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The tropical seagrass Halophila stipulacea invaded the Eastern Mediterranean Sea in the late nineteenth century and progressively spread throughout the basin ever since. Its spread is expected to continue north-westward as the Mediterranean Sea becomes warmer, potentially changing the seagrass biogeography of the basin. Given the power of genomics to assess invasion dynamics in non-model species, we report the first ddRAD-seq study of H. stipulacea and small-scale population genomic analysis addressing its century-old Mediterranean invasion. Based on 868 SNPs and 35 genotyped native (Red Sea) and exotic (from Cyprus, Greece, and Italy) samples, results suggest that genetic structure was high, especially between major geographic discontinuities, and that exotic populations maintain comparably lower genetic diversity than native populations, despite 130 years of invasion. The evidence of high heterozygosity excess, coupled with previously reported male-dominated and rare flowering records in the exotic range, suggests that clonal propagation likely played a pivotal role in the successful colonization and spread of H. stipulacea in the Mediterranean. This shift in reproductive strategy, particularly evident in the Italian populations located closest to the western boundary and representing more recent establishments, underscores the importance of this cost-effective mode of reproduction, especially during the initial stages of invasion, raising questions about the species future expansion trajectory. Our findings serve as a catalyst for future research into the species' invasion dynamics, including deciphering the intricate roles of acclimatization and rapid adaptation, important for a comprehensive assessment of invasion risks and improving management strategies aimed at conserving seagrass ecosystems. [ABSTRACT FROM AUTHOR]

Haematococcus pluvialis is a green microalga of commercial interests due to its ability to produce a high value ketocarotenoid, astaxanthin. As a non-model species that lacks a well annotated genome, omics analyses such as transcriptomics and proteomics analysis have often been used together with physiological and biochemical analysis to explore pathways of interest. However, interpretation of these datasets remains challenging. In this work, TMT-based proteomics and phosphoproteomics analyses were conducted on Haematococcus cells grown under favorable conditions (green stage biomass) and high-light stress conditions (red stage biomass). Phosphoproteins were enriched using titanium dioxide before LC–MS/MS analysis. Our proteomics and phosphoproteomics analyses identified 1394 proteins and 569 phosphosites on 366 phosphoproteins, respectively. Of these, 1315 proteins and 396 phosphosites on 314 phosphoproteins were quantifiable, among which 370 proteins and 121 phosphosites on 94 phosphoproteins were differentially expressed. Using an improved analysis pipeline that combines Blast2GO, KEGG, and DAVID to analyze differentially expressed proteins and phosphoproteins, total identified proteins increased from 255 to 322 and total identified phosphoproteins increased from 59 to 70, which were 26.28% and 18.64%, respectively, higher than with the UniProt analysis alone. Using this pipeline, a previously uncharacterized protein and phosphoprotein were identified as an ATPase subunit B and a phosphofructokinase, respectively, and further confirmed with translated genomic and transcriptomic data. This work provides an example of phosphoproteomics analysis in H. pluvialis, while the proteomics and phosphoproteomics analysis pipelines described here may be useful to analyze omics data from other non-model algal species. [ABSTRACT FROM AUTHOR]

Microsatellite markers were developed for the tree peony Paeonia delavayi to investigate fine scale population genetics of this species. Using ddRAD-seq data from twenty individuals of P. delavayi, we identified 529 polymorphic microsatellite loci, of which 195 were suitable for designing microsatellite primers. Of the 120 microsatellite loci selected for validation, 20 were successfully amplified with clear peaks and displayed polymorphism. Three populations were genotyped using the 20 polymorphic microsatellites. The number of alleles per locus ranged from two to thirteen. Observed and expected heterozygosity ranged from 0 to 0.941 and 0 to 0.834 respectively. The cross-species amplification test using five individuals from a population of P. ludlowii showed that 15 of the 20 polymorphic loci were successfully amplified, and four loci showed polymorphism. Among the 22 alleles occurring in P. ludlowii across fifteen loci, eight alleles across five loci were exclusive to P. ludlowii. The results demonstrate that ddRAD-seq is an efficient method for the development of microsatellite markers for non-model organisms with large genomes. The newly developed markers will be valuable tools to investigate the genetic diversity, genetic structure, and gene flow of P. delavayi from local to regional spatial scales. [ABSTRACT FROM AUTHOR]

Our pioneering data provide the first comprehensive view of placental transcriptome of the beaver during single and multiple gestation. RNA-Seq and a de novo approach allowed global pattern identification of C. fiber placental transcriptome. Non-redundant beaver transcriptome comprised 211,802,336 nt of placental transcripts, grouped into 128,459 contigs and clustered into 83,951 unigenes. An Ensembl database search revealed 14,487, 14,994, 15,004, 15,267 and 15,892 non-redundant homologs for Ictidomys tridecemlineatus, Rattus norvegicus, Mus musculus, Homo sapiens and Castor canadensis, respectively. Due to expression levels, the identified transcripts were divided into two sets: non-redundant and highly expressed (FPKM > 2 in at least three examined samples), analysed simultaneously. Among 17,009 highly expressed transcripts, 12,147 had BLASTx hits. GO annotations (175,882) were found for 4301 transcripts that were assigned to biological process (16,386), cellular component (9149) and molecular function (8338) categories; 666 unigenes were also classified into 122 KEGG pathways. Comprehensive analyses were performed for 411 and 3078 highly expressed transcripts annotated with a list of processes linked to 'placenta' (31 GO terms) or 'embryo' (324 GO terms), respectively. Among transcripts with entire CDS annotation, 281 (placenta) and 34 (embryo) alternative splicing events were identified. A total of 8499 putative SNVs (~ 6.2 SNV/transcript and 1.7 SNV/1 kb) were predicted with 0.1 minimum frequency and maximum variant quality (p value 10e−9). Our results provide a broad-based characterization of the global expression pattern of the beaver placental transcriptome. Enhancement of transcriptomic resources for C. fiber should improve understanding of crucial pathways relevant to proper placenta development and successful reproduction. [ABSTRACT FROM AUTHOR]

The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied. [ABSTRACT FROM AUTHOR]

As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective 'RAD-seq-Assembly-Microsatellite' approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design. A total of 121,750 RAD contigs were generated with a mean length of 522 bp, and 19,782 contigs contained microsatellite motifs. A total of 156,150 primer pairs were successfully designed based on 16,497 contigs containing priming sites. Experimental validation of 52 randomly selected microsatellite loci demonstrated that 45 (86.54%) loci were successfully amplified and polymorphic in two geographically isolated populations of T. fasciatus. Compared with traditional approaches based on DNA cloning and other approaches based on next-generation sequencing, our newly developed approach could yield thousands of microsatellite loci with much higher successful amplification rate and lower costs, especially for non-model species with shallow background of genomic information. The 'RAD-seq-Assembly-Microsatellite' approach holds great promise for microsatellite development in future ecological and evolutionary studies of non-model species. [ABSTRACT FROM AUTHOR]

Evolutionary developmental biology often combines methods for examining morphology (e.g., scanning electron microscopy, SEM) with analyses of gene expression (e.g., RNA in situ hybridization). Due to differences in tissue preparation for SEM and gene expression analyses, the same specimen cannot be used for both sets of techniques. To aid in the understanding of morphological variation, it would be particularly useful to have a high-magnification image of the very same sample in which gene expression is subsequently analyzed. To address this need, we developed a method that couples extended depth of field (EDF) epi-illumination microscopy to in situ hybridization in a sequential format, enabling both surface microscopy and gene expression analyses to be carried out on the same specimen. We first created a digital image of inflorescence apices using epi-illumination microscopy and commercially available EDF software. We then performed RNA in situ hybridizations on photographed apices to assess the expression of two developmental genes: Knotted1 ( Kn1) in Zea mays (Poaceae) and a PISTILLATA ( PI) homolog in Musa basjoo (Musaceae). We demonstrate that expression signal is neither altered nor reduced in the imaged apices as compared with the unphotographed controls. The demonstrated method reduces the amount of sample material necessary for developmental research, and enables individual floral development to be placed in the context of the entire inflorescence. While the technique presented here is particularly relevant to floral developmental biology, it is applicable to any research where observation and description of external features can be fruitfully linked with analyses of gene expression. [ABSTRACT FROM AUTHOR]

The potential use of single nucleotide polymorphism markers (SNPs) in conservation genetics is widely recognized; however, methods for discovering large numbers of SNPs typically rely on relatively expensive, genome-wide, species-specific research projects which limits their development in many taxa. Here we describe the use of high-density SNP genotyping arrays designed for cattle to discover SNPs in two antelope species. From a total of 54,001 SNP markers on the array, the analysis yielded 148 polymorphic markers in the scimitar-horned oryx and 149 in the Arabian oryx. The results represent a first step toward developing SNP marker panels for ongoing projects on each species. As high density genotyping arrays become available for an increasing number of model species, this approach has the potential to generate SNP markers, rapidly and affordably, in a broad range of species for conservation genetic research. [ABSTRACT FROM AUTHOR]

Abstract: We present 151 SNPs (single nucleotide polymorphisms) identified in Tatra and Alpine chamois individuals after genotyping with the Bovine SNP50 Genotyping BeadChip (Illumina®). Population structure analysis based on the identified 151 SNPs as well as a subset of 48 SNPs were able to give information about geographic origin of each individual making the markers suitable for future evaluation and monitoring of the genetic status of the Tatra and Alpine chamois. Our study demonstrates how it is possible to quickly identify informative SNPs in non-model organisms based on a SNP marker panel created for a related domestic species. [Copyright &y& Elsevier]