Beneficial and pathogenic Arabidopsis root-interacting fungi differently affect auxin levels and responsive genes during early infection

Auxin (indole-3-acetic acid, IAA) is an important phytohormone involved in root growth and development. Root-interacting beneficial and pathogenic fungi utilize auxin and its target genes to manipulate the performance of their hosts for their own needs. In order to follow and visualize auxin effects in fungi-colonized Arabidopsis roots, we used the dual auxin reporter construct DR5::EGFP-DR5v2::tdTomato and fluorescence microscopy as well as LC-MS-based phytohormone analyses. We demonstrate that the beneficial endophytic fungi Piriformospora indica and Mortierella hyalina produce and accumulate IAA in their mycelia, in contrast to the phytopathogenic biotrophic fungus Verticillium dahliae and the necrotrophic fungus Alternaria brassicicola. Within three hours after exposure of Arabidopsis roots to the pathogens, the signals of the auxin-responsive reporter genes disappeared. When exposed to P. indica, significantly higher auxin levels and stimulated expression of auxin-responsive reporter genes were detected both in lateral root primordia and the root elongation zone within one day. Elevated auxin levels were also present in the M. hyalina/Arabidopsis root interaction, but no downstream effects on auxin-responsive reporter genes were observed. However, the jasmonate level was strongly increased in the colonized roots. We propose that the lack of stimulated root growth upon infection with M. hyalina is not caused by the absence of auxin, but an inhibitory effect mediated by high jasmonate content

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.</p

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts.

Funder: National Institute for Basic Biology (NIBB) Collaborative Research Program (13-710)Funder: The Forschungskredit of the University of Zurich The University Research Priority Program “Evolution in Action” of the University of Zurich The Georges and Antoine Claraz Foundation (Switzerland)Funder: Spanish Ministry of Science, Innovation and Universities (BFU2016-80621-P)Funder: The Georges and Antoine Claraz Foundation (Switzerland) The Research Priority Program “Evolution in Action” of the University of ZurichFunder: Foundation of German Business (sdw), Georges and Antoine Claraz Foundation, URPP Evolution in Action of the University of ZurichFunder: Special Grant for Innovation in Research Program of the Technical University of Dresden (Germany).Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants

Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica

Understanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, the relative contribution of these two processes to radical morphological shifts is still poorly understood. Here, we use the model system of two mosses, Funaria hygrometrica and Physcomitrium (Physcomitrella) patens, to investigate the molecular mechanisms underlying contrasting sporophyte architectures. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that large-scale differences in sporophytic architecture are mainly governed by orthologous (i.e., shared) genes frequently experiencing temporal gene expression shifts between the two species. While the absolute number of species-specific genes expressed during sporophyte development is somewhat smaller, we observed a significant increase of their proportion in preferentially sporophyte expressed genes, suggesting a fundamental role in the sporophyte phase. However, further functional studies are necessary to determine their contribution to diverging sporophyte morphologies. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators

Non-canonical structure, function and phylogeny of the B-sister MADS-box gene OsMADS30 of rice (Oryza sativa)

B-sister MADS-box genes play key roles in female reproductive organ and seed development throughout seed plants. This view is supported by their high conservation in terms of sequence, expression and function. In grasses, there are three subclades of B-sister genes: the OsMADS29-, the OsMADS30-and the OsMADS31-like genes. Here, we report on the evolution of the OsMADS30-like genes. Our analyses indicate that these genes evolved under relaxed purifying selection and are rather weakly expressed. OsMADS30, the representative of the OsMADS30-like genes from rice (Oryza sativa), shows strong sequence deviations in its 30 region when compared to orthologues from other grass species. We show that this is due to a 2.4-kbp insertion, possibly of a hitherto unknown helitron, which confers a heterologous C-terminal domain to OsMADS30. This putative helitron is not present in the OsMADS30 orthologues from closely related wild rice species, pointing to a relatively recent insertion event. Unlike other B-sister mutants O. sativa plants carrying a T-DNA insertion in the OsMADS30 gene do not show aberrant seed phenotypes, indicating that OsMADS30 likely does not have a canonical 'B-sister function'. However, imaging-based phenotyping of the T-DNA carrying plants revealed alterations in shoot size and architecture. We hypothesize that sequence deviations that accumulated during a period of relaxed selection in the gene lineage that led to OsMADS30 and the alteration of the C-terminal domain might have been a precondition for a potential neo-functionalization of OsMADS30 in O. sativa

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Funder: National Institute for Basic Biology (NIBB) Collaborative Research Program (13-710)Funder: The Forschungskredit of the University of Zurich The University Research Priority Program “Evolution in Action” of the University of Zurich The Georges and Antoine Claraz Foundation (Switzerland)Funder: Spanish Ministry of Science, Innovation and Universities (BFU2016-80621-P)Funder: The Georges and Antoine Claraz Foundation (Switzerland) The Research Priority Program “Evolution in Action” of the University of ZurichFunder: Foundation of German Business (sdw), Georges and Antoine Claraz Foundation, URPP Evolution in Action of the University of ZurichFunder: Special Grant for Innovation in Research Program of the Technical University of Dresden (Germany).Abstract: Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants