PlantRNA 2.0 : an updated database dedicated to tRNAs of photosynthetic eukaryotes

PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 48 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. Transfer RNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, circa 35 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, putative unconventional splicing sites in the D- or T- regions of tRNA molecules were experimentally determined to strengthen the quality of the database. As for PlantRNA 1.0, comprehensive biological information including flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.

Coleopteran Pollinators of Annonaceae in the Brazilian Cerrado—A Review

The evolutionary trajectories of insects and angiosperms appear to be intimately interconnected. Increases in the diversity of phytophagous beetles and angiosperms co-occur in the Mesozoic fossil record, and there is fossil evidence of pollinivory and pollination by insects, both in flowering plants and in gymnosperms. The oldest records of angiosperm pollination indicate flies as pollen vectors. A basal group of angiosperms, the order Magnoliales, has retained plesiomorphic characters such as dozens of pistils and stamens spiraling around the receptacle. In a family of this order, Annonaceae, over 90% of species are pollinated by beetles. In many Annonaceae species, flowers display wide spaces, referred to as floral chambers, where beetles can find shelter from weather conditions and predators, food in the form of pollen and tissues, and a mating site. Two basic types of floral chambers can be distinguished: small chambers visited by small beetles (Nitidulidae, Staphylinidae, Chrysomelidae, and Curculionidae) with diurnal and/or nocturnal activity and large and thermogenic floral chambers visited by beetles of the tribe Cyclocephalini (Scarabaeoidea, Melolonthidae). In the latter case, the heat that the flowers produce may serve as a resource for the beetles that visit them, resulting in smaller endothermy costs for the scarabs. This study reviewed the literature including PhD and MSc theses on cantharophilous Annonaceae in the Cerrado. In this biome, both types of associations are found, although cantharophilous Annonaceae represent a small portion of the plant species (<5%). Cantharophilous Annonaceae in the Cerrado share attributes according to the beetles that pollinate them: species pollinated by small beetles, for instance, may flower throughout the year, whereas Annonaceae pollinated by Cyclocephalini normally flower in the beginning of the rainy season (October/November), in synchrony with the phenological patterns of their pollinators. Cantharophilous Annonaceae flowers, regardless of their size, tend to have light colors and sweet and fruity odors. In addition to the lack of studies on the attraction of beetles by these floral characters, the taxonomic composition of the beetles that pollinate Annonaceae in the Cerrado is poorly known. This review attempts to discuss, in light of what has already been published, potential fields of investigation concerning pollinating beetles’ behavior and evolution.

Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

Whole genome phylogeny of Cyanobacteria documents a distinct evolutionary trajectory of marine picocyanobacteria

During their 2.7 Gyr long evolution cyanobacteria radiated into a large number of different lineages. To better understand the evolution of cyanobacteria we compared a whole genome phylogenetic tree using 1,047 concatenated single copy orthologues of Prochlorococcus marinus MIT9313 obtained from 93 reference prokaryotic species with traditional phylogenies inferred from 16S rRNA gene and 109 genes found in all used genomes. In contrast to the traditional phylogeny, our genome wide analysis shows a split between picocyanobacteria encompassing all marine Prochlorococcus species, marine Synechococcus species, and members of freshwater Cyanobium genus (altogether referred here as the PSC clade) and the remaining groups of extant cyanobacteria. To determine the influence of the horizontal gene transfer on the overall tree topology we removed the 374 genes identified as potentially transferred genes. A newly calculated tree utilizing the remaining 673 genes displayed the same topology as the former whole genome tree with the PSC clade as a basal group of all cyanobacteria. The picocyanobacteria also exhibited distinctly larger similarity to reference bacteria's cell and genome size, carboxyzome architecture, various metabolic pathways, and chlorophyll synthesis than to the other cyanobacteria. Potentially horizontally transferred genes were found in connected chains throughout fundamental metabolic pathways suggesting that evolution of these genes was severely limited and or brought to a standstill. The environment related genes connected with metabolism of nitrogen, sulfur, and scarce seawater metals were more conserved in PSC group as they were already best tuned for its poor and stable environment. Other genes were found predominantly sequentially static as they were already accurately adapted with rare beneficial mutations. The PSC clade thus represents an isolated cyanobacterial lineage which followed a distinct evolutionary trajectory driven by its specific environment.

Hipparion Datum Implies Miocene Palaeoecological Pattern

Here, we report well–preserved skulls and postcranial specimens of the subgenus Hippotherium from the Linxia Basin, Gansu, China. Based on morphological comparison, the species of subgenus Hippotherium in China, Hipparion weihoense and Hipparion chiai, should be ascribed to the same species, H. weihoense. The species Hipparion prostylum (later Hipparion aff. brachypus) from Maragheh, Iran should also be ascribed to H. weihoense. Phylogenetic analysis shows the subgenus Hippotherium derived from the North American genus Cormohipparion, and as a basal group of Hipparion in Eurasia, representing the Hipparion Datum. Analysis on locomotive ability indicates that H. weihoense likely lived in an open habitat, whereas other species of subgenus Hippotherium likely lived in closed habitats. This result indicates a palaeoecological pattern in the early Late Miocene in Eurasia: influenced by a series of geological events, aridification of mid–latitude Asia progressed, whereas Europe and North Africa remained relatively humid; as the genus originated from East Asia, Hipparion divided rapidly into different groups with differing functional morphology to occupy diverse niches.

An Optimized Transformation System and Functional Test of CYC-Like TCP Gene CpCYC in Chirita pumila (Gesneriaceae)

The development of an ideal model plant located at a key phylogenetic node is critically important to advance functional and regulatory studies of key regulatory genes in the evolutionary developmental (evo-devo) biology field. In this study, we selected Chirita pumila in the family Gesneriaceae, a basal group in Lamiales, as a model plant to optimize its genetic transformation system established previously by us through investigating a series of factors and further conduct functional test of the CYC-like floral symmetry gene CpCYC. By transforming a RNAi:CpCYC vector, we successfully achieved the desired phenotypes of upright actinomorphic flowers, which suggest that CpCYC actually determines the establishment of floral zygomorphy and the horizontal orientation of flowers in C. pumila. We also confirmed the activities of CpCYC promoter in dorsal petals, dorsal/lateral staminodes, as well as the pedicel by transferring a CpCYC promoter:GUS vector into C. pumila. Furthermore, we testified the availability of a transient gene expression system using C. pumila mesophyll protoplasts. The improved transformation system together with the inherent biological features would make C. pumila an attractive new model in functional and regulatory studies for a broad range of evo-devo issues.

Effect of Supplementing Seaweed Extracts to Pigs until d35 Post-Weaning on Performance and Aspects of Intestinal Health

The objective of this study was to examine the effects of feeding laminarin (LAM) and fucoidan (FUC) enriched seaweed extracts up to d35 post-weaning on measures of animal performance, intestinal microbial and transcriptome profiles. 75 pigs were assigned to one of three groups: (1) basal diet; (2) basal diet + 250 ppm fucoidan; (3) basal diet + 300 ppm laminarin with 7 replicates per treatment group. Measures of performance were collected weekly and animals sacrificed on d35 post-weaning for the sampling of gastrointestinal tissue and digesta. Animal performance was similar between the basal group and the groups supplemented with FUC and LAM (P > 0.05). Pigs fed the basal diet had higher alpha diversity compared to both the LAM and FUC supplemented pigs (P < 0.05). Supplementation with LAM and FUC increased the production of butyric acid compared to basal fed pigs (P < 0.05). At genus level pigs fed the LAM supplemented diet had the greatest abundance of Faecalbacterium, Roseburia and the lowest Campylobacter of the three experimental treatments (P< 0.05). While neither extract had beneficial effects on animal performance, LAM supplementation had a positive influence on intestinal health through alterations in the gastrointestinal microbiome and increased butyrate production.

Resolving the early divergence pattern of teleost fish using genome-scale data

Regarding the phylogenetic relationship of the three primary groups of teleost fishes, Osteoglossomorpha (bonytongues and others), Elopomorpha (eels and relatives), Clupeocephala (the remaining teleost fish), early morphological studies hypothesized the first divergence of Osteoglossomorpha, whereas the recent prevailing view is the first divergence of Elopomorpha. Molecular studies supported all the possible relationships of the three primary groups. This study analyzed genome-scale data from four previous studies: (1) 412 genes from 12 species, (2) 772 genes from 15 species, (3) 1,062 genes from 30 species, and (4) 491 UCE loci from 27 species. The effects of the species, loci, and models used on the constructed tree topologies were investigated. In the analyses of the datasets (1) - (3), although the first divergence of Clupeocephala that left the other two groups in a sister relationship was supported by concatenated sequences and gene trees of all the species and genes, the first divergence of Elopomorpha among the three groups was supported using species and/or genes with low divergence of sequence and amino-acid frequencies. This result corresponded to that of the UCE dataset (4), whose sequence divergence was low, which supported the first divergence of Elopomorpha with high statistical significance. The increase in accuracy of the phylogenetic construction by using species and genes with low sequence divergence was predicted by a phylogenetic informativeness approach and confirmed by computer simulation. These results supported that Elopomorpha was the first basal group of teleost fish to have diverged, consistent with the prevailing view of recent morphological studies.

Cranial morphology of the middle Permian pareiasaur Nochelesaurus alexanderi from the Karoo Basin of South Africa

ABSTRACT Pareiasaurs were globally distributed, abundant, herbivorous parareptiles with the basal-most members found only in the mid-Permian of South Africa. These basal forms form a monophyletic group and were locally abundant and became extinct at the top of the Tapinocephalus Assemblage Zone at the end of the Guadalupian. Four species of basal pareiasaurs are currently recognised: Bradysaurus baini, B. seeleyi, Embrithosaurus schwarzi and Nochelesaurus alexanderi, but they are all poorly understood and there remains historic uncertainty as to their validity. In this paper, our second contribution designed to improve understanding of the basal group, we present the first detailed cranial description and updated diagnosis for Nochelesaurus alexanderi and demonstrate that it is a distinct taxon based on one cranial autapomorphy, a large transversely wide postparietal, and a combination of cranial characters. Within the local group of mid-Permian pareiasaurs, we recognise new dental features of Nochelesaurus alexanderi: non-symmetrical marginal cusp arrangements on upper and lower teeth resulting from an extra basal mesial cusp; an incipient horizontal cingulum on lower jaw teeth, sometimes with one or two tiny medial cingular cusps; and up to ten marginal cusps. Our study demonstrates that tooth morphology and orientation, cranial ornamentation, morphology of the cheek bosses, shape of the postfrontal and postparietal, and morphology of the distal paroccipital process of the opisthotic are the most useful to identify South African mid-Permian pareiasaurs.

Mutational Dynamics of Aroid Chloroplast Genomes II

The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.