Water scarcity, resulting from climate change, poses a significant threat to ecosystems. We sequenced the genome of The genome was assembled into 12 chromosomes encompassing 21 169 protein‐coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation‐associated gene families, and highlighted genome‐level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)‐responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of the The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation.
- Award ID(s):
- 1753811
- NSF-PAR ID:
- 10232663
- Date Published:
- Journal Name:
- Gigabyte
- Volume:
- 2020
- ISSN:
- 2709-4715
- Page Range / eLocation ID:
- 1 to 9
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Summary Syntrichia ruralis , a dryland desiccation‐tolerant moss, provides valuable insights into survival of water‐limited conditions.S. ruralis , conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relativeS. caninervis . We took a genetic approach to characterize the role of anS. ruralis transcription factor, identified in transcriptomic analyses, inArabidopsis thaliana .S. ruralis ortholog of ABA‐insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized inArabidopsis , acts as a negative regulator of an ABA‐dependent stress response inArabidopsis . -
Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. However, aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ~9 terrestrial insect genomes. Instead, ~24 terrestrial insect genomes have been sequenced for every aquatic insect genome. This discrepancy is even more dramatic if the quality of genomic resources is considered; for instance, while no aquatic insect genome has been assembled to the chromosome level, 29 terrestrial insect genomes spanning four orders have. We argue that a lack of aquatic insect genomes is not due to any underlying difficulty (e.g., small body sizes or unusually large genomes), yet it is severely hampering aquatic insect research at both fundamental and applied scales. By expanding the availability of aquatic insect genomes, we will gain key insight into insect diversification and empower future research for a globally important taxonomic group.more » « less
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Summary Recent studies have shown that correlations between chromatin modifications and transcription vary among eukaryotes. This is the case for marked differences between the chromatin of the moss
Physcomitrium patens and the liverwortMarchantia polymorpha . Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with land plants. We aimed to describe chromatin in hornworts to establish synapomorphies across bryophytes and approach a definition of the ancestral chromatin organization of land plants.We used genomic methods to define the 3D organization of chromatin and map the chromatin landscape of the model hornwort
Anthoceros agrestis .We report that nearly half of the hornwort transposons were associated with facultative heterochromatin and euchromatin and formed the center of topologically associated domains delimited by protein coding genes. Transposons were scattered across autosomes, which contrasted with the dense compartments of constitutive heterochromatin surrounding the centromeres in flowering plants.
Most of the features observed in hornworts are also present in liverworts or in mosses but are distinct from flowering plants. Hence, the ancestral genome of bryophytes was likely a patchwork of units of euchromatin interspersed within facultative and constitutive heterochromatin. We propose this genome organization was ancestral to land plants.
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Premise Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution.
Methods We employed diverse likelihood‐based analyses to infer large‐scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (
Aneura mirabilis ) and a putatively mycoheterotrophic moss (Buxbaumia ), and compared 15 bryophyte plastomes for major structural rearrangements.Results Overall land‐plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four‐taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of
RNA edit sites restores cases of unexpected non‐monophyly to monophyly forTakakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophicAneura but notBuxbaumia . Plastid genome structure is nearly invariant across bryophytes, but thetuf A locus, presumed lost in embryophytes, is unexpectedly retained in several mosses.Conclusions A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily
RNA ‐edited taxa. TheBuxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophicAneura . Autotrophic bryophyte plastomes, includingBuxbaumia , hardly vary in overall structure. -
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Abstract Mosses (Bryophyta) are a key group occupying an important phylogenetic position in land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage, containing more than 95% of modern mosses, whereas other classes are species‐poor. Two branches with large numbers of gene duplications were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida, and Tetraphidopsida. The analysis of the phylogenetic progression of duplicated paralogs retained on genomic syntenic regions in the
Physcomitrella patens genome confirmed that the whole‐genome duplication events WGD1 and WGD2 were re‐recognized as the ψ event and the Funarioideae duplication event, respectively. The ψ polyploidy event was tightly associated with the early diversification of Bryopsida, in the ancestor of Bryidae, Dicranidae, Timmiidae, and Funariidae. Together, four branches with large numbers of gene duplications were unveiled in the evolutionary past ofP. patens . Gene retention patterns following the four large‐scale duplications in different moss lineages were analyzed and discussed. Recurrent significant retention of stress‐related genes may have contributed to their adaption to distinct ecological environments and the evolutionary success of this early‐diverging land plant lineage.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.46471/gigabyte.8
