One or three species in Megadenia (Brassicaceae): insight from molecular studies

Out of the Qinghai-Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae)

Numerous high-elevation alpine plants of the Qinghai-Tibet Plateau (QTP) also have disjunct distribution in adjacent low-altitude mountains. The out-of-QTP versus into-the-QTP hypothesis of alpine plants provide strong evidence for the highly disputed assumption of the massive ice sheet developed in the central plateau during the Last Glacial Maximum (LGM). In this study, we sequenced the genomes of most known populations of Megadenia, a monospecific alpine genus of Brassicaceae distributed primarily in the QTP, though rarely found in adjacent low-elevation mountains of north China and Russia (NC-R). All sequenced samples clustered into four geographic genetic groups: one pair was in the QTP and another was in NC-R. The latter pair is nested within the former, and these findings support the out-of-QTP hypothesis. Dating the four genetic groups and niche distribution suggested that Megadenia migrated out of the QTP to adjacent regions during the LGM. The NC-R group showed a decrease in the effective population sizes. In addition, the genes with high genetic divergences in the QTP group were mainly involved in habitat adaptations during low-altitude colonization. These findings reject the hypothesis of development massive ice sheets, and support glacial survival of alpine plants within, as well as further migration out of, the QTP.

Dynamic enhancer transcription associates with reprogramming of immune genes during pattern triggered immunity in Arabidopsis

Background

Enhancers are cis-regulatory elements present in eukaryote genomes, which constitute indispensable determinants of gene regulation by governing the spatiotemporal and quantitative expression dynamics of target genes, and are involved in multiple life processes, for instance during development and disease states. The importance of enhancer activity has additionally been highlighted for immune responses in animals and plants; however, the dynamics of enhancer activities and molecular functions in plant innate immunity are largely unknown. Here, we investigated the involvement of distal enhancers in early innate immunity in Arabidopsis thaliana.

Results

A group of putative distal enhancers producing low-abundance transcripts either unidirectionally or bidirectionally are identified. We show that enhancer transcripts are dynamically modulated in plant immunity triggered by microbe-associated molecular patterns and are strongly correlated with open chromatin, low levels of methylated DNA, and increases in RNA polymerase II targeting and acetylated histone marks. Dynamic enhancer transcription is correlated with target early immune gene expression patterns. Cis motifs that are bound by immune-related transcription factors, such as WRKYs and SARD1, are highly enriched within upregulated enhancers. Moreover, a subset of core pattern-induced enhancers are upregulated by multiple patterns from diverse pathogens. The expression dynamics of putative immunity-related enhancers and the importance of WRKY binding motifs for enhancer function were also validated.

Conclusions

Our study demonstrates the general occurrence of enhancer transcription in plants and provides novel information on the distal regulatory landscape during early plant innate immunity, providing new insights into immune gene regulation and ultimately improving the mechanistic understanding of the plant immune system.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01362-8.

Taxonomic Composition of Iris Subser. Chrysographes (Iridaceae) Inferred from Chloroplast DNA and Morphological Analyses

The species of Iris subser. Chrysographes are herbaceous perennials found mainly in southwestern and central China and also in the Eastern Himalayas. To date, six species have been recognized in this group. In the framework of its taxonomic revision, we have carried out molecular and morphological studies. For this, we have sequenced four chloroplast DNA regions (trnS-trnG, trnL-trnF, rps4-trnSGGA, and psbA-trnH) for 25 samples across the major distribution ranges of the six species. Our phylogenetic analyses evidence that I. subser. Chrysographes is indeed a monophyletic group, which is sister to I. subser. Sibiricae. Within I. subser. Chrysographes, we have recovered four divergent lineages further supported by diagnosable morphological traits and geographical distributions. In this context, our data confirm the recognition of I. clarkei, I. delavayi, and I. wilsonii in their traditional concepts. Furthermore, both molecular and morphological data support the close affinities and similar distribution ranges of I. bulleyana, I. chrysographes, and I. forrestii, which suggests including I. chrysographes and I. forrestii as color forms in I. bulleyana. A revised taxonomic treatment for the group, including the notes on the species distributions and habitats, and also an identification key to the species are provided.

Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species

Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5'-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.

The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae)

Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was assembled for Megadenia pygmaea using Nanopore long reads and high-throughput chromosome conformation capture (Hi-C). The assembled genome is 215.2 Mb and is anchored on six pseudochromosomes. We annotated a total of 25,607 high-confidence protein-coding genes and corroborated the phylogenetic affinity of Megadenia with the Brassicaceae expanded lineage II, containing numerous agricultural crops. We dated the divergence of Megadenia from its closest relatives to 27.04 (19.11-36.60) million years ago. A reconstruction of the chromosomal composition of the species was performed based on the de novo assembled genome and comparative chromosome painting analysis. The karyotype structure of M. pygmaea is very similar to the previously inferred proto-Calepineae karyotype (PCK; n = 7) of the lineage II. However, an end-to-end translocation between two ancestral chromosomes reduced the chromosome number from n = 7 to n = 6 in Megadenia. Our reference genome provides fundamental information for karyotypic evolution and evolutionary study of this genus.

Plastome phylogeny and early diversification of Brassicaceae

Background

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.

Results

Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.

Conclusions

Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3555-3) contains supplementary material, which is available to authorized users.

Plastome phylogeny and early diversification of Brassicaceae

BACKGROUND

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.

RESULTS

Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.

CONCLUSIONS

Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

Non-monophyly of Siberian Erythronium (Liliaceae) leads to the recognition of the formerly neglected Erythronium sajanense

Four Erythronium species have been traditionally recognised within Eurasia based on their disjunct distributions and the slight morphological divergence between them: E. dens-canis, E. caucasicum, E. sibiricum and E. japonicum. The range of E. sibiricum includes adjacent parts of southern Siberia, Kazakhstan, China and Mongolia in the Altai-Sayan mountain region. Despite several recently proposed taxa within the range of E. sibiricum (E. sajanense, E. sibiricum subsp. altaicum, E. sibiricum subsp. sulevii), this species has never been tested for genetic subdivisions. We here used nucleotide sequence variation in one nuclear (internal transcribed spacer) and two plastid (rpl32-trnL, rps15-ycf1) regions to test for genetic divisions within Siberian Erythronium and, in particular, to examine the phylogenetic position of E. sajanense. The plastid phylogeny revealed a basal polytomy among E. japonicum, E. sibiricum populations pertaining to E. sajanense and a third strongly supported lineage that includes E. dens-canis, E. caucasicum and the remainder of E. sibiricum, thus rendering Siberian Erythronium non-monophyletic. The nuclear topology agrees with the plastid one in recovering E. sajanense as a distinct lineage that is weakly supported as sister to E. japonicum. Topological incongruences exist between the plastid and nuclear phylogenies but these do not affect the taxonomic recognition of E. sajanense (endemic to the Western Sayan Mts.). This species is morphologically distinguishable on the basis of its subulate stamen filaments. Whereas nuclear phylogeny failed to resolve any genetic grouping within E. sibiricum s. str., plastid data recovered a deep (possibly phylogeographically meaningful) lineage from samples referred to as E. sibiricum subsp. altaicum.