Reference genome facilitates trait development for faba beans.

Reference genomes facilitate trait improvement by aiding in the elucidation of causal genetic elements. Thanks to the recent release of a reference sequence for the faba bean, breeders and geneticists are poised to accelerate precision breeding and genetic improvement of this important crop.

A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane.

Erianthus produces substantial biomass, exhibits a good Brix value, and shows wide environmental adaptability, making it a potential biofuel plant. In contrast to closely related sorghum and sugarcane, Erianthus can grow in degraded soils, thus releasing pressure on agricultural lands used for biofuel production. However, the lack of genomic resources for Erianthus hinders its genetic improvement, thus limiting its potential for biofuel production. In the present study, we generated a chromosome-scale reference genome for Erianthus fulvus Nees. The genome size estimated by flow cytometry was 937 Mb, and the assembled genome size was 902 Mb, covering 96.26% of the estimated genome size. A total of 35 065 protein-coding genes were predicted, and 67.89% of the genome was found to be repetitive. A recent whole-genome duplication occurred approximately 74.10 million years ago in the E. fulvus genome. Phylogenetic analysis showed that E. fulvus is evolutionarily closer to S. spontaneum and diverged after S. bicolor. Three of the 10 chromosomes of E. fulvus formed through rearrangements of ancestral chromosomes. Phylogenetic reconstruction of the Saccharum complex revealed a polyphyletic origin of the complex and a sister relationship of E. fulvus with Saccharum sp., excluding S. arundinaceum. On the basis of the four amino acid residues that provide substrate specificity, the E. fulvus SWEET proteins were classified as mono- and disaccharide sugar transporters. Ortho-QTL genes identified for 10 biofuel-related traits may aid in the rapid screening of E. fulvus populations to enhance breeding programs for improved biofuel production. The results of this study provide valuable insights for breeding programs aimed at improving biofuel production in E. fulvus and enhancing sugarcane introgression programs.

Evaluation of genome size and phylogenetic relationships of the Saccharum complex species.

"Saccharum complex" is a hypothetical group of species, which is supposed to be involved in the origin of modern sugarcane, and displays large genomes and complex chromosomal alterations. The utilization of restricted parents in breeding programs of modern cultivated sugarcane has resulted in a genetic blockage, which controlled its improvement because of the limited genetic diversity. The use of wild relatives is an effective way to broaden the genetic composition of cultivated sugarcane. Due to the infrequent characterization of genomes, the potential of wild relatives is diffused in improving the cultivated sugarcane. To characterize the genomes of the wild relatives, the genome size and phylogenetic relationships among eight species, including Saccharum spontaneum, Erianthus arundinaceus, E. fulvus, E. rockii, Narenga porphyrocoma, Miscanthus floridulus, Eulalia quadrinervis, and M. sinensis were evaluated based on flow cytometry, genome surveys, K-mer analysis, chloroplast genome sequencing, and whole-genome SNPs analysis. We observed highly heterozygous genomes of S. spontaneum, E. rockii, and E. arundinaceus and the highly repetitive genome of E. fulvus. The genomes of Eulalia quadrinervis, N. porphyrocoma, M. sinensis, and M. floridulus were highly complex. Phylogenetic results of the two approaches were dissimilar, however, both indicate E. fulvus displayed closer relationships to Miscanthus and Saccharum than other species of Saccharum complex. Eulalia quadrinervis was more closely related to M. floridulus than M. sinensis; E. arundinaceus differ significantly from Miscanthus, Narenga, and Saccharum, but was relatively close to Erianthus. We proved the point of E. rockii and E. fulvus should not be classified as one genus, and E. fulvus should be classified as the Saccharum genus. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03338-5.

Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding.

Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to which their efficiency in crop breeding is reduced. In this regard, the bulk segregant analysis sequencing (BSA-seq) and its related approaches, viz., quantitative trait locus (QTL)-seq, bulk segregant RNA-Seq (BSR)-seq, and MutMap, have emerged as efficient methods to identify the genomic loci/QTLs controlling specific traits at high resolution, accuracy, reduced time span, and in a high-throughput manner. These approaches combine BSA with next-generation sequencing (NGS) and enable the rapid identification of genetic loci for qualitative and quantitative assessments. Many previous studies have shown the successful identification of the genetic loci for different plant traits using BSA-seq and its related approaches, as discussed in the text with details. However, the efficiency and accuracy of the BSA-seq depend upon factors like sequencing depth and coverage, which enhance the sequencing cost. Recently, the rapid reduction in the cost of NGS together with the expected cost reduction of third-generation sequencing in the future has further increased the accuracy and commercial applicability of these approaches in crop improvement programs. This review article provides an overview of BSA-seq and its related approaches in crop breeding together with their merits and challenges in trait mapping.

Corrigendum: Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments.

[This corrects the article DOI: 10.3389/fmicb.2021.821546.].

Reference-grade Taxus genome unleashes its pharmacological potential.

The genus Taxus is well known for its anticancer metabolite, paclitaxel. Recent releases of chromosome-scale reference genomes for two Taxus species (Xiong et al. and Cheng et al.) now provide novel insights on genome structure and phylogenomics and the origin and evolution of the paclitaxel biosynthesis pathway.

Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing.

There is a special interaction between the environment, soil microorganisms, and tea plants, which constitute the ecosystem of tea plantations. Influenced by environmental factors and human management, the changes in soil microbial community affected the growth, quality, and yield of tea plants. However, little is known about the composition and structure of soil bacterial and fungal communities in 100-year-old tea plantations and the mechanisms by which they are affected. In this regard, we characterized the microbiome of tea plantation soils by considering the bacterial and fungal communities in 448 soil samples from 101 ancient tea plantations in eight counties of Lincang city, which is one of the tea domestication centers in the world. 16S and Internal Transcribed Spacer (ITS) rRNA high-throughput amplicon sequencing techniques were applied in this study. The results showed that the abundance, diversity, and composition of the bacterial and fungal communities have different sensitivity with varying pH, altitude, and latitude. pH and altitude affect soil microbial communities, and bacterial communities are more sensitive than fungi in terms of abundance and diversity to pH. The highest α-diversity of bacterial communities is shown in the pH 4.50-5.00 and 2,200-m group, and fungi peaked in the pH 5.00-5.50 and 900-m group. Because of environmental and geographical factors, all microbes are similarly changing, and further correlations showed that the composition and structure of bacterial communities are more sensitive than fungal communities, which were affected by latitude and altitude. In conclusion, the interference of anthropogenic activities plays a more important role in governing fungal community selection than environmental or geographical factors, whereas for the bacterial community, it is more selective to environment adaptation than to adaptation to human activities.

Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana.

Ulmus wallichiana is a traditional medicinal plant listed as a vulnerable in the IUCN red list data. Genomic and transcriptomic resources for this species are lacking, hindering its genetic exploration. Further, no polymorphic marker resource is available for this species, thus limiting the elucidation of its underlying genetic diversity, which is a pre-requisite for its conservation. This study was therefore aimed to generate a functionally annotated transcriptomic resource and screen it for SSR regions. We used paired-end Illumina based RNAseq technology and trinity based de novo assembly approach to generate full length transcripts, which were screened for SSR regions and functionally annotated. Around 6.6 million raw reads were de novo assembled transcripts, which were clustered into 146,083 unigenes. 19,909 transcripts were provided with 3986 unique KEGG ids, 70,519 transcripts with 6621 unique Pfam domains, and 45,125 transcripts with 7302 unique INTERPRO domains. 1456 transcripts were identified as transcriptions factors (TFs). Further, 8868 unique GO terms were obtained for the unigenes. The transcripts mapped to 23,056 known pre-determined orthology clusters in the eggNOG database. A total of 16,570 SSRs were identified from the unigenes. Out of the 90 SSRs selected for characterization on 20 genotypes, 28 were polymorphic. Mean effective alleles (Ne) of 2.53, mean observed heterozygosity (Ho) of 0.77, and average polymorphic information content (PIC) of 0.57 were found. This study may facilitate the genetic exploration of this species. The polymorphic SSRs would prove useful to explore its genetic diversity patterns, required for its conservation.

Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments.

Wheat is an important cereal crop species consumed globally. The growing global population demands a rapid and sustainable growth of agricultural systems. The development of genetically efficient wheat varieties has solved the global demand for wheat to a greater extent. The use of chemical substances for pathogen control and chemical fertilizers for enhanced agronomic traits also proved advantageous but at the cost of environmental health. An efficient alternative environment-friendly strategy would be the use of beneficial microorganisms growing on plants, which have the potential of controlling plant pathogens as well as enhancing the host plant's water and mineral availability and absorption along with conferring tolerance to different stresses. Therefore, a thorough understanding of plant-microbe interaction, identification of beneficial microbes and their roles, and finally harnessing their beneficial functions to enhance sustainable agriculture without altering the environmental quality is appealing. The wheat microbiome shows prominent variations with the developmental stage, tissue type, environmental conditions, genotype, and age of the plant. A diverse array of bacterial and fungal classes, genera, and species was found to be associated with stems, leaves, roots, seeds, spikes, and rhizospheres, etc., which play a beneficial role in wheat. Harnessing the beneficial aspect of these microbes is a promising method for enhancing the performance of wheat under different environmental stresses. This review focuses on the microbiomes associated with wheat, their spatio-temporal dynamics, and their involvement in mitigating biotic and abiotic stresses.

Comprehensive temporal reprogramming ensures dynamicity of transcriptomic profile for adaptive response in Taxus contorta.

Plants respond to the environmental perturbations by triggering the dynamic changes within the transcriptome. The assessment of these oscillations within the transcriptome would offer insights into the ecological adaptation of the plants. We evaluated how the transcriptome of Taxus contorta swings under natural conditions to elucidate its adaptive response. Thus, our study provides new insights into the performance of T. contorta under a changing environment during different seasons. The abundance estimation using the RNAseq approach revealed 6727 differentially expressed genes. Comprehensive reprogramming was observed in Taxol biosynthesis, maintenance of redox homeostasis, and generation of effective shield to UV-B, high light intensity, and temperature. Besides differential expression, the alternative splicing (AS) and single nucleotide variations (SNVs) also confer flexibility to the transcriptome of T. contorta. 1936 differentially expressing transcripts were also found to exhibit Differential Exon Usage (DEU) as well as differential SNVs. LC-MS-based untargeted metabolic analysis revealed 7774 ion features, among which around 334 putatively identified metabolites were differentially regulated. Our results showed that the swing and the oscillations of the transcriptome and metabolome of T. contorta ensure adaptability and better survival under changing environment. In addition, varying patterns of AS and SNVs compliment the adaptation provided by differential expression.

Selection constraints determine preference for A/U-ending codons in Taxus contorta.

Unequal utilization of synonymous codons is a well-known phenomenon among living organisms. This phenomenon plays a major role in the enhancement of the accuracy and efficiency of translation. Gymnosperms are rarely paid attention in this aspect. Understanding the degree of and determining the forces influencing codon usage bias (CUB) in Taxus contorta, an endangered Himalayan gymnosperm, will prove useful in interpreting the evolutionary characteristics of this species. Using RNAseq data, 93 790 assembled transcripts were clustered into 32 701 unigenes. Around 13 061 full-length sequences were utilized for the analysis of CUB. Compositional properties showed that GC-content ranged from 28.76% to 65.22%, with an average value of 44.28%, suggesting an AT-rich genome. The mean effective number of codons (ENC) value revealed that CUB is not strong in T. contorta. The preferred codons tended to be A/U ending, whereas the avoided codons tended to be G/C ending. A P2 index of 0.54 and a Mutation Responsive Index (MRI) value of -0.02 in addition to the results revealed by the neutrality, ENC, and parity plots showed that natural selection is a predominating factor governing CUB. Mutational pressure, gene length, hydropathiciy, aromaticity, and nucleotide composition influence CUB weakly.

RNAseq-based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae.

Taxaceae and Cephalotaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within Cephalotaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq-based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 single-copy complete orthologous groups were selected for phylogenetic analysis. Maximum-likelihood, maximum-parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and Cephalotaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within Cephalotaxaceae.

Exploring microRNA profiles for circadian clock and flowering development regulation in Himalayan Rhododendron.

miRNA is a non-coding, yet crucial entity in remodeling the genetic architecture. Rhododendron arboreum of Himalayas grows and even flower under fluctuating climate. sRNA from leaves of vegetative and reproductive periods was sequenced to elucidate its seasonal associations. Conserved (256) and novel (210) miRNAs and their precursors were located based on homology with plant databases and transcriptome of the species. 27,139 predicted targets were involved with metabolism, reproduction, and response to abiotic stimuli. A comparative analysis showed differential expression of 198 miRNAs with season-specific abundance of 103 miRNAs. Specific isoforms of 11 miRNA families exhibited a temporal expression and targeted different genes implying a complex regulation. The variable miRNA expression among the tissues of different conditions can be associated with the adaptability of the species, which will prove essential for further study on miRNAs mediating seasonal response. Moreover, exogenous cues also mediate phase transition via networking of flowering pathways and their components. In this context, 18 known families and 77 novel miRNAs modulating 117 genes crucial in circadian entrainment were filtered. A negative correlation was obtained between the expression of 18 of these miRNAs and their targets when tested through quantitative-PCR. It highlighted the role of miRNA-target pairs in perceiving environmental variabilities and monitoring flowering growth. Furthermore, a phylogenetic clustering was performed, which supported the lineage-specific evolution and function of putative miR156 sequence in the species. This documentation of genome-wide profiling of miRNA, their targets, and expression will enhance the understanding of developmental and climate-tolerance strategies in high-altitude trees.

Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum).

Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina's platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.