The poplar pangenome provides insights into the evolutionary history of the genus

Zhang, Bingyu; Zhu, Wenxu; Wu, Xiaojuan; Lu, Junqian; Ding, Changjun; Su, Xiaohua

doi:10.1038/s42003-019-0474-7

Cited by 47 publications

(37 citation statements)

References 46 publications

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“…recently made it possible to conduct whole genome sequencing, allowing the generation of a large number of genome-wide markers [65][66][67]. Population genetics studies of the silver birch have identified genetic variations in genes that are associated with local adaptations to different environmental conditions [42].…”

Section: Plos Onementioning

confidence: 99%

Identification and analysis of key genes involved in methyl salicylate biosynthesis in different birch species

Singewar¹,

Moschner²,

Hartung³

et al. 2020

PLoS ONE

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Species of the perennial woody plant genus Betula dominate subalpine forests and play a significant role in preserving biological diversity. In addition to their conventional benefits, birches synthesize a wide range of secondary metabolites having pharmacological significance. Methyl salicylate (MeSA) is one of these naturally occurring compounds constitutively produced by different birch species. MeSA is therapeutically important in human medicine for muscle injuries and joint pain. However, MeSA is now mainly produced synthetically due to a lack of information relating to MeSA biosynthesis and regulation. In this study, we performed a comprehensive bioinformatics analysis of two candidate genes mediating MeSA biosynthesis, SALICYLIC ACID METHYLTRANSFERASE (SAMT) and SALICYLIC ACID-BINDING PROTEIN 2 (SABP2), of high (B. lenta, B. alleghaniensis, B. medwediewii, and B. grossa) and low (B. pendula, B. utilis, B. alnoides, and B. nana) MeSA-producing birch species. Phylogenetic analyses of SAMT and SABP2 genes and homologous genes from other plant species confirmed their evolutionary relationships. Multiple sequence alignments of the amino acid revealed the occurrence of important residues for substrate specificity in SAMT and SABP2. The analysis of cis elements in different birches indicated a functional multiplicity of SAMT and SABP2 and provided insights into the regulation of both genes. We successfully developed six prominent single nucleotide substitution markers that were validated with 38 additional birch individuals to differentiate high and low MeSA-producing birch species. Relative tissue-specific expression analysis of SAMT in leaf and bark tissue of two high and two low MeSA-synthesizing birches revealed a high expression in the bark of both high MeSA-synthesizing birches. In contrast, SABP2 expression in tissues revealed indifferent levels of expression between species belonging to the two groups. The comparative expression and bioinformatics analyses provided vital information that could be used to apply plant genetic engineering technology in the mass production of organic MeSA.

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Section: Plos Onementioning

confidence: 99%

Identification and analysis of key genes involved in methyl salicylate biosynthesis in different birch species

Singewar¹,

Moschner²,

Hartung³

et al. 2020

PLoS ONE

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“…First introduced in bacteria (Tettelin et al, 2005), it is highly relevant to plant research with more than 50% of genes in some species being variable (accessory), found in some individuals but not others (Golicz et al, 2020). Pangenomes have been constructed for key crop species, such as rice, soybean, bread wheat, and oilseed rape (Li et al, 2014;Golicz et al, 2016b;Contreras-Moreira et al, 2017;Gordon et al, 2017;Montenegro et al, 2017;Zhou et al, 2017;Hurgobin et al, 2018;Ou et al, 2018;Zhao et al, 2018b;Gao et al, 2019;Zhang et al, 2019a). Plant accessory genes have been shown to be over-represented in functions related to signaling and disease resistance as well as abiotic stress response (Golicz et al, 2016b;Montenegro et al, 2017;Hurgobin et al, 2018;Wang et al, 2018b), perhaps contributing to environmental adaptation and phenotypic plasticity and providing promising targets for crop improvement.…”

Section: Beyond Single Reference Genomics -The Pan-genome Approachmentioning

confidence: 99%

Global Role of Crop Genomics in the Face of Climate Change

et al. 2020

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The development of climate change resilient crops is necessary if we are to meet the challenge of feeding the growing world's population. We must be able to increase food production despite the projected decrease in arable land and unpredictable environmental conditions. This review summarizes the technological and conceptual advances that have the potential to transform plant breeding, help overcome the challenges of climate change, and initiate the next plant breeding revolution. Recent developments in genomics in combination with high-throughput and precision phenotyping facilitate the identification of genes controlling critical agronomic traits. The discovery of these genes can now be paired with genome editing techniques to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value. Utilizing the genetic potential of crop wild relatives (CWRs) enables the domestication of new species and the generation of synthetic polyploids. The high-quality crop plant genome assemblies and annotations provide new, exciting research targets, including long non-coding RNAs (lncRNAs) and cis-regulatory regions. Metagenomic studies give insights into plant-microbiome interactions and guide selection of optimal soils for plant cultivation. Together, all these advances will allow breeders to produce improved, resilient crops in relatively short timeframes meeting the demands of the growing population and changing climate.

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“…The abundant and diverse expressed genes in the early invasion stage assure MULT to accommodate or infect successfully more diverse poplar hosts than MONO (Frantzeskakis et al, 2019;Morris and Moury, 2019). In nature, Populus sections Aigeiros and Tacamahaca host most modern species, abundant with genetically modified varieties or highly hybridized species for woody crops with industrial, ecological, and bio-energy purposes (McKown and Guy, 2018;Zanewich et al, 2018;Zhang et al, 2019). These diverse host selective forces from diverse species hosts possibly drove multigermtubi forma specialis to evolve more diverse pathogen-associated molecular patterns (PAMPs) and effectors for dismissing the evolving diverse host pattern recognition receptors (PRRs) and R genes defenses (Nurnberger and Kemmerling, 2009;Frantzeskakis et al, 2019).…”

Section: The Gene Expression Profiles Showing Formae Speciales Specifmentioning

confidence: 99%

“…These diverse host selective forces from diverse species hosts possibly drove multigermtubi forma specialis to evolve more diverse pathogen-associated molecular patterns (PAMPs) and effectors for dismissing the evolving diverse host pattern recognition receptors (PRRs) and R genes defenses (Nurnberger and Kemmerling, 2009;Frantzeskakis et al, 2019). The poplar hosts in section Leuce of monogermtubi fungi were also earlier lineage with low abundant species and few intrasectional crossed hybridized varieties in a slow evolutionary pace compared to other subgenus poplars in Populus genus (Christe et al, 2016;Zhang et al, 2019). Monogermtubi fungi also were in earlier evolution than the multigermtubi fungi (Han et al, 1998b(Han et al, , 2000Sun et al, 2015).…”

Section: The Gene Expression Profiles Showing Formae Speciales Specifmentioning

confidence: 99%

“…P. alba, a host from section Leuce, responded with the most abundant DEGs at the necrotrophic stage to a monogermtubi fungus infection (Zhang et al, 2018b). The unique pattern of the specific DEG's expression of Marssonina formae speciales could have stemmed on the co-evolutionary forces from its own poplar hosts (Christe et al, 2016;Frantzeskakis et al, 2019;Taylor and Larson, 2019;Zhang et al, 2019). Interestingly, nearly half a hundred of DEGs expressed in the initial invasion and biotrophic stages to MULT were discovered to have their homologous or same unigenes expressed in the necrotrophic stage to MONO with the same NCBI-NR function annotation ( Supplementary Table S15).…”

Section: The Gene Expression Profiles Showing Formae Speciales Specifmentioning

confidence: 99%

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Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea

Ren

Yan

et al. 2020

Front. Microbiol.

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The knowledge on the host specificity of a pathogen underlying an interaction is becoming an urgent necessity for global warming. In this study, the gene expression profiles and the roles of effectors in host specificity were integrally characterized with two formae speciales, multigermtubi and monogermtubi, of a hemibiotrophic pathogen Marssonina brunnea when they were infecting respective susceptible poplar hosts. With a functional genome comparison referring to a de novo transcriptome of M. brunnea and Pathogen-Host Interaction database functional annotations, the multigermtubi strain showed abundant and significant differentially expressed unigenes (DEGs) (more than 40%) in colonizing the initial invasion stage and in the necrotrophic stage. The monogermtubi strain induced less than 10% of DEGs in the initial invasion stage but which abruptly increased to more than 80% DEGs in the necrotrophic stage. Both strains induced the least DEGs in the biotrophic stage compared to the initial invasion and necrotrophic stages. The orthologs of the effector genes Ecp6, PemG1, XEG1, ACE1, and Mg3LysM were exclusively induced by one of the two formae speciales depending on the infection stages. Some unigenes homologous to carbohydrate lytic enzyme genes, especially pectate lyases, were notably induced with multigermtubi forma specialis infection but not expressed in the monogermtubi forma specialis at an earlier infection stage. The extraordinary differences in the functional genome level between the two formae speciales of M. brunnea could be fundamental to exploring their host specificity determinant and evolution. This study also firstly provided the fungal transcriptome of the monogermtubi forma specialis for M. brunnea.

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The poplar pangenome provides insights into the evolutionary history of the genus

Cited by 47 publications

References 46 publications

Identification and analysis of key genes involved in methyl salicylate biosynthesis in different birch species

Identification and analysis of key genes involved in methyl salicylate biosynthesis in different birch species

Global Role of Crop Genomics in the Face of Climate Change

Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea

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