Molecular evidence for segmental duplication across chromosomes of soybean using transcription factor gene family

Duplication of genome is an important genetic innovation. Large genome size (1.1 Gb) along with ancient and recent duplication events make the soybean genome more complex. Analyzing the distribution and duplication event in soybean transcription family genes, the segmental duplication within chromosomes was revealed. Our study provides a strong evidence that the large segmental duplication event in genome architecture and evolution of soybean genome using simple method of sequence and order analysis of TF genes. Finally, a scheme for interrelationship of different chromosomes has been proposed.

Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production

Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7 Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 Mb and 966.80 Mb, respectively. Phylogenomic analyses show that T. yunnanensis is most closely related to Sequoiadendron giganteum among the sampled taxa, with an estimated divergence time of 133.4−213.0 MYA. As with most gymnosperms, and unlike most angiosperms, there is no evidence of a recent whole-genome duplication in T. yunnanensis. Repetitive sequences, especially long terminal repeat retrotransposons, are prevalent in the T. yunnanensis genome, contributing to its large genome size. We further integrated genomic and transcriptomic data to unveil clusters of genes involved in Taxol synthesis, located on the chromosome 12, while gene families encoding hydroxylase in the Taxol pathway exhibited significant expansion. Our study contributes to the further elucidation of gymnosperm relationships and the Taxol biosynthetic pathway.

A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum

Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

SUMMARYIn this study, we aim to identify genomic traits of the transitions to the ectomycorrhizal ecology within the Boletales, one of the most diverse lineages of symbiotrophic fungi.We sequenced the genomes and compared the gene repertoires of symbiotrophic Boletales species to their saprotrophic brown-rot relatives. We also reconstructed gene duplication/loss histories along a time-calibrated phylogeny.We showed that the rate of gene duplication is constant along the backbone of Boletales phylogeny with large loss events in lineages leading to several families. The rate of gene family expansion sharply increased in the late Miocene and mostly took place in Boletaceae.Most of the ectomycorrhizal Boletales are characterized by a large genome size due to transposable element (TE) expansions and a reduction in the diversity of plant cell wall degrading enzymes (PCWDEs) compared to their brown-rot relatives. However, several species in the Boletaceae, Paxillaceae and Boletinellaceae have kept a substantial set of endoglucanases and LPMOs acting on cellulose/hemicellulose and fungal polysaccharides suggesting that they may partly decompose organic matter by a combined activity of oxidative and hydrolytic enzymes.The present study provides novel insights on our understanding of the mechanisms that influence the evolutionary diversification of boletes and symbiosis evolution.

A Combinatorial Approach of High-Throughput Genomics and Mass Proteomics for Understanding the Regulation and Expression of Secondary Metabolite Production in Actinobacteria

Secondary metabolites produced by Actinobacteria are an important source of antibiotics, drugs, and antimicrobial peptides. However, the large genome size of actinobacteria with high gene coding density makes it difficult to understand the complex regulation of biosynthesis of such critically and economically important products.

Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

A chromosome-level genome sequence of a model chrysanthemum: evolution and 1 reference for hexaploid cultivated chrysanthemum

Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspread repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to a relatively large genome size. Furthermore, we identified aretrotransposon, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

Genomics and molecular physiology for improvement of drought tolerance in wheat.

This chapter discusses the complexity of drought tolerance in wheat focusing the morphological, biochemical, physiological and molecular responses. The breeding approaches, such as traditional and genomics-assisted strategies, for drought tolerance in wheat are described. Future perspectives are also mentioned. Before wheat genome sequencing, it was very difficult to dissect drought tolerance genomic regions because of large genome size and repetitive sequences. But with the availability of sequencing approaches, a large number of genomic resources has become available which extend the scope of utilization of advanced genomics approaches such as GWAM and GS, MutMap+, etc. A new genome editing approach, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPRassociated protein 9 (Cas9) system, can also be utilized for enhancement of drought tolerance in wheat. Therefore, integration of genomic approaches with precise phenotyping is the need of the hour for improving drought tolerance in wheat.

Stress Ecology in Mining Landscape: Postindustrial Deposits in Comparison with their Surroundings as the Environments for Selection of Plants with Small and Large Genome Size

This pilot case study compares genome sizes of two groups of species (conspecific plants) which spontaneously colonize interior space within abandoned industrial area and/or deposits, and those ones occurred in adjacent vicinity. Testing of the hypothesis “There is functional significance of small versus large genomes of plant species by comparing their occurrence in unreclaimed toxic deposits as an example of stressed environment and in their populations from neighbouring habitats” confirmed this idea.