Phylogenetic analyses in cornus substantiate ancestry of xylem supercooling freezing behavior and reveal lineage of desiccation related proteins

An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data

PREMISE

A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group.

METHODS

We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis.

RESULTS

A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode.

CONCLUSIONS

Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.

De novo sequencing, characterization, and comparison of inflorescence transcriptomes of Cornus canadensis and C. florida (Cornaceae)

BACKGROUND

Transcriptome sequencing analysis is a powerful tool in molecular genetics and evolutionary biology. Here we report the results of de novo 454 sequencing, characterization, and comparison of inflorescence transcriptomes of two closely related dogwood species, Cornus canadensis and C. florida (Cornaceae). Our goals were to build a preliminary source of genome sequence data, and to identify genes potentially expressed differentially between the inflorescence transcriptomes for these important horticultural species.

RESULTS

The sequencing of cDNAs from inflorescence buds of C. canadensis (cc) and C. florida (cf), and normalized cDNAs from leaves of C. canadensis resulted in 251799 (ccBud), 96245 (ccLeaf) and 114648 (cfBud) raw reads, respectively. The de novo assembly of the high quality (HQ) reads resulted in 36088, 17802 and 21210 unigenes for ccBud, ccLeaf and cfBud. A reference transcriptome for C. canadensis was built by assembling HQ reads of ccBud and ccLeaf, containing 40884 unigenes. Reference mapping and comparative analyses found 10926 sequences were putatively specific to ccBud, and 6979 putatively specific to cfBud. Putative differentially expressed genes between ccBud and cfBud that are related to flower development and/or stress response were identified among 7718 shared sequences by ccBud and cfBud. Bi-directional BLAST found 87 (41.83% of 208) of Arabidopsis genes related to inflorescence development had putative orthologs in the dogwood transcriptomes. Comparisons of the shared sequences by ccBud and cfBud yielded 65931 high quality SNPs between two species. The twenty unigenes with the most SNPs are listed as potential genetic markers for evolutionary studies.

CONCLUSIONS

The data provide an important, although preliminary, information platform for functional genomics and evolutionary developmental biology in Cornus. The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and/or disease resistance in dogwoods for future analyses. Results of the study also provide markers useful for dogwood phylogenomic studies.

MS-desi, a desiccation-related protein in the floral nectar of the evergreen velvet bean (Mucuna sempervirens Hemsl): molecular identification and characterization

Plant desiccation-related proteins (DRPs) were first identified as pcC13-62 from the resurrection plant Craterostigma plantagineum and it has been suggested they are involved in plant desiccation tolerance. We identified and characterized a plant DRP, which we called MS-desi, in the floral nectar of a subtropical bean species, Mucuna sempervirens (MS). MS-desi is a major nectar protein (nectarin) of the bean plant and expresses exclusively in the stylopodium, where the nectary is located. The full-length MS-desi gene encodes for a protein of 306 amino acids with a molecular mass of 33,248 Da, and possesses a ferritin-like domain and a signal peptide of 30 amino acids. Structural and phylogenetic analysis demonstrated MS-desi has high similarity to members of the plant DRPs, including pcC 13-62 protein. MS-desi has a similar hydropathy profile to that of pcC13-62 with a grand average of hydropathy index of 0.130 for MS-desi and 0.106 for pcC13-62 protein, which is very different from those of dehydrins and late embryogenesis abundant proteins. The protein's secondary structures, both predicted from the amino acid sequence and directly analysed by far UV circular dichroism, showed that MS-desi is mainly composed of alpha helices and is relatively temperature dependent. The structure change is reversible within a wide range of temperatures. Purified MS-desi and raw MS floral nectar showed dose-dependent citrate synthase inhibition activity, but insensitivity to lactate dehydrogenase, suggesting that, unlike dehydrins, it does not act as a chaperone. The overall results constitute, to our knowledge, the first study on a desiccation-related protein in plant floral nectar.

Adaptation to seasonality and the winter freeze

Flowering plants initially diversified during the Mesozoic era at least 140 million years ago in regions of the world where temperate seasonal environments were not encountered. Since then several cooling events resulted in the contraction of warm and wet environments and the establishment of novel temperate zones in both hemispheres. In response, less than half of modern angiosperm families have members that evolved specific adaptations to cold seasonal climates, including cold acclimation, freezing tolerance, endodormancy, and vernalization responsiveness. Despite compelling evidence for multiple independent origins, the level of genetic constraint on the evolution of adaptations to seasonal cold is not well understood. However, the recent increase in molecular genetic studies examining the response of model and crop species to seasonal cold offers new insight into the evolutionary lability of these traits. This insight has major implications for our understanding of complex trait evolution, and the potential role of local adaptation in response to past and future climate change. In this review, we discuss the biochemical, morphological, and developmental basis of adaptations to seasonal cold, and synthesize recent literature on the genetic basis of these traits in a phylogenomic context. We find evidence for multiple genetic links between distinct physiological responses to cold, possibly reinforcing the coordinated expression of these traits. Furthermore, repeated recruitment of the same or similar ancestral pathways suggests that land plants might be somewhat pre-adapted to dealing with temperature stress, perhaps making inducible cold traits relatively easy to evolve.

Deacclimation kinetics and carbohydrate changes in stem tissues of Hydrangea in response to an experimental warm spell

Temperate winters are becoming progressively milder due to climate warming, and temperature patterns are becoming increasingly irregular with risk of unseasonable warm spells. Warm spells may cause premature loss of plant cold hardiness and increase the risk of subsequent freezing injury. This study investigated the timing and rate of deacclimation and associated changes in soluble carbohydrates and water status in stems of Hydrangea macrophylla ssp. macrophylla (Thunb.) Ser. 'Alma' and Hydrangea paniculata Sieb. 'Vanille Fraise' in response to a simulated warm spell (22 °C/17 °C day/night). In H. macrophylla, deacclimation kinetics showed a sigmoid course with a short lag-phase followed by a fast deacclimation rate. In H. paniculata, the deacclimation pattern could not be determined precisely, but H. paniculata, the hardier genotype based on mid-winter freezing tolerance, deacclimated to a greater extent than H. macrophylla. These results imply that dehardening resistance is not related to mid-winter hardiness. In both species deacclimation was associated with rehydration and decreasing sugar levels, but species-specific quantitative and qualitative differences in the accumulation patterns of specific sugars were observed. In H. paniculata cold hardiness may be associated with 1-kestose, an oligofructan frequently associated with overwintering in herbaceous plants, but not previously related to freezing tolerance in woody perennials.

The role of botanical gardens in climate change research

Botanical gardens have a unique set of resources that allows them to host important climate change research projects not easily undertaken elsewhere. These resources include controlled growing conditions, living collections with broad taxonomic representation, meticulous record-keeping, networks spanning wide geographic areas, and knowledgeable staff. Indeed, botanical gardens have already contributed significantly to our understanding of biological responses to climate change, particularly the effects of temperature on the timing of flowering and leaf-out. They have also made significant contributions to the understanding of the relationships among climate, physiology, and anatomy. Gardens are finding new uses for traditional research tools such as herbarium specimens and historical photographs, which are increasingly being used to obtain information on past plant behavior. Additional work on invasive species and comparative studies of responses to climatic variation are providing insights on important ecological, evolutionary, and management questions. With their large collections of plant species from throughout the world and excellent herbaria, botanical gardens are well positioned to expand their current activities to continue to provide leadership in climate change research and education.

Expressed sequence tag analysis of the response of apple (Malus x domestica'Royal Gala') to low temperature and water deficit

Leaf, bark, xylem and root tissues were used to make nine cDNA libraries from non-stressed (control) 'Royal Gala' apple trees, and from 'Royal Gala' trees exposed to either low temperature (5 degrees C for 24 h) or water deficit (45% of saturated pot mass for 2 weeks). Over 22 600 clones from the nine libraries were subjected to 5' single-pass sequencing, clustered and annotated using blastx. The number of clusters in the libraries ranged from 170 to 1430. Regarding annotation of the sequences, blastx analysis indicated that within the libraries 65-72% of the clones had a high similarity to known function genes, 6-15% had no functional assignment and 15-26% were completely novel. The expressed sequence tags were combined into three classes (control, low-temperature and water deficit) and the annotated genes in each class were placed into 1 of 10 different functional categories. The percentage of genes falling into each category was then calculated. This analysis indicated a distinct downregulation of genes involved in general metabolism and photosynthesis, while a significant increase in defense/stress-related genes, protein metabolism and energy was observed. In particular, there was a three-fold increase in the number of stress genes observed in the water deficit libraries indicating a major shift in gene expression in response to a chronic stress. The number of stress genes in response to low temperature, although elevated, was much less than the water deficit libraries perhaps reflecting the shorter (24 h) exposure to stress. Genes with greater than five clones in any specific library were identified and, based on the number of clones obtained, the fold increase or decrease in expression in the libraries was calculated and verified by semiquantitative polymerase chain reaction. Genes, of particular note, that code for the following proteins were overexpressed in the low-temperature libraries: dehydrin and metallothionein-like proteins, ubiquitin proteins, a dormancy-associated protein, a plasma membrane intrinsic protein and an RNA-binding protein. Genes that were upregulated in the water deficit libraries fell mainly into the functional categories of stress (heat shock proteins, dehydrins) and photosynthesis. With few exceptions, the overall differences in downregulated genes were nominal compared with differences in upregulated genes. The results of this apple study are similar to other global studies of plant response to stress but offer a more detailed analysis of specific tissue response (bark vs xylem vs leaf vs root) and a comparison between an acute stress (24-h exposure to low temperature) and a chronic stress (2 weeks of water deficit).

JrSUT1, a putative xylem sucrose transporter, could mediate sucrose influx into xylem parenchyma cells and be up-regulated by freeze-thaw cycles over the autumn-winter period in walnut tree (Juglans regia L.)

Sucrose has been reported to play multiple roles in the winter biology of temperate woody species. However, no report on the molecular basis of sucrose transport in xylem tissue has yet been made. In the walnut tree, it is demonstrated that during the autumn-winter period, active absorption of sucrose from xylem vessels to parenchyma cells (sucrose influx) is much higher when samplings were taken shortly after a period of freezing temperatures. Here, the question of whether this increased sucrose influx mirrors a regulation of sucrose transporters in xylem tissue was tested. A putative sucrose transporter cDNA (JrSUT1: Juglans regia sucrose transporter 1) was isolated. Over the autumn-winter period, JrSUT1 transcripts and respective proteins were present in xylem parenchyma cells and highly detected when samplings were performed shortly after a freeze-thaw cycle. This up-regulation of JrSUT1 level was confirmed in controlled conditions and was not obtained in bark. Immunolocalization studies showed that JrSUT1 and plasma membrane H+ -ATPase (JrAHA) were colocalized to vessel-associated cells (VACs), which control solute exchanges between parenchyma cells and xylem vessels. We propose that JrSUT1 could be involved in the retrieval of sucrose from xylem vessel. All these data are discussed with respect to the winter biology of the walnut tree.