The Gibberellin perception system evolved to regulate a pre-existing GAMYB-mediated system during land plant evolution

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

Background

The moss Physcomitrella patens as a model species provides an important reference for early-diverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies. The usability of a reference genome greatly depends on the quality of the annotation and the availability of centralized community resources. Therefore, in the light of accumulating evidence for missing genes, fragmentary gene structures, false annotations and a low rate of functional annotations on the original release, we decided to improve the moss genome annotation.

Results

Here, we report the complete moss genome re-annotation (designated V1.6) incorporating the increased transcript availability from a multitude of developmental stages and tissue types. We demonstrate the utility of the improved P. patens genome annotation for comparative genomics and new extensions to the cosmoss.org resource as a central repository for this plant “flagship” genome. The structural annotation of 32,275 protein-coding genes results in 8387 additional loci including 1456 loci with known protein domains or homologs in Plantae. This is the first release to include information on transcript isoforms, suggesting alternative splicing events for at least 10.8% of the loci. Furthermore, this release now also provides information on non-protein-coding loci. Functional annotations were improved regarding quality and coverage, resulting in 58% annotated loci (previously: 41%) that comprise also 7200 additional loci with GO annotations. Access and manual curation of the functional and structural genome annotation is provided via the http://www.cosmoss.org model organism database.

Conclusions

Comparative analysis of gene structure evolution along the green plant lineage provides novel insights, such as a comparatively high number of loci with 5’-UTR introns in the moss. Comparative analysis of functional annotations reveals expansions of moss house-keeping and metabolic genes and further possibly adaptive, lineage-specific expansions and gains including at least 13% orphan genes.

Flowering time control in ornamental gloxinia (Sinningia speciosa) by manipulation of miR159 expression

BACKGROUND AND AIMS

Gloxinia (Sinningia speciosa) is a popular commercial plant for its attractive and colourful flowers. However, the genetic mechanism of flowering time regulation in gloxinia is largely unknown. Recent studies on model plants have elucidated that miR159 acts as a negative regulator of floral transition in short-day photoperiods. The aim of this study was to investigate whether genetic modification of miR159 expression can offer an effective approach for regulation of flowering characteristics in gloxinia.

METHODS

Transgenic gloxinia plants were generated that over-express or suppress miR159 by means an efficient Agrobacterium-mediated transformation system in order to study the effect of miR159 on flowering time. In addition, the full-length cDNA of gloxinia GAMYB (SsGAMYB) was also cloned, and was verified to be a target of miR159 by modified RNA ligase-mediated 5' rapid amplification of cDNA ends.

KEY RESULTS

Transgenic gloxinia plants that over-express or suppress miR159 exhibited significantly late or early flowering, respectively. During flower development, the expression level of miR159 was negatively correlated with SsGAMYB in gloxinia. MiR159-mediated SsGAMYB expression affected the expression levels of SsLEAFY (SsLFY) and three MADS-box genes (SsAP1, SsAP3 and SsAG), which regulated floral transition downstream of GAMYB. In addition, suppression of miR159 caused a conversion of petals and sepals in a few transgenic plants.

CONCLUSIONS

miR159-regulated GAMYB expression is an effective pathway of flowering time control in gloxinia. Transgenic manipulation of miR159 can be used as an applicable strategy to regulate flowering time in commercial ornamental plants.

Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

In recent years, there has been a significant increase in the number of completely sequenced plant genomes. The comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. The aldehyde dehydrogenase (ALDH) gene superfamily comprises a group of enzymes involved in the NAD(+)- or NADP(+)-dependent conversion of various aldehydes to their corresponding carboxylic acids. ALDH enzymes are involved in processing many aldehydes that serve as biogenic intermediates in a wide range of metabolic pathways. In addition, many of these enzymes function as 'aldehyde scavengers' by removing reactive aldehydes generated during the oxidative degradation of lipid membranes, also known as lipid peroxidation. Plants and animals share many ALDH families, and many genes are highly conserved between these two evolutionarily distinct groups. Conversely, both plants and animals also contain unique ALDH genes and families. Herein we carried out genome-wide identification of ALDH genes in a number of plant species-including Arabidopsis thaliana (thale crest), Chlamydomonas reinhardtii (unicellular algae), Oryza sativa (rice), Physcomitrella patens (moss), Vitis vinifera (grapevine) and Zea mays (maize). These data were then combined with previous analysis of Populus trichocarpa (poplar tree), Selaginella moellindorffii (gemmiferous spikemoss), Sorghum bicolor (sorghum) and Volvox carteri (colonial algae) for a comprehensive evolutionary comparison of the plant ALDH superfamily. As a result, newly identified genes can be more easily analyzed and gene names can be assigned according to current nomenclature guidelines; our goal is to clarify previously confusing and conflicting names and classifications that might confound results and prevent accurate comparisons between studies.