriched mRNAs isolated from from various Brassica napus tissues in our analysis. Results A total of 8905 lncRNA loci were identified, including 7100 long intergenic noncoding RNA (lincRNA) loci and 1805 loci generating long noncoding natural antisense transcript (lncNAT). Many lncRNAs were identified only in the ssRNA-seq and poly(A) RNA-seq dataset, suggesting that B. napus has a large lncRNA repertoire and it is necessary to use libraries prepared from different tissues and developmental stages as well as different library preparation approaches to capture the whole spectrum of lncRNAs. Analysis of coexpression networks revealed that among the regulatory modules are networks containing lncRNAs and protein-coding genes related to oil biosynthesis indicating a possible role of lncRNAs in the control of lipid metabolism. One such example is that several lncRNAs are potential regulators of BnaC08g11970D that encodes oleosin1, a protein found in oil bodies and involved in seed lipid accumulation. We also observed that the expression levels of B. napus lncRNAs is positively correlated with their conservation levels. Conclusions We demonstrated that the B. napus genome has a large number of lncRNA and that these lncRNAs are expressed broadly across many developmental times and in different tissue types. We also provide evidence indicating that specific lncRNAs appear to be important regulators of lipid biosynthesis forming regulatory networks with transcripts involved in lipid biosynthesis. We also provide evidence that these lncRNAs are conserved in other species of the Brassicaceae family