Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species. Three short-read-based strategies for plant pan-genome construction include iterative individual, iteration pooling, and map-to-pan. Their performance is very different under various conditions, while comprehensive evaluations have yet to be conducted nowadays. Here, we evaluate the performance of these three pan-genome construction strategies for plants under different sequencing depths and sample sizes. Also, we indicate the influence of length and repeat content percentage of novel sequences on three pan-genome construction strategies. Besides, we compare the computational resource consumption among the three strategies. Our findings indicate that map-to-pan has the greatest recall but the lowest precision. In contrast, both two iterative strategies have superior precision but lower recall. Factors of sample numbers, novel sequence length, and the percentage of novel sequences’ repeat content adversely affect the performance of all three strategies. Increased sequencing depth improves map-to-pan’s performance, while not affecting the other two iterative strategies. For computational resource consumption, map-to-pan demands considerably more than the other two iterative strategies. Overall, the iterative strategy, especially the iterative pooling strategy, is optimal when the sequencing depth is less than 20X. Map-to-pan is preferable when the sequencing depth exceeds 20X despite its higher computational resource consumption.
Warming affects leaf light use efficiency and functional traits in alpine plants: evidence from a 4-year in-situ field experiment
Light use efficiency (LUE) is a crucial determinant of plant productivity, while leaf functional traits directly affect ecosystem functions. However, it remains unclear how climate warming affects LUE and leaf functional traits of dominant species in alpine meadows.
We conducted a 4-year in-situ field warming experiment to investigate the eco-physiological characteristics for a dominant species (
Experimental warming increased the leaf LUE, maximum photochemical efficiency, non-photochemical quenching, relative water content and specific leaf area for both species. However, there was a decrease in leaf and soil element content. Different species exhibit varying adaptability to warming. Increasing temperature significantly increased the photosynthetic rate, stomatal conductance, transpiration rate, total water content, and specific leaf volume of
Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis
An important strategy to combat yield loss challenge is the development of varieties with increased tolerance to drought to maintain production. Improvement of crop yield under drought stress is critical to global food security.
In this study, we performed multiomics analysis in a collection of 119 diverse rapeseed (
The results of the genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within drought tolerance-related gene
The results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought-tolerant varieties.
Post-anthesis dry matter and nitrogen accumulation, partitioning, and translocation in maize under different nitrate–ammonium ratios in Northwestern China
An appropriate supply of ammonium (NH4+) in addition to nitrate (NO3−) can greatly improve plant growth and promote maize productivity. However, knowledge gaps exist regarding the mechanisms by which different nitrogen (N) fertilizer sources affect the enzymatic activity of nitrogen metabolism and non-structural carbohydrates during the post-anthesis period.
A field experiment across 3-year was carried out to explore the effects of four nitrateammonium ratio (NO3−/NH4+ = 1:0 (N1), 1:1 (N2), 1:3 (N3), and 3:1 (N4)) on postanthesis dry matter (DM) and N accumulation, partitioning, transportation, and grain yield in maize.
NO3-/NH4+ ratio with 3:1 improved the enzymatic activity of N metabolism and non-structural carbohydrate accumulation, which strongly promoted the transfer of DM and N in vegetative organs to reproductive organs and improved the pre-anthesis DM and nitrogen translocation efficiency. The enzymatic activities of nitrate reductase, nitrite reductase, glutamine synthetase, glutamine oxoglutarate aminotransferase, and non-structural carbohydrate accumulation under N4 treatment were increased by 9.30%–32.82%, 13.19%–37.94%, 4.11%–16.00%, 11.19%–30.82%, and 14.89%–31.71% compared with the other treatments. Mixed NO3−-N and NH4+-N increased the total DM accumulation at the anthesis and maturity stages, simultaneously decreasing the DM partitioning of stem, increasing total DM, DM translocation efficiency (DMtE), and contribution of pre-anthesis assimilates to the grain (CAPG) in 2015 and 2017, promoting the transfer of DM from stem to grain. Furthermore, the grain yield increased by 3.31%–9.94% (2015), 68.6%–26.30% (2016), and 8.292%–36.08% (2017) under the N4 treatment compared to the N1, N2, and N3 treatments.
The study showed that a NO3−/NH4+ ratio of 3:1 is recommended for high-yield and sustainable maize management strategies in Northwestern China.
Identification of plant microRNAs using convolutional neural network
MicroRNAs (miRNAs) are of significance in tuning and buffering gene expression. Despite abundant analysis tools that have been developed in the last two decades, plant miRNA identification from next-generation sequencing (NGS) data remains challenging. Here, we show that we can train a convolutional neural network to accurately identify plant miRNAs from NGS data. Based on our methods, we also present a user-friendly pure Java-based software package called Small RNA-related Intelligent and Convenient Analysis Tools (SRICATs). SRICATs encompasses all the necessary steps for plant miRNA analysis. Our results indicate that SRICATs outperforms currently popular software tools on the test data from five plant species. For non-commercial users, SRICATs is freely available at
Whole-transcriptome profiling and identification of cold tolerance-related ceRNA networks in japonica rice varieties
Low-temperature stress negatively impacts rice yield, posing a significant risk to food security. While previous studies have explored the physiological and linear gene expression alterations in rice under low-temperature conditions, the changes in competing endogenous RNA (ceRNA) networks remain largely unexamined.
We conducted RNA sequencing on two
We identified 364 differentially expressed circular RNAs (circRNAs), 224 differentially expressed microRNAs (miRNAs), and 12,183 differentially expressed messenger RNAs (mRNAs).
We identified
Mosses and vascular plants show diverging diversity patterns along a latitudinal gradient in boreal bogs and fens
Latitudinal patterns of plant diversity were studied in boreal peatlands. Vascular plant diversity decreased with latitude in fens, whereas moss diversity increased in bogs and fens. Community uniqueness decreased with latitude in both habitats. Taxonomic and functional composition were primarily structured by contrasting local conditions in bogs and fens, whereas climatic variations along the latitudinal gradient played a secondary role.
Abstract
Questions
The latitudinal biodiversity gradient; i.e., the increase in biodiversity towards the equator, is one of the most prominent biodiversity patterns. Nevertheless, many questions remain to be answered about the influence of multiple environmental factors on the latitudinal biodiversity gradient, especially for mosses, and the functional diversity of mosses and vascular plants. This study aims at evaluating the influence of latitude, climate, environmental variables, and habitat types (bog vs fen) on taxonomic and functional diversity (α-diversity and β-diversity) and the composition of vascular plant and moss species.
Location
49° N to 55° N in Northwestern Quebec, Canada.
Taxon
Mosses, vascular plants.
Methods
We used a database containing 376 phytosociological plots (400 m2) sampled in boreal peatlands located along a 600-km latitudinal gradient. We evaluated changes in α-diversity and β-diversity in response to latitude, longitude, climate, and local abiotic variables for both taxonomic groups using linear mixed effect models. We evaluated the effects of these variables on taxonomic and functional composition using variance partitioning by redundancy analysis.
Results
Moss diversity increased with latitude, although the effects were masked by environmental variables, whereas vascular plant diversity decreased with latitude in fens and did not vary with latitude in bogs. We observed a decrease in taxonomic and functional uniqueness with latitude. Moss and vascular plant taxonomic and functional composition were primarily structured by contrasting local conditions in bogs and fens, whereas climatic variations along the latitudinal gradient played a secondary role.
Conclusions
Our results highlight the contrasting biodiversity patterns in both peatland types and the importance of local habitat conditions in structuring vascular plant and moss diversity. These patterns varied depending on the diversity indicator used, as α- and β-diversity and functional and taxonomic diversity were often decoupled. Future studies should therefore include more than one diversity indicator and consider the differences between ecosystems and taxon groups.
Physiological and biochemical assortment in different wheat genotypes (Triticum aestivum L.) under rain fed conditions
Syeda Okasha Javed, Shahid Iqbal Awan, Sania Shouket, Kotb A. Attia, Zhu Xi, Arif Ahmed Mohammed, Sher Aslam Khan, Sayeda Tanavish Javed, Yasir Majeed - Volume 51(4)
Estimating the frequency of virulence against an Stb gene in Zymoseptoria tritici populations by bulk phenotyping on checkerboard microcanopies of wheat near‐isogenic lines
The BCP method leverages the relationship between the ratio of Zymoseptoria tritici lesions on wheat near-isogenic lines differing by one resistance gene (Stb16q) and the frequency of virulent strains in the inoculated population.
Abstract
Monitoring virulent strains within pathogen populations is crucial to improve host resistance deployment strategies. Such monitoring increasingly involves field pathogenomics studies of molecular polymorphisms in pathogen genomes based on high-throughput screening technologies. However, it is not always straightforward to predict virulence phenotypes from these polymorphisms, and in planta phenotyping remains necessary. We developed a method for ‘bulk phenotyping on checkerboard microcanopies of wheat near-isogenic lines’ (BPC) for estimating the frequency of virulence against a resistance gene in mixed populations of the fungal pathogen Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB) in wheat, without the need for strain-by-strain pathogen phenotyping. Our method involves the uniform inoculation of a microcanopy of two wheat lines—one with the target resistance gene and the other without it—with a multistrain mixture of isolates representative of the population to be characterized, followed by the differential quantification of infection points (lesions). Using Stb16q, a wheat resistance gene that has recently broken down in Europe, we found a robust correlation between the ratio of the mean number of lesions on each wheat line and the frequency of virulent strains in the inoculum. Using pairs of virulent and avirulent strains, as well as synthetic populations consisting of 10 virulent strains and 10 avirulent strains mixed in different proportions, we validated the principle of the method and established standard curves at virulence frequencies close to those observed in natural conditions. We discuss the potential of this method for virulence monitoring in combination with molecular methods.
No safe haven: Loss of avirulence in the plant pathogen Leptosphaeria maculans by DNA duplication and repeat‐induced point mutation
Unlike other avirulence genes in canola pathogen Leptosphaeria maculans, AvrLm2 is protected from repeat-induced point mutation (RIP): here fungal populations were identified with RIP in AvrLm2, due to a DNA duplication event.
Abstract
Microbes can overcome the ability of plant resistance genes to confer protection against disease by mutating their corresponding avirulence genes. The fungus Leptosphaeria maculans causes blackleg disease on canola crops and subverts Brassica napus resistance genes through several DNA mutation mechanisms. One of these is repeat-induced point (RIP) mutation, which can ‘leak’ into the avirulence genes from the adjacent repetitive sequences that the mutation process is targeting. Here, we identified populations of L. maculans in Australia that have extensive RIP mutations in the avirulence gene AvrLm2 and show that this has been triggered by a duplication of the gene and surrounding DNA that includes the distant (>55 kb in total) AvrLm6 gene. This finding provides another mechanism of mutation by which pathogens can overcome host resistance, and more broadly contributes to understanding the complex balance between gene duplication and genome defence.