Floral Development of Rhamnaceae and Origin of Its Unique Floral Features

Rhamnaceae flowers have a peculiar morphology, including keeled sepals, one stamen whorl closely related to the petals, and a broad perigynous hypanthium that supports a voluminous nectary. In the present investigation, we detailed the flower development of five Rhamnaceae species to understand the origin of such specific floral characteristics. Floral buds and flowers were processed for surface and histological analyses. The sepals emerge in sequential order and the other organs in simultaneous order. The development of the perigynous hypanthium renders the floral apex broad and concave. The sepals undergo abaxial thickening early on, forming a keel and strongly influencing the floral merosity. Petals and stamens appear close to each other on the same radius in a very short plastochron. The carpels unite soon after their emergence, forming a syncarpous ovary and free style branches. Differences in intercalary carpel growth promote the formation of inferior (Gouania virgata) and semi-inferior ovaries (Colubrina glandulosa, Hovenia dulcis, and Sarcomphalus joazeiro). Rhamnidium elaeocarpum does not undergo such growth, and the resulting ovary is superior. The keeled sepals promote the isolation of the petal-stamen pair inside the flower bud. The possibility of a common primordium that the originates petal and stamen is refuted. Comparisons with other Rosales families provide insights into the floral origin and diversification of Rhamnaceae.

Three new species of Elatostema (Urticaceae) from Thailand

Three new species of Elatostema (Urticaceae) from Thailand, E.kaweesakii Triyutth. & L.F.Fu, sp. nov., E.rubricaule Triyutth. & L.F.Fu, sp. nov. and E.saxatile Triyutth. & L.F.Fu, sp. nov., are newly described and illustrated. These new species can be distinguished by the presence of rhizome. Elatostemakaweesakii is similar to E.atroviride. Elatostemakaweesakii is a lithophyte growing in limestone crevices. It differs from E.atroviride by its large swollen rhizome, glabrous stem, glabrous receptacle, number of tepal in staminate flower, absence of tepal in pistillate flower, presence of staminodes in pistillate flower and smooth achene. Elatostemarubricaule and E.saxatile are found on sandstone habitats. They have distinct flattened and disk-like rhizome. Elatostemarubricaule is distinguished by its distinct sulcate and reddish stem with flattened and disc-like rhizome and chartaceous leaves with entire margin. Elatostemasaxatile resembles E.bulbiferum but differs by its flattened and disc-like rhizome, acute leaf apex, glabrous receptacle in pistillate inflorescences, presence of staminodes in pistillate flower, and its sandstone habitat. Descriptions, distribution, ecological and phenological data are provided.

Ficusmotuoensis (Moraceae), a new species from southwest China

A new climbing species, Ficusmotuoensis Zhen Zhang & Hong Qing Li in Moraceae from southwest China has been described and illustrated in this paper. The new species resembles F.disticha, F.diversiformis and F.hederacea, but differs from these in the medium-sized acrophylls, shorter peduncle, as well as larger and spotted syconium. According to the morphological traits and phylogenetic placement, the new species belongs to Ficussubg.Synoeciasect.Apiosycea. Besides, the new species deviates from the common distribution pattern compared to the other members of sect. Apiosycea, indicating that it could be very useful for exploring the biogeography of sect. Apiosycea.

Diversification in the Rosales is influenced by dispersal, geographic range size, and pre-existing species richness

PREMISE

Biodiversity results from origination and extinction, justifying interest in identifying traits that influence this balance. Traits implicated in the success or failure of lineages include dispersal, colonization ability, and geographic range size. We investigated the impact of dispersal and range size on contemporary diversity in the Rosales.

METHODS

We used the multiple-state speciation and extinction (MuSSE) method to explore the effects on genus-level diversification of two genus-level traits (geographic range size and within-genus proclivity to speciate) and two species traits (seed dispersal and growth habit) and the multiple hidden-state speciation and extinction (MuHiSSE) method for species-level associations. Finally, we conducted a PGLS (phylogenetic least-squares) analysis to distinguish between speciation within genera versus origination of new genera.

RESULTS

At the species level, animal dispersal enhances diversification rate in both woody and herbaceous lineages, while woody lineages without animal dispersal have higher extinction rates than speciation rates. At the genus level, herbaceous taxa have positive diversification rates regardless of other character states. Diversification rate variation is also explained by two interactions: (1) a three-way interaction between large geographic range, animal-mediated dispersal, and high within-genus species richness, whereby genera possessing all three traits have high diversification rates, and (2) a four-way interaction by which the three-way interaction is stronger in woody genera than in herbaceous genera.

CONCLUSIONS

Colonization ability may underlie the relationship between dispersal type and range size and may influence past diversification rates by decreasing extinction rates during late Cenozoic climate volatility. Thus, colonization ability could be used to predict future extinction risk to aid conservation.

Codon usage patterns across seven Rosales species

BACKGROUND

Codon usage bias (CUB) analysis is an effective method for studying specificity, evolutionary relationships, and mRNA translation and discovering new genes among various species. In general, CUB analysis is mainly performed within one species or between closely related species and no such study has been applied among species with distant genetic relationships. Here, seven Rosales species with high economic value were selected to conduct CUB analysis.

RESULTS

The results showed that the average GC1, GC2 and GC3 contents were 51.08, 40.52 and 43.12%, respectively, indicating that the A/T content is more abundant and the Rosales species prefer A/T as the last codon. Neutrality plot and ENc plot analysis revealed that natural selection was the main factor leading to CUB during the evolution of Rosales species. All 7 Rosales species contained three high-frequency codons, AGA, GTT and TTG, encoding Arg, Val and Leu, respectively. The 7 Rosales species differed in high-frequency codon pairs and the distribution of GC3, though the usage patterns of closely related species were more consistent. The results of the biclustering heat map among 7 Rosales species and 20 other species were basically consistent with the results of genome data, suggesting that CUB analysis is an effective method for revealing evolutionary relationships among species at the family or order level. In addition, chlorophytes prefer using G/C as ending codon, while monocotyledonous and dicotyledonous plants prefer using A/T as ending codon.

CONCLUSIONS

The CUB pattern among Rosales species was mainly affected by natural selection. This work is the first to highlight the CUB patterns and characteristics of Rosales species and provides a new perspective for studying genetic relationships across a wide range of species.

Uncovering the Neglected Floral Secretory Structures of Rhamnaceae and Their Functional and Systematic Significance

Rhamnaceae flowers are notably recognized by their fleshy nectary. Other types of floral secretory structures have been scarcely reported for this family. Thus, the objective of the present study was to update the occurrence of these structures in the family and to contribute to the knowledge of their morphology and systematic significance. To this end, we carried out an extensive bibliographic search on the secretory structures of the family and obtained data for 257 taxa. Additionally, we presented here novel data (surface, anatomy, and ultrastructure) for six species belonging to the main clades within Rhamnaceae. The family has a wide diversity of types of mucilage-secreting structures: epidermis, hypodermis, idioblasts, cavities, and ducts. Mucilage and phenolic idioblasts are widely distributed among the floral organs. Colleters are present in all sampled species, and these are the first reports of their occurrence in floral organs of Rhamnaceae. The information obtained about the structure, secreted content, and occurrence of the secretory structures of Rhamnaceae helped us to understand the assertive folk use of its species. The absence of mucilage and the presence of resin or mucilage cavities and ducts in some taxa may have intrafamily systematic significance.

Complete plastome sequence of Elaeagnus glabra (Elaeagnaceae): an Asian endemic plant species

Elaeagnus glabra is an evergreen vine or climbing shrub with 5 m height. It is widespread in southern China. It grows in the sunny forests or forest margins below 1000 m a.s.l. In this paper, we report and describe the complete plastome of E. glabra in order to provide useful genomic data for its systematic research. The complete plastome of E. glabra is 152,555 bp with a typical quadripartite structure of angiosperms. It contains two Inverted Repeats (IRs) of 25,918 bp, a large single-copy (LSC) of 82,408 bp, and a small single-copy (SSC) region of 18,311 bp. The complete plastome contains 129 genes, including 83 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The overall A/T content in the chloroplast genome of E. glabra is 62.90%. The phylogenetic analysis indicated that E. glabra is close to E. loureirii within Elaeagnaceae. The complete plastome of E. glabra will provide useful resources for the development and utilization of this species and the phylogenetic study of Rosales.

Anatomy solves the puzzle of explosive pollen release in wind-pollinated urticalean rosids

PREMISE OF THE STUDY

This study details the unusual synorganization of the staminate flower in wind-pollinated urticalean rosids to add the missing pieces that complete the puzzle of the explosive mechanism of pollen release in this group.

METHODS

Flower buds and flowers were analyzed using light and scanning electron microscopy.

KEY RESULTS

The pistillode, stamens, and sepals form a floral apparatus that explosively releases pollen to be carried by the wind. The anthers dehisce when the stamens are still inflexed on the floral bud and are enveloped by the sepals and supported by an inflated pistillode. The distension of the filaments presses the pistillode, which decreases the pressure exerted on the anthers by releasing the air accumulated internally through its apical orifice. The extended filaments and the dehiscent free anthers move rapidly outward from the center of the flower. This movement of the filaments is then blocked by the robust basally united sepals, which causes a rapid inversion of the anther position, thus hurling the pollen grains far from the flower. The pollen grains are released grouped by the mucilage produced in high quantity in the cells found in all floral organs.

CONCLUSIONS

The anatomical structure of the pistillode and the finding of mucilaginous cells are the main features that help in the understanding the explosive mechanism of pollen release in urticalean rosids. The pistillode can be considered an exaptation because it was evolved later to provide a new role in the plant, optimizing male fitness.

Climatic Changes and Orogeneses in the Late Miocene of Eurasia: The Main Triggers of an Expansion at a Continental Scale?

Migrations from the Qinghai-Tibetan Plateau (QTP) to other temperate regions represent one of the main biogeographical patterns for the Northern Hemisphere. However, the ages and routes of these migrations are largely not known. We aimed to reconstruct a well-resolved and dated phylogeny of Hippophae L. (Elaeagnaceae) and test hypothesis of a westward migration of this plant out of the QTP across Eurasian mountains in the Miocene. We produced two data matrices of five chloroplast DNA (cpDNA) and five nuclear DNA markers for all distinct taxa of Hippophae. These matrices were used to reconstruct phylogenetic relationships in the genus. In dating analyses, we first estimated the stem node age of Elaeagnaceae using five fossil records evenly distributed across a tree of Rosales. We used this estimate and two fossil records to calibrate the cpDNA and nDNA phylogenies of Hippophae. The same phylogenies were used to reconstruct ancestral areas within the genus. The monophyly of Hippophae, all five species, and most of subspecies was strongly supported by both plastid and nuclear data sets. Diversification of Hippophae likely started in central Himalayas/southern Tibet in the early Miocene and all extant distinct species had probably originated by the middle Miocene. Diversification of Hippophae rhamnoides likely started in the late Miocene east of the QTP from where this species rapidly expanded to central and western Eurasia. Our findings highlight the impact of different stages in uplift of the QTP and Eurasian mountains and climatic changes in the Neogene on diversification and range shifts in the highland flora on the continent. The results provide support to the idea of an immigration route for some European highland plants from their ancestral areas on the QTP across central and western mountain ranges of Eurasia in the late Miocene.

The complete chloroplast genome sequence of Spyridium parvifolium var. parvifolium (family Rhamnaceae; tribe Pomaderreae)

We assembled the complete chloroplast genome of the Australian shrub Spyridium parvifolium var. parvifolium. The genome was 161,012 bp in length, with a pair of inverted repeats (IRs) of 26,515 bp, separated by a large single copy (LSC) region of 88,814 bp and a small single copy region (SCC) of 19,168 bp. The GC content was 36.9%. In total, 130 genes were annotated, including 86 protein coding genes, 36 tRNA genes and 8 rRNA genes. Phylogenetic analysis of 56 chloroplast genes placed this genome of S. parvifolium var. parvifolium within the family Rhamnaceae.

Horizontal transfers of LTR retrotransposons in seven species of Rosales

Horizontal transposable element transfer (HTT) events have occurred among a large number of species and play important roles in the composition and evolution of eukaryotic genomes. HTTs are also regarded as effective forces in promoting genomic variation and biological innovation. In the present study, HTT events were identified and analyzed in seven sequenced species of Rosales using bioinformatics methods by comparing sequence conservation and K_a/K_s value of reverse transcriptase (RT) with 20 conserved genes, estimating the dating of HTTs, and analyzing the phylogenetic relationships. Seven HTT events involving long terminal repeat (LTR) retrotransposons, two HTTs between Morus notabilis and Ziziphus jujuba, and five between Malus domestica and Pyrus bretschneideri were identified. Further analysis revealed that these LTR retrotransposons had functional structures, and the copy insertion times were lower than the dating of HTTs, particularly in Mn.Zj.1 and Md.Pb.3. Altogether, the results demonstrate that LTR retrotransposons still have potential transposition activity in host genomes. These results indicate that HTT events are another strategy for exchanging genetic material among species and are important for the evolution of genomes.

Major intrinsic proteins repertoire of Morus notabilis and their expression profiles in different species

Leaf moisture content in Morus is a significant trait regulating the yield of silk production. Studies have shown that fresh leaves or leaves with high water content are preferably eaten by silk worm. Water and certain other molecules transport in plants is known to be regulated by aquaporins or Major Intrinsic Proteins (MIPs). Members of the MIP gene family have also been implicated in plant development and stress responsiveness. To understand how members of MIP gene family are regulated and evolved, we carried out an extensive analysis of the gene family. We identified a total of 36 non redundant MIPs in Morus notabilis genome, belonging to five subfamilies PIPs, TIPs, NIPs, XIPs and SIPs) have been identified. We performed a Gene ontology (GO) term enrichment analysis and looked at distribution of cis elements in their 2K upstream regulatory region to reveal their putative roles in various stresses and developmental aspects. Expression analysis in developmental stages revealed their tissue preferential expression pattern in diverse vegetative and reproductive tissues. Comparison of expression profiles in the leaves of three species including Morus notabilis, Morus serrata and Morus laevigata led to identification of differential expression in these species. In all, this study elaborates a basic insight into the structure, function and evolutionary analysis of MIP gene family in Morus which is hitherto unavailable. Our analysis will provide a ready reference to the mulberry research community involved in the Morus improvement program.

Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae)

Ziziphus jujuba is an important woody plant with high economic and medicinal value. Here, we analyzed and characterized the complete chloroplast (cp) genome of Z. jujuba, the first member of the Rhamnaceae family for which the chloroplast genome sequence has been reported. We also built a web browser for navigating the cp genome of Z. jujuba ( http://bio.njfu.edu.cn/gb2/gbrowse/Ziziphus_jujuba_cp/ ). Sequence analysis showed that this cp genome is 161,466 bp long and has a typical quadripartite structure of large (LSC, 89,120 bp) and small (SSC, 19,348 bp) single-copy regions separated by a pair of inverted repeats (IRs, 26,499 bp). The sequence contained 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The genome structure, gene order, GC content, and codon usage are similar to other typical angiosperm cp genomes. A total of 38 tandem repeats, two forward repeats, and three palindromic repeats were detected in the Z. jujuba cp genome. Simple sequence repeat (SSR) analysis revealed that most SSRs were AT-rich. The homopolymer regions in the cp genome of Z. jujuba were verified and manually corrected by Sanger sequencing. One-third of mononucleotide repeats were found to be erroneously sequenced by the 454 pyrosequencing, which resulted in sequences of 1-4 bases shorter than that by the Sanger sequencing. Analyzing the cp genome of Z. jujuba revealed that the IR contraction and expansion events resulted in ycf1 and rps19 pseudogenes. A phylogenetic analysis based on 64 protein-coding genes showed that Z. jujuba was closely related to members of the Elaeagnaceae family, which will be helpful for phylogenetic studies of other Rosales species. The complete cp genome sequence of Z. jujuba will facilitate population, phylogenetic, and cp genetic engineering studies of this economic plant.

Genome-wide analysis, expression dynamics and varietal comparison of NAC gene family at various developmental stages in Morus notabilis

NAC genes are important transcription factors and forms a large family in plants. They have shown to play an important role in growth and development and have also been shown to involve in regulation of stress-responsive genes. In the present study, a repertoire of NAC genes in recently published mulberry genome has been identified which consists of a total of 79 members. Structural analysis revealed that most of the NAC genes in mulberry contain two introns. The proteins encoded by them show a wide range of isoelectric points suggestive of their varied roles in varying microcellular environment. Phylogenetic and conserved motif analysis elucidate the presence of 15 sub-groups of these genes along with two novel sub-groups having distinct conserved motifs which are not present in Arabidopsis. Gene ontology term enrichment analysis and cis-element identification from their putative 1 K upstream regulatory region indicates their possible role in important biological processes like organ formation, meristem establishment, senescence, and various biotic and abiotic stresses. Expression analysis across various developmental stages led to identification of their preferential expression in diverse tissues. Taken together, this work provides a solid background information related to structure, function, expression and evolution of NAC gene family in mulberry.