Search

Soil functioning is closely linked to the interactions between biological communities with the physical environment. Yet, the impact of plant community attributes on metabolic processes promoting soil nutrient cycling remains largely unknown. We hypothesized that the plant community acts as a regulating agent of nutrient mobilization in soils according to the phylogenetic and morpho-functional traits of plant species of which it is composed. Rhizosphere soils were collected in autumn and spring under 32 tree and shrub species in two Mediterranean mixed forests (four plots in each) located in southern Spain, and nine soil enzymatic activities related to C, N and P mobilization were assessed. Phylogeny and morpho-functional traits of plant species were recorded and their imprint in soil enzymatic activities across forests was determined. The results showed a plant phylogenetic signal for N mobilization in both forests, while it varied across forests for non-labile C and P mobilization. The plant phylogenetic signals were primarily driven by lineages that diversified through the Miocene, about 25 Myr ago. In addition, leaf traits and plant's mycorrhizal type explained soil enzymatic activities independently from phylogeny. C and P mobilization increased under ectomycorrhizal plants, whilst enhanced N mobilization did occur under arbuscular mycorrhizal ones. The plant community composition led to a different carbon and nutrient mobilization degree, which in turn was mediated by distinct microbial communities mirroring differentiated resource-acquisition strategies of plants. Our results highlight the role of plant traits and mycorrhizal interactions in modulating carbon and nutrient cycling in Mediterranean mixed forest soils. [ABSTRACT FROM AUTHOR]

WRKY transcription factors play an important role in the immune system and the innate defense response of plants. WRKY transcription factors have great feedback on nitrogen stress. In this study, bioinformatics was used to detect the WRKYs of Panax notoginseng (PnWRKYs). The response of PnWRKYs under nitrogen stress was also well studied. PnWRKYs were distributed on 11 chromosomes. According to PnWRKY and Arabidopsis thaliana WRKY (AtWRKY) domains, these PnWRKY proteins were divided into three groups by phylogenetic analysis. MEME analysis showed that almost every member contained motif 1 and motif 2. PlantCARE online predicted the cis-acting elements of the promoter. PnWRKY gene family members obtained 22 pairs of repeat fragments by collinearity analysis. The expression levels of PnWRKYs in different parts (roots, flowers, and leafs) were analyzed by the gene expression pattern. They reflected tissue-specific expressions. The qRT-PCR experiments were used to detect 74 PnWRKYs under nitrogen stress. The results showed that the expression levels of 8 PnWRKYs were significantly induced. The PnWRKY gene family may be involved in biotic/abiotic stresses and hormone induction. This study will not only lay the foundation to explore the functions of PnWRKYs but also provide candidate genes for the future improvement of P. notoginseng. [ABSTRACT FROM AUTHOR]

The phylogenetic diversity (PD) can be used as a proxy for measures of functional diversity (FD); this relationship between PD and FD is premised on the reasonable assumption that evolutionary diversification has generated trait diversification, which in turn may result in greater niche complementarity. Functional traits have been used in various applications, from assemblage ecology looking at the relationship between functional diversity, environmental filtering, and assemblage structure. We used a trait-based approach, quantifying variations in the leaf-height-seed (LHS) scheme and functional and phylogenetic indices in semi-arid communities from three different habitats (grasslands, shrubland, and mixed habitats). To do so, three functional traits including specific leaf area (SLA), vegetation height (VH), and seed mass (SM) were measured in three habitats. We calculated at the plot scale, community weighted means (CWM) for each trait, species richness, Faith's phylogenetic diversity index (PD), functional richness (Frich), functional and phylogenetic mean pairwise dissimilarities (MPD), and nutrient concentration. The results showed that the first Soil_PCA axis (explaining 37.1% of the total variance) showed a high loading of soil nutrients (N, P, K, OM) and pH, while the second axis (which explained 22.1% 224 of the variance) exhibited a high loading of pH at the top and K at the bottom. Also, the higher soil nutrient concentration and pH were significant and positively related with species and functional richness and Faith's phylogenetic diversity. [ABSTRACT FROM AUTHOR]

Background: Plant nitrogen use efficiency (NUE) is an important ecological indicator that reflects the capacity of a plant to transform nitrogen into production, which is essential for further elucidating plant growth and terrestrial ecosystem productivity. Although there are a growing number of studies that address NUE changes at local scales, the variations of NUE over large spatial scales remain unclear. In this study, we analyzed the geographic patterns of NUE and explored its phylogenic and environmental drivers across 1452 species at 1102 sites in China. Results: NUE tended to decrease with latitude (r = − 0.56), whereas it increased with longitude (r = 0.54), and varied widely in different ecosystems and plant life forms. Furthermore, NUE was negatively correlated with plant foliar phosphorus concentration (r = − 0.53), soil pH (r = − 0.10), soil total phosphorus (r = − 0.13) and available phosphorus (r = − 0.05), but positively with the mean annual temperature (r = 0.32), annual precipitation (r = 0.27), and aridity index (r = 0.26). NUE was significantly altered with phylogeny and evolved toward a lower value (r = − 0.28), which may have been due to increasing nitrogen deposition and fixation in biogeochemical evolution. Overall, the combination of foliar phosphorus concentration, phylogeny, climate, and soil properties accounted for 52.7% of the total variations of NUE. In particular, foliar phosphorus concentration was the most important factor, whereas plant evolutionary history was second in contributing to NUE variations. Conclusions: Our study emphasizes the pivotal role of plant stoichiometry and phylogeny in nitrogen cycling and suggests incorporating them into earth system models to better understanding plant growth and nitrogen cycling in the context of environmental changes. [ABSTRACT FROM AUTHOR]

In February 2020, stem cankers and necrotic lesions were observed on Fatsia japonica in the Khuzestan province, Iran. Four identical isolates were obtained from symptomatic tissue and identified as Botryosphaeria dothidea based on morphology and phylogenetic analysis of the ITS and tef1 gene regions. The pathogenicity of the isolates was confirmed by inoculating healthy shrubs of F. japonica. [ABSTRACT FROM AUTHOR]

The E3 ubiquitin ligases have been known to intrigue many researchers to date, due to their heterogenicity and substrate mediation for ubiquitin transfer to the protein. HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ligases are spatially and temporally regulated for substrate specificity, E2 ubiquitin-conjugating enzyme interaction, and chain specificity during ubiquitylation. However, the role of the HECT E3 ubiquitin ligase in plant development and stress responses was rarely explored. We have conducted an in-silico genome-wide analysis to identify and predict the structural and functional aspects of HECT E3 ligase members in tomato. Fourteen members of HECT E3 ligases were identified and analyzed for the physicochemical parameters, phylogenetic relations, structural organizations, tissue-specific gene expression patterns, and protein interaction networks. Our comprehensive analysis revealed the HECT domain conservation throughout the gene family, close evolutionary relationship with different plant species, and active involvement of HECT E3 ubiquitin ligases in tomato plant development and stress responses. We speculate an indispensable biological significance of the HECT gene family through extensive participation in several plant cellular and molecular pathways. [ABSTRACT FROM AUTHOR]

During March 2016, leaf blight, followed by death, was observed on yard-long bean plants (Vigna unguiculata subsp. sesquipedalis) in Brazil. Based on morphological characteristics and phylogenetic analysis, the pathogen was identified as Rhizoctonia solani AG-1 IA. Koch's postulates were fulfilled. All accessions studied were classified as susceptible. This is the first report of Rhizoctonia solani AG1-IA infecting yard-long bean. [ABSTRACT FROM AUTHOR]

Gleditsia sinensis is an endemic species widely distributed in China with high economic and medicinal value. To explore the genomic evolution and phylogenetic relationships of G. sinensis, the complete mitochondrial (mt) genome of G. sinensis was sequenced and assembled, which was firstly reported in Gleditsia. The mt genome was circular and 594,121 bp in length, including 37 protein-coding genes (PCGs), 19 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. The overall base composition of the G. sinensis mt genome was 27.4% for A, 27.4% for T, 22.6% for G, 22.7% for C. The comparative analysis of PCGs in Fabaceae species showed that most of the ribosomal protein genes and succinate dehydrogenase genes were lost. In addition, we found that the rps4 gene was only lost in G. sinensis, whereas it was retained in other Fabaceae species. The phylogenetic analysis based on shared PCGs of 24 species (22 Fabaceae and 2 Solanaceae) showed that G. sinensis is evolutionarily closer to Senna species. In general, this research will provide valuable information for the evolution of G. sinensis and provide insight into the phylogenetic relationships within the family Fabaceae. [ABSTRACT FROM AUTHOR]

Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia. [ABSTRACT FROM AUTHOR]

The genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus. [ABSTRACT FROM AUTHOR]

We assembled new plastomes of 19 species of Mikania and of Ageratina fastigiata, Litothamnus nitidus, and Stevia collina, all belonging to tribe Eupatorieae (Asteraceae). We analyzed the structure and content of the assembled plastomes and used the newly generated sequences to infer phylogenetic relationships and study the effects of different data partitions and inference methods on the topologies. Most phylogenetic studies with plastomes ignore that processes like recombination and biparental inheritance can occur in this organelle, using the whole genome as a single locus. Our study sought to compare this approach with multispecies coalescent methods that assume that different parts of the genome evolve at different rates. We found that the overall gene content, structure, and orientation are very conserved in all plastomes of the studied species. As observed in other Asteraceae, the 22 plastomes assembled here contain two nested inversions in the LSC region. The plastomes show similar length and the same gene content. The two most variable regions within Mikania are rpl32-ndhF and rpl16-rps3, while the three genes with the highest percentage of variable sites are ycf1, rpoA, and psbT. We generated six phylogenetic trees using concatenated maximum likelihood and multispecies coalescent methods and three data partitions: coding and non-coding sequences and both combined. All trees strongly support that the sampled Mikania species form a monophyletic group, which is further subdivided into three clades. The internal relationships within each clade are sensitive to the data partitioning and inference methods employed. The trees resulting from concatenated analysis are more similar among each other than to the correspondent tree generated with the same data partition but a different method. The multispecies coalescent analysis indicate a high level of incongruence between species and gene trees. The lack of resolution and congruence among trees can be explained by the sparse sampling (~ 0.45% of the currently accepted species) and by the low number of informative characters present in the sequences. Our study sheds light into the impact of data partitioning and methods over phylogenetic resolution and brings relevant information for the study of Mikania diversity and evolution, as well as for the Asteraceae family as a whole. [ABSTRACT FROM AUTHOR]

Adrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla. [ABSTRACT FROM AUTHOR]

Marseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T). [ABSTRACT FROM AUTHOR]

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference. [ABSTRACT FROM AUTHOR]

Phaseolus vulgaris (L.), commonly known as bean or common bean, is considered a promiscuous legume host since it forms nodules with diverse rhizobial species and symbiovars. Most of the common bean nodulating rhizobia are mainly affiliated to the genus Rhizobium, though strains belonging to Ensifer, Pararhizobium, Mesorhizobium, Bradyrhizobium, and Burkholderia have also been reported. This is the first report on the characterization of bean-nodulating rhizobia at the species and symbiovar level in Greece. The goals of this research were to isolate and characterize rhizobia nodulating local common bean genotypes grown in five different edaphoclimatic regions of Greece with no rhizobial inoculation history. The genetic diversity of the rhizobial isolates was assessed by BOX-PCR and the phylogenetic affiliation was assessed by multilocus sequence analysis (MLSA) of housekeeping and symbiosis-related genes. A total of fifty fast-growing rhizobial strains were isolated and representative isolates with distinct BOX-PCR fingerpriniting patterns were subjected to phylogenetic analysis. The strains were closely related to R. anhuiense, R. azibense, R. hidalgonense, R. sophoriradicis, and to a putative new genospecies which is provisionally named as Rhizobium sp. I. Most strains belonged to symbiovar phaseoli carrying the α-, γ-a and γ-b alleles of nodC gene, while some of them belonged to symbiovar gallicum. To the best of our knowledge, it is the first time that strains assigned to R. sophoriradicis and harbored the γ-b allele were found in European soils. All strains were able to re-nodulate their original host, indicating that they are true microsymbionts of common bean. [ABSTRACT FROM AUTHOR]

Three gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement. [ABSTRACT FROM AUTHOR]

The 2′,3′-cycling ribonuclease (RNase) genes are catalysts of RNA cleavage and include the RNase T2 gene family. RNase T2 genes perform important roles in plants and have been conserved in the genome of eukaryotic organisms. In this study we identified 21 EURNS genes in Eucommia ulmoides Oliver (E. ulmoides) and analyzed their structure, chromosomal location, phylogenetic tree, gene duplication, stress-related cis-elements, and expression patterns in different tissues. The length of 21 predicted EURNS proteins ranged from 143 to 374 amino acids (aa), their molecular weight (MW) ranged from 16.21 to 42.38 kDa, and their isoelectric point (PI) value ranged from 5.08 to 9.09. Two classifications (class I and class III) were obtained from the conserved domains analysis and phylogenetic tree. EURNS proteins contained a total of 15 motifs. Motif 1, motif 2, motif 3, and motif 7 were distributed in multiple sequences and were similar to the conserved domain of RNase T2. EURNS genes with similar structure and the predicted EURNS proteins with conserved motif compositions are in the same group in the phylogenetic tree. The results of RT-PCR and transcription data showed that EURNS genes have tissue-specific expression and exhibited obvious trends in different developmental stages. Gene duplication analysis results indicated that segment duplication may be the dominant duplication mode in this gene family. This study provides a theoretical basis for research on the RNase T2 gene family and lays a foundation for the further study of EURNS genes. [ABSTRACT FROM AUTHOR]

In Rosaceae species, two gametophytic self-incompatibility (GSI) mechanisms are described, the Prunus self-recognition system and the Maleae (Malus/Pyrus/Sorbus) non-self- recognition system. In both systems the pistil component is a S-RNase gene, but from two distinct phylogenetic lineages. The pollen component, always a F-box gene(s), in the case of Prunus is a single gene, and in Maleae there are multiple genes. Previously, the Rosa S-locus was mapped on chromosome 3, and three putative S-RNase genes were identified in the R. chinensis 'Old Blush' genome. Here, we show that these genes do not belong to the S-locus region. Using R. chinensis and R. multiflora genomes and a phylogenetic approach, we identified the S-RNase gene, that belongs to the Prunus S-lineage. Expression patterns support this gene as being the S-pistil. This gene is here also identified in R. moschata, R. arvensis, and R. minutifolia low coverage genomes, allowing the identification of positively selected amino acid sites, and thus, further supporting this gene as the S-RNase. Furthermore, genotype–phenotype association experiments also support this gene as the S-RNase. For the S-pollen GSI component we find evidence for multiple F-box genes, that show the expected expression pattern, and evidence for diversifying selection at the F-box genes within an S-haplotype. Thus, Rosa has a non-self-recognition system, like in Maleae species, despite the S-pistil gene belonging to the Prunus S-RNase lineage. These findings are discussed in the context of the Rosaceae GSI evolution. Knowledge on the Rosa S-locus has practical implications since genes controlling floral and other ornamental traits are in linkage disequilibrium with the S-locus. [ABSTRACT FROM AUTHOR]

Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members' specifically A. marina and related species. [ABSTRACT FROM AUTHOR]

Background: The identification of banana cultivars genome is needed to provide a valid identity from the accession of bananas which are used as basic data in the management of in situ and ex situ banana conservation as well as for further breeding of banana cultivars. Results: The size of PCR-amplified matK ranged from 844 to 860 bp and showed a high variability. The haplotype diversity was 0.9048 with nine haplotypes. Haplotype distribution map revealed the lineage patterns of banana cultivars from Java. Reconstruction of genetic relationships using the maximum likelihood, maximum parsimony and Bayesian inference algorithms produces tree topologies and classifications that are grouped according to their genomic groups, into three main clades, i.e., AA/AAA, AAB and ABB. Based on the previously derived age constraints and fossil data, we estimate (Musaceae) that genetic divergence times of all samples occurred during the Eocene (95% HPD: 51.9 Mya), Musa acuminata group (AA, AAA, AAB) with Musa balbisiana group (BB and ABB) occurred during the Oligocene (95% HPD: 26 Mya), and the separation on each banana cultivars occurred during the Middle Miocene to Pliocene (95% HPD: 16.5–2.5 Mya). Conclusions: From this study, we conclude that all studied cultivars are closely related according to its genomic groups with high variation. Genetic variation among those cultivars creates nine haplotypes. The development of variety which leads to the formation of different banana cultivars had suggested to be occurred long ago along with human migration and domestication. [ABSTRACT FROM AUTHOR]

Welwitschia mirabilis is one of the most extraordinary plant species on earth. With a fossil record of 112 My and phylogenetically isolated within the order Gnetales, the monotypic genus Welwitschia has survived only in the northern Namib Desert in Angola and Namibia. Despite its iconic role, the biogeography, ecological niche, and evolutionary history of the species remain poorly understood. Here we present the first comprehensive map of the strongly disjunct species range, and we explore the genetic relationships among all range fragments based on six SSR markers. We also assess the variation of the environmental niche and habitat preference. Our results confirm genetic divergence, which is consistent with the hypothetical existence of two subspecies within Welwitschia. We identify an efficient geographical barrier separating two gene pools at 18.7°S in northern Namibia. We also identify further diversification within each of the two subspecies, with several different gene pools in ten isolated range fragments. Given the presence of well-isolated populations with unique gene pools and the association with different bioclimatic variables, rock types, and habitats within arid river catchments, we can hypothesize that the present intraspecific diversity may have evolved at least in part within the present refuge of the northern Namib Desert. [ABSTRACT FROM AUTHOR]

Plants have evolved genetic and physiological mechanisms to mitigate the adverse effects of high temperature. CARBOXYL TERMINUS OF THE HSC70-INTERACTING PROTEINS (CHIP) is a conserved chaperone-dependent ubiquitin E3 ligase that targets misfolded proteins. Here, we report functional analysis of the SlCHIP gene from tomato (Solanum lycopersicum) in heat tolerance. SlCHIP encodes a CHIP protein with three tandem tetracopeptide repeat (TPR) motifs and a C-terminal U box domain. Phylogenetic analysis of CHIP homologs from animals, spore-bearing and seed plants revealed a tree topology similar to the evolutionary tree of the organisms. Expression of SlCHIP was induced under high temperature and was also responsive to plant stress hormones. Silencing of SlCHIP in tomato reduced heat tolerance based on increased heat stress symptoms, reduced photosynthetic activity, elevated electrolyte leakage and accumulation of insoluble protein aggregates. The accumulated protein aggregates in SlCHIP-silenced plants were still highly ubiquitinated, suggesting involvement of other E3 ligases in ubiquitination. SlCHIP restored the heat tolerance of Arabidopsis chip mutant to the wild type levels. These results indicate that tomato SlCHIP plays a critical role in heat stress responses most likely by targeting degradation of misfolded proteins that are generated during heat stress. [ABSTRACT FROM AUTHOR]

Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree. [ABSTRACT FROM AUTHOR]

Purified occlusion bodies (OBs) of Mythimna (formerly Pseudaletia) unipuncta (the true armyworm) granulovirus Hawaiian strain (MyunGV-A) were observed, showing typical GV morphological characteristics under scanning and transmission electron microscopy (EM). The genome of MyunGV-A was completely sequenced and analysed. The genome is 176,677 bp in size, with a G+C content of 39.79%. It contains 183 open reading frames (ORFs) encoding 50 or more amino acids with minimal overlap. Comparison of MyunGV-A with TnGV, XcGV, and HearGV genomes revealed extensive sequence similarity and collinearity, and the four genomes contain the same nine homologous regions (hrs) with conserved structures and locations. Three unique genes, 12 baculovirus repeated ORF (bro), 2 helicase, and 3 enhancin genes, were identified. In particular, two repeated genes (ORF39 and 49) are present in the genome, in reverse and complementarily orientations. Twenty-four OB proteins were identified from the putative protein database of MyunGV-A. In addition, MyunGV-A belongs to the Betabaculovirus group and is most closely related to TnGV (99% amino acid identity) according to a phylogenetic tree based on the combined amino acid sequences of 38 core gene contents. [ABSTRACT FROM AUTHOR]

A recent survey in Germany revealed the wide presence of 'Candidatus Phytoplasma ulmi' in native elm stands. Accessions were studied for their genetic variability and phylogenetic relationship based on the conserved groEL and the variable imp gene. While the groEL sequences revealed a high intraspecific homology of more than 99%, the homology of the imp gene dropped to 71% between distantly related sequences. Twenty-nine groEL and 74 imp genotypes were distinguished based on polymorphic sites. Phylogenetic analysis of the groEL gene clustered all 'Ca. P. ulmi' strains and separated them from related phytoplasmas of the 16SrV group. The inferred phylogeny of the imp gene resulted in a different tree topology and separated the 'Ca. P. ulmi' genotypes into two clusters, one closely related to the flavescence dorée phytoplasma strain FD-D (16SrV-D), the other affiliated with the flavescence dorée phytoplasma strains FD-C and FD70 and the alder yellows phytoplasma (16SrV-C). In both phylograms, 'Ca. P. ulmi' genotypes from Scots elm trees formed a coherent cluster, while genotypes from European white elms and field elms grouped less strictly. The regional distribution pattern was congruent for some of the groEL and imp genotypes, but a strict linkage for all genotypes was not apparent. [ABSTRACT FROM AUTHOR]

The genus Paramignya (Rutaceae) comprises about 30 species typically distributing in tropical Asia. Like other genera of the family Rutaceae, the significant variation in the morphology of Paramignya species makes the taxonomic study and accurate identification become difficult. In Vietnam, Paramignya species have been mostly found in Khanh Hoa and Lam Dong provinces and used as traditional medicines. Recently, Paramignya trimera, a species of the genus Paramignya with local name "Xao tam phan" has been drawn attention and intensively exploited to treat liver diseases and cancers. However, the significant variations in the morphology and different local names of P. trimera have caused confusion and difficulty in the accurate identification and application of this plant for medicine. In this study, the combination of both morphological and DNA sequence data has effectively supported the taxonomic identification of P. trimera and some relatives collected in Khanh Hoa and Lam Dong provinces. The comparison of the morphology and analysis of the phylogenetic trees suggested that there was a significant variation of P. trimera. In addition, some accessions of P. trimera with morphological characteristics similar and Atalantia buxifolia were likely the intergeneric hybrids between the two species. Analysis of genetic variation, interspecific and intraspecific distances using ITS, matK and rbcL sequences shown that P. trimera was closely related to A. buxifolia, Severinia monophylla and Luvunga scandens. In addition, matK sequences represented as the effective candidate DNA barcode to identify and distinguish Paramignya species from others of the family Rutaceae. [ABSTRACT FROM AUTHOR]

This study reassesses the taxonomic status of the Malayan water shrew, Chimarrogale hantu Harrison 1958 as a distinct species and reclassifies it as the genus Crossogale through genetic and morphological analyses. We construct phylogenetic trees using both mitochondrial (cyt b) and nuclear markers (ApoB and RAG2). Chimarrogale hantu formed a distinct clade that diverged from other Chimarrogale species and other genera in the tribe Nectogalini (Nectogale, Neomys, Pseudosoriculus, Episoriculus, Chodsigoa, and Soriculus clades). The C. hantu clade is closely related to the Bornean water shrew, Crossogale phaeura with a K2P genetic distance of 7%. High K2P genetic distance (> 15% K2P) was also observed when compared to other Chimarrogale species (C. platycephalus, C. himalayica, C. styani, C. varennei and C. leander) as well as other genera from the tribe Nectogalini (> 20% K2P). We proved that C. hantu genetically and morphologically merits species rank. We suggest classifying C. hantu in the genus Crossogale along with Cr. phaeura, while the rest of the Asiatic shrews remain in the genus Chimarrogale. Future comprehensive reviews of the Sundaic water shrew group should include Chimarrogale sumatrana from Sumatra, Indonesia, for a comprehensive understanding on the relationship of water shrews between Sundaland and the rest of the Asiatic region. [ABSTRACT FROM AUTHOR]

Background: Fabaceae is considered as the third largest family, which includes more than 727 genera and 20,000 species. The genus Vicia has from 180 to 210 species. Vicia species have a great economical and agricultural importance. Karyotype study of chromosomes and SDS-PAGE for seed storage proteins (soluble and non-soluble proteins) were carried out on five Vicia species (Vicia macrocarpa, Vicia sativa, Vicia narbonensis, Vicia ervilia) collected from IPK, Germany, and Vicia faba from Agriculture Research Centre, Giza, Egypt, to find out the phylogenetic relationships among these species. Result: From karyotype of studied Vicia species chromosomes, it was found that V. macrocarpa, V. sativa, and V. faba had six pairs of chromosome (2n = 12) while V. narbonensis and V. ervilia had seven pairs of chromosome (2n = 14). The most related species was found between V. ervilia and V. narbonensis (77.8%) depending on seed soluble protein similarity level, but between V. narbonensis and V. macrocarpa was 70.0% depending on seed non-soluble protein similarity level, while between V. ervilia and V. narbonensis, the most related species was 69.0% depending on collective data of both soluble and non-soluble seed storage protein. Conclusion: The phylogenetic relationships between the studied species depending on collective data of protein markers and karyotype characteristic were as follows: V. ervilia is closely related to V. narbonensis, while V. narbonensis is related to V. macrocarpa and V. ervilia, but the degree of relation between V. narbonensis and V. macrocarpa is less than the relation between V. narbonensis and V. ervilia. Equally, while V. sativa is closely related to V. macrocarpa, but V. faba is distant from all other studied species. [ABSTRACT FROM AUTHOR]

Kobresia plants are important forage resources in the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. Therefore, it is beneficial to obtain Kobresia genome resources and study the adaptive characteristics of Kobresia plants in the Qinghai-Tibetan Plateau. We assembled the genome of Kobresia littledalei C. B. Clarke, which was about 373.85 Mb in size. 96.82% of the bases were attached to 29 pseudo-chromosomes, combining PacBio, Illumina and Hi-C sequencing data. Additional investigation of the annotation identified 23,136 protein-coding genes. 98.95% of these were functionally annotated. According to phylogenetic analysis, K. littledalei in Cyperaceae separated from Poaceae about 97.6 million years ago after separating from Ananas comosus in Bromeliaceae about 114.3mya. For K. littledalei, we identified a high-quality genome at the chromosome level. This is the first time a reference genome has been established for a species of Cyperaceae. This genome will help additional studies focusing on the processes of plant adaptation to environments with high altitude and cold weather. Measurement(s) genome • DNA • sequence_assembly • sequence feature annotation Technology Type(s) DNA sequencing • sequence assembly process • sequence annotation Factor Type(s) sequencing platform Sample Characteristic - Organism Carex littledalei Sample Characteristic - Location Tibetan Plateau Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12326612 [ABSTRACT FROM AUTHOR]

Mitochondrial genomes are valuable for making inferences regarding population genetics, phylogenetics and recently in understanding adaptive variation in OXPHOS genes. Ribbon fish, Trichiurus lepturus is distributed in the Indian Ocean and contributes to a major share of pelagic fish landings. Considering the importance, we characterized the complete mitogenome of large head hairtail T. lepturus from Indian waters by PCR amplification and sequencing. The entire mitogenome is 16,840 bp in length, with 13 protein coding genes, 2 subunit ribosomal RNA genes, and 1 control region similar to other vertebrates. Genome contains only 21 tRNAs (tRNAPro is absent) as against 22 tRNAs reported in other vertebrates. The putative origin of L-strand replication (OL) was located in a cluster of five tRNA genes (WANCY region) and may not be functional due to the variation of conserved motif (5′-GCCGG-3′) and loop. These two unusual features are common for Trichiurus mitogenomes. Phylogenetic analysis supported the monophyly of Trichiuridae. This study will provide information for further studies on taxonomy, phylogeny and patterns of adaptive evolution in the mitogenome of Trichiurus species. [ABSTRACT FROM AUTHOR]

Heat shock transcription factor (Hsf) plays a transcriptional regulatory role in plants during heat stress and other abiotic stresses. 31 non-redundant ZmHsf genes from maize were identified and clustered in the reference genome sequenced by Single Molecule Real Time (SMRT). The amino acid length, chromosome location, and presence of functional domains and motifs of all ZmHsfs sequences were analyzed and determined. Phylogenetics and collinearity analyses reveal gene duplication events in Hsf family and collinearity blocks shared by maize, rice and sorghum. The results of RNA-Seq analysis of anthesis and post-anthesis periods in maize show different expression patterns of ZmHsf family members. Specially, ZmHsf26 of A2 subclass and ZmHsf23 of A6 subclass were distinctly up-regulated after heat shock (HS) at post-anthesis stage. Nanopore transcriptome sequencing of maize seedlings showed that alternative splicing (AS) events occur in ZmHsf04 and ZmHsf17 which belong to subclass A2 after heat shock. Through sequence alignment, semi-quantitative and quantitative RT-PCR, we found that intron retention events occur in response to heat shock, and newly splice isoforms, ZmHsf04-II and ZmHsf17-II, were transcribed. Both new isoforms contain several premature termination codons in their introns which may lead to early termination of translation. The ZmHsf04 expression was highly increased than that of ZmHsf17, and the up-regulation of ZmHsf04-I transcription level were significantly higher than that of ZmHsf04-II after HS. [ABSTRACT FROM AUTHOR]

Despite application of genome-scale datasets, the phylogenetic placement of scorpions within arachnids remains contentious between two different phylogenetic data classes. Paleontologists continue to recover scorpions in a basally branching position, partly owing to their morphological similarity to extinct marine orders like Eurypterida (sea scorpions). Phylogenomic datasets consistently recover scorpions in a derived position, as the sister group of Tetrapulmonata (a clade of arachnids that includes spiders). To adjudicate between these hypotheses using a rare genomic change (RGC), we leveraged the recent discovery of ancient paralogy in spiders and scorpions to assess phylogenetic placement. We identified homologs of four transcription factors required for appendage patterning (dachshund, homothorax, extradenticle, and optomotor blind) in arthropods that are known to be duplicated in spiders. Using genomic resources for a spider, a scorpion, and a harvestman, we conducted gene tree analyses and assayed expression patterns of scorpion gene duplicates. Here we show that scorpions, like spiders, retain two copies of all four transcription factors, whereas arachnid orders like mites and harvestmen bear a single copy. A survey of embryonic expression patterns of the scorpion paralogs closely matches those of their spider counterparts, with one paralog consistently retaining the putatively ancestral pattern found in the harvestman, as well as the mite, and/or other outgroups. These data comprise a rare genomic change in chelicerate phylogeny supporting the inference of a distal placement of scorpions. Beyond demonstrating the diagnostic power of developmental genetic data as a phylogenetic data class, a derived placement of scorpions within the arachnids, together with an array of stem-group Paleozoic scorpions that occupied marine habitats, effectively rules out a scenario of a single colonization of terrestrial habitat within Chelicerata, even in tree topologies contrived to recover the monophyly of Arachnida. [ABSTRACT FROM AUTHOR]

The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes. [ABSTRACT FROM AUTHOR]

Pectins, the major components of cell walls in plants, are synthesized and secreted to cell walls as highly methyl-esterified polymers and then demethyl-esterified by pectin methylesterases (PMEs). The PMEs are spatially regulated by pectin methylesterase inhibitors (PMEIs). In this study, 43 and 49 putative PME and PMEI genes were identified in maize, respectively. Gene structure and motif analysis revealed that members in the same paralogous pairs or in the same subgroup generally had common motif compositions and gene structure patterns, which indicates functional similarity between the closely related ZmPME/PMEI genes. Gene ontology annotation analysis showed that most of the ZmPME/PMEI genes are involved in cell wall modification and pectin catabolic process with molecular functions of pectinesterase or pectinesterase inhibitor activities. There are 35 ZmPME/PMEI genes expressed higher in anthers than in other tissues from the NimbleGen maize microarray data, and the semiq-RT-PCR assay revealed most of these ZmPME/PMEIs specially expressed in anthers and pollens, indicating they possibly had role in anther and pollen development. In addition, these ZmPME/PMEI genes were highly expressed in the fertile anthers, while lowly or no expressed in sterile anthers. This further indicated these genes might be involved in the development of anther and pollen. [ABSTRACT FROM AUTHOR]

Fatty acid desaturases can catalyze saturated or unsaturated fatty acids to form a double bond at various locations in the hydrocarbon chain. In the present study, a total of 20 full-length desaturase genes were identified from rice genome. An exhaustive analysis was performed to describe their chromosomal locations, gene structures, phylogeny, cis-regulatory elements, sub-cellular localizations and expression patterns. The rice desaturase genes were distributed on ten of 12 chromosomes and phylogenetically classified into six subfamilies with the Arabidopsis counterparts, FAB2, FAD2, FAD3/7/8, FAD6, DES1 and SLD1. Among of them, 9 members were expanded via chromosomal tandem or segmental duplications. The gene structures and motif constituents were evolutionarily conserved in the same subfamilies. The majority of desaturase genes showed tissue-specific expression patterns and response to abiotic stresses and hormones based on microarray data and qRT-PCR analyses. This study will provide useful clues for functional validation of desaturase genes and contribute to produce nutritionally important fatty acids by genetic modification in rice. [ABSTRACT FROM AUTHOR]

Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment. [ABSTRACT FROM AUTHOR]

The present paper reports for the first time the characteristics of the complete plastid genome of Surianaceae (Suriana maritima L.) in the order Fabales. The circular complete plastid genome is 163,747 bp in length with a typical quadripartite organization containing 115 unique genes, of which 80 are protein-coding genes, 31 tRNA genes and four rRNA genes. The plastid genome of S. maritima is characterized by absence of intron in the atpF gene, which has never been reported for any other species of the Fabales. The gene content and their orders in the plastid genome of Surianaceae are similar to the basal lineages of the legume family (Cercidoideae, Detarioideae) and Quillajaceae, supporting a likely common ancestor for the three families. Phylogenetic analysis supported the sister relationship between Surianaceae and Leguminosae, with strongly supported by Bayesian method and moderately supported by likelihood method. The complete plastid genome of Surianaceae could provide potential benefit in resolving the long-standing unresolved interfamily relationships of Fabales when a more comprehensive sampling from Polygalaceae and Leguminosae is available for future studies. [ABSTRACT FROM AUTHOR]

For many years, methods based on the molecular analysis of conservative genome segments have been used to solve controversial issues of phylogeny by calculating the divergence of organisms. In the present study, a marker fragment of the 12S rRNA gene was used to clarify the phylogenetic position of a poorly studied faunistic group, ancient leech-like parasites of the genus Acanthobdella. The mosaic combination of oligochaete (Oligochaeta) and modern leech (Hirudinea) traits points to the intermediate evolutionary position of acanthobdells. Our results suggest that the 12S marker fragment is efficient for phylogenetic analysis at the genus and species levels. The phylogenetic history of acanthobdellids reconstructed in the present study is not consistent with the results of earlier studies. Low statistical support suggests that the 12S marker is not efficient for phylogenetic analysis at the supergenus level. [ABSTRACT FROM AUTHOR]

Echinostomes are important intestinal foodborne parasites. Despite their significance as pathogens, characterization of the molecular biology and phylogenetics of these parasites are limited. In the present study, we determined the entire mitochondrial (mt) genome of the echinostome Echinostoma miyagawai (Hunan isolate) and examined the phylogenetic relationship with selected members of the suborder Echinostomata. The complete mt genome of E. miyagawai (Hunan isolate) was 14,468 bp in size. This circular mt genome contained 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region. The gene order and genomic content were identical with its congeners. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) based on the concatenated amino acid sequences of 12 protein-coding genes strongly supported monophyly for the genus Echinostoma; however, they rejected monophyly for the family Echinostomatidae and the genus Fasciola. The mt genomic data described in this study provides useful genetic markers for studying the population genetics, molecular biology, and phylogenetics of these echinostomes. [ABSTRACT FROM AUTHOR]

Ottelia, a pantropical genus of aquatic plants belonging to the family Hydrocharitaceae, includes several narrowly distributed taxa in Asia. Although the Asian species have received comparatively more research attention than congeners in other areas, various key taxonomic questions remain unaddressed, especially with regards to apparent cryptic diversity within O. alismoides, a widespread species complex native to Asia, northern Australia and tropical Africa. Here we test taxonomic concepts and evaluate species boundaries using a phylogenetic framework. We sampled five of the seven species of Ottelia in Asia as well as each species endemic to Africa and Australia; multiple samples of O. alismoides were obtained from across Asia. Phylogenetic trees based on five plastid DNA markers and the nuclear ITS region shared almost identical topologies. A Bayesian coalescent method of species delimitation using the multi-locus data set discerned one species in Africa, one in Australia and four in Asia with the highest probability. The results lead us to infer that a population sampled in Thailand represents a hitherto unrecognised cryptic taxon within the widespread species complex, although the apparent lack of unambiguous diagnostic characters currently precludes formal description. Conversely, no molecular evidence for distinguishing O. cordata and O. emersa was obtained, and so the latter is synonymised under the former. Two accessions that exhibit inconsistent positions among our phylogenetic trees may represent cases of chloroplast capture, however incomplete lineage sorting or polyploidy are alternative hypotheses that ought to be tested using other molecular markers. [ABSTRACT FROM AUTHOR]

Coussareeae are a Neotropical clade of morphologically heterogeneous plants in the subfamily Rubioideae of the coffee family (Rubiaceae). The tribe encompasses about 330 species assigned to ten genera: Bradea, Coccocypselum, Coussarea, Cruckshanksia, Declieuxia, Faramea, Heterophyllaea, Hindsia, Oreopolus, and Standleya. Historically, the genera of Coussareeae have rarely been considered closely related, and the widely defined Coussareeae were delimited based on molecular systematics without proposed morphological synapomorphies. In order to assess the tribe's monophyly, as well as the generic limits, infrageneric relationships, and suprageneric relationships, multiple specimens per genus were sampled whenever possible and analyzed using multiple molecular loci with the Bayesian and maximum likelihood methods. The results of the phylogenetic analyses (all genera represented by multiple terminals are monophyletic, all genera are resolved with respect to each other, and three major suprageneric clades are resolved), coupled with herbarium and literature studies, were used to identify potential synapomorphic features. Non-molecular diagnostic features remain elusive for Coussareeae as a whole, but we have identified multiple diagnostic features and potential synapomorphies for each of the three major suprageneric clades: (1) Coussarea and Faramea (e.g., porate pollen grains with annuli bordering the pores); (2) Bradea, Coccocypselum, Declieuxia, Hindsia, and Standleya (e.g., colporate pollen grains with complex reticulate tecta); and 3) Cruckshanksia, Heterophyllaea, and Oreopolus (e.g., chartaceous, loculicidal capsules). The latter clade, distributed in different biomes of the Andes, is sister to the former two, both widely distributed in the Neotropics. [ABSTRACT FROM AUTHOR]

In tropical dry forests, a high interspecific variation in the strategies of fruiting phenology has been documented. Therefore, phenological responses may be mediated by influence of environmental variables, functional plant attributes or phylogenetic inertia. During 2 years, we recorded the fruiting phenology of 151 species belonging to 5 different growth forms of a Neotropical dry forest in Mexico. We evaluated the relationships between fruiting phenology, abiotic factors (precipitation, temperature, day-length) and functional attributes (growth form, dispersal syndrome, size and time for fruit development) using phylogenetic least squares models (PGLS). More species had ripe fruits during the dry season (92%) than during rainy months and dispersed their seeds by autochory and endozoochory. We found that fruit development time was positively correlated with fruit size and together the morphological fruit traits (size and dispersal syndrome) showed an important relationship with the growth form, but with a strong phylogenetic signal. Environmental seasonality had a strong influence on fruit ripening time, without a relevant association to the phylogeny of plant species. However, the phenological response to the environment (rainfall and day-length) at the community level was mediated by growth form. In woody species, we documented a high interspecific fruiting variation linked with the different dispersal syndromes. In herbaceous species, fruiting phenology is a trait restricted by the duration of their life cycle by rainfall seasonality, which in turn might have selected some traits (e.g., dry fruit, presence of spines, explosive dehiscence) for maximizing seed dispersal during the dry season. [ABSTRACT FROM AUTHOR]

Oligopeptide transporters (OPT) are integral cell membrane proteins that play a critical role in the transport of small peptides, secondary amino acids, glutathione conjugates, and mineral uptake. In the present study, 67 putative wheat yellow stripe-like transporter (YSL) proteins belonging to the subfamily of OPT transporters were identified. Phylogeny analysis resulted in the distribution of wheat YSLs into four discrete clades. The highest number of YSLs was present on the A genome and the chromosome 2 of hexaploid wheat. The identified wheat YSL genes showed differential expression in different tissues and during grain development suggesting the importance of this subfamily. Gene expression pattern of TaYSLs during iron starvation experiments suggested an early high transcript accumulation of TaYS1A, TaYS1B, TaYSL3, TaYSL5, and TaYSL6 in roots. In contrast, delayed expression was observed in shoots for TaYS1A, TaYS1B, TaYSL5, TaYSL12, and TaYSL19 as compared to control. Further, their expression under biotic and abiotic response emphasized their alternative functions during the plant growth and development. In conclusion, this work is the first comprehensive study of wheat YSL transporters and would be an important resource for prioritizing genes towards wheat biofortification. [ABSTRACT FROM AUTHOR]

The genus Machaerophorus includes three perennial species (M. arequipa, M. laticarpus, and M. matthioloides) inhabiting the southern Peruvian Andes. However, based on the morphological data, this genus has been reduced for more than one hundred years to synonymy of several genera of various tribes, and its phylogenetic placement using molecular data has never been studied. Therefore, in this study we explored the phylogenetic placement of Machaerophorus to test its generic status and tribal assignment, using for this purpose ribosomal nuclear (ITS) and chloroplast (trnL-F, trnH-psbA, rps16 intron) data together with a comprehensive sampling of taxa. Results obtained here demonstrated that Machaerophorus represents a well-differentiated lineage within the South American Cremolobeae-Eudemeae-Schizopetaleae clade, and hence, the genus is reinstated and excluded from the placements in Sibara and Mathewsia. Based on molecular data and morphological affinities, we included it within the tribe Schizopetaleae. A key to Machaerophorus and the genera of Schizopetaleae is also presented. [ABSTRACT FROM AUTHOR]

Fargesia, a temperate woody bamboo genus, is one of the largest genera and constitutes a taxonomically problematic group due to unusual life cycles and the rarity of flowering. We explored phylogenetic relationships within Fargesia and its allies based on sequence data from three cpDNA regions (matK, psbA-trnH and trnL-trnF) and one nuclear region (nrITS). A representative sample of 49 species, including 36 Fargesia and nine Yushania, were sampled, and maximum parsimony, maximum likelihood and Bayesian inference were used to reconstruct the phylogeny of Fargesia. The results suggest that Fargesia is polyphyletic, with F. crassinoda and F. damuniu in the Thamnocalamus clade, F. ampullaris, F. semiorbiculata, F. gyirongensis and F. collaris in the Drepanostachyum + Himalayacalamus clade, and the rest of species of Fargesia and all sampled species of Yushania in a Fargesia + Yushania clade, which was further divided into weakly supported Fargesia spathe and non-spathe clades. Species in the Fargesia spathe clade have the derived "spathe-like leaf sheath syndrome," which may have evolved as a result of an adaptive advantage of compressed inflorescences in colder temperatures. [ABSTRACT FROM AUTHOR]

In spite of their success during the past several millions of years, recent analyses indicate that polyploid species may have higher extinction rates than their diploid relatives. The idea that neopolyploid species are relatively short-lived is antithetical to the notion of polyploid exceptionalism. I propose that young, established polyploid species have unusually high extinction rates due to demographic and genetic challenges and that early demise accounts for the elevated extinction of polyploid species as a whole. Polyploid species are composed of conspecific lineages (each of an independent origin). Each origin is associated with a genetic and demographic bottleneck which reduces their abilities to cope with environment perturbations. The greater the number of independently originated lineages, the longer a polyploid species is likely to persist, given that the lineages are genetically/ecologically divergent. Autopolyploids appear to have much higher extinction rates than allopolyploids, even though the formation frequency in autopolyploids may be orders of magnitude greater. Niche differences between polyploids and their progenitors may be enhanced via the differential survival of the most divergent polyploids relative to their progenitors. It seems to be the rarely successful polyploid that flourishes during times of environmental alteration and that leaves an enduring genomic legacy. [ABSTRACT FROM AUTHOR]

A comprehensive study of critical South Asian species Seseli diffusum (Umbelliferae—Apioideae—Apieae) was carried out to determine the most suitable taxonomic position of the species, based on morphology (carpoanatomy, micromorphology of the fruit indumentum and some vegetative characters) and molecular data from nrDNA ITS region sequencing. Comparison with certain other species of Seseli and several provisionally related Apieae genera showed a close affinity of S. diffusum to the genus Psammogeton and more distant relationships with some species of Trachyspermum, clearly polyphyletic genus. No species of Seseli, even in broad sense, was found to be closely related to S. diffusum. It was proposed to transfer this species into Psammogeton, while separating a new section, Pseudoseseli, within the latter. [ABSTRACT FROM AUTHOR]

Despite progress in prevention and management of biological invasions, challenges remain, including difficulties with assessing future invasion risks. Predicting the identity of potentially damaging invaders is complex because they are often unknown as pests in their natural range. We used a plant sentinel approach to assess host ranges of invasive aphids across 62 conifer species from around the world in Christchurch Botanic Gardens, as a model for risk assessment such as for the 'International Plant Sentinel Network'. Using standardised sampling, we obtained ca. 600 observations of aphid abundances (4731 individuals), mainly of the pine aphids Eulachnus brevipilosus and Essigella californica and the spruce aphids Cinara pilicornis and Elatobium abietinum. These aphids were highly genus-specific, despite the spatially mixed distribution of genera. A phylogenetic analysis of pine aphid host preferences showed that abundances of species varied among pine subgenera and the geographic origin of trees, with significantly more aphids on pines in the subgenus Pinus than the subgenus Strobus. Essigella californica occurred abundantly on many pines across most subsections in the subgenus Pinus whereas E. brevipilosus was largely restricted to a few species in the subsection Pinus. Our study revealed several new host records (previously unknown aphid-host relationships) including the abundant occurrence of E. brevipilosus on Japanese red pine, P. densiflora, and of E. californica on P. yunnanensis, P. serotina, P. brutia, and P. nigra, among others. Our study identified numerous novel insect-plant interactions that are likely to materialise if these aphids colonise new host plants, confirming the utility of the plant sentinel approach. [ABSTRACT FROM AUTHOR]

A new species of Asplundia from the Cordillera Central in Colombia is described and illustrated. Asplundia callejasii is placed in A. subg. Asplundia, based on the morphology of the staminate flowers. The most distinctive characteristic of A. callejasii is its long leaves, with the blade unicostate, oblanceolate, shallowly divided, and very lustrous, with the plicate nerves forming roughly 45° angles with the midrib. These features give it a unique aspect that sets it apart from any other species within the family. [ABSTRACT FROM AUTHOR]