Evolution of the NANOG pseudogene family in the human and chimpanzee genomes

BACKGROUND: The NANOG gene is expressed in mammalian embryonic stem cells where it maintains cellular pluripotency. An unusually large family of pseudogenes arose from it with one unprocessed and ten processed pseudogenes in the human genome. This article compares the NANOG gene and its pseudogenes in the human and chimpanzee genomes and derives an evolutionary history of this pseudogene family. RESULTS: The NANOG gene and all pseudogenes except NANOGP8 are present at their expected orthologous chromosomal positions in the chimpanzee genome when compared to the human genome, indicating that their origins predate the human-chimpanzee divergence. Analysis of flanking DNA sequences demonstrates that NANOGP8 is absent from the chimpanzee genome. CONCLUSION: Based on the most parsimonious ordering of inferred source-gene mutations, the deduced evolutionary origins for the NANOG pseudogene family in the human and chimpanzee genomes, in order of most ancient to most recent, are NANOGP6, NANOGP5, NANOGP3, NANOGP10, NANOGP2, NANOGP9, NANOGP7, NANOGP1, and NANOGP4. All of these pseudogenes were fixed in the genome of the human-chimpanzee common ancestor. NANOGP8 is the most recent pseudogene and it originated exclusively in the human lineage after the human-chimpanzee divergence. NANOGP1 is apparently an unprocessed pseudogene. Comparison of its sequence to the functional NANOG gene's reading frame suggests that this apparent pseudogene remained functional after duplication and, therefore, was subject to selection-driven conservation of its reading frame, and that it may retain some functionality or that its loss of function may be evolutionarily recent

Elevated genetic diversity in an F2:6 population of quinoa (<i>Chenopodium quinoa</i>) developed through an inter-ecotype cross

Quinoa (Chenopodium quinoa) is a seed crop of the Andean highlands and Araucanian coastal regions of South America that has recently expanded in use and production beyond its native range. This is largely due its superb nutritional value, consisting of protein that is rich in essential amino acids along with vitamins and minerals. Quinoa also presents a remarkable degree of tolerance to saline conditions, drought, and frost. The present study involved 72 F2:6 recombinant inbred lines (RIL) and parents developed through hybridization between highland (0654) and coastal (NL-6) germplasm groups. The purpose was to characterize the quinoa germplasm developed, to assess the discriminating potential of 21 agro-morpho phenological traits, and to evaluate the extent of genetic variability recovered through selfing. A vast amount of genetic variation was detected among the 72 lines evaluated for quantitative and qualitative traits. Impressive transgressive segregation was measured for seed yield (22.42 g/plant), while plant height and maturity had higher heritabilities (73 and 89%, respectively). Other notable characters segregating in the population included panicle and stem color, panicle form, and resistance to downy mildew. In the Principal Component analysis, the first axis explained 74% of the total variation and was correlated to plant height, panicle size, stem diameter, biomass, mildew reaction, maturation, and seed yield; those traits are relevant discriminatory characters. Yield correlated positively with panicle length and biomass. UPGMA based cluster analysis identified three groups: one consisting of late, mildew-resistant, high yielding lines; one having semi-late lines with intermediate yield and mildew susceptibility; and a third cluster consisting of early to semi-late accessions with low yield and mildew susceptibility. This study highlighted the extended diversity regenerated among the 72 accessions and helped to identify potentially adapted quinoa genotypes for production in the Moroccan coastal environment

Development and mapping of SNP assays in allotetraploid cotton

A narrow germplasm base and a complex allotetraploid genome have made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypiumhirsutum). To generate sequence for SNP discovery, we conducted a genome reduction experiment (EcoRI, BafI double digest, followed by adapter ligation, biotin–streptavidin purification, and agarose gel separation) on two accessions of G. hirsutum and two accessions of G. barbadense. From the genome reduction experiment, a total of 2.04 million genomic sequence reads were assembled into contigs with an N50 of 508 bp and analyzed for SNPs. A previously generated assembly of expressed sequence tags (ESTs) provided an additional source for SNP discovery. Using highly conservative parameters (minimum coverage of 8× at each SNP and 20% minor allele frequency), a total of 11,834 and 1,679 non-genic SNPs were identified between accessions of G. hirsutum and G. barbadense in genome reduction assemblies, respectively. An additional 4,327 genic SNPs were also identified between accessions of G. hirsutum in the EST assembly. KBioscience KASPar assays were designed for a portion of the intra-specific G. hirsutum SNPs. From 704 non-genic and 348 genic markers developed, a total of 367 (267 non-genic, 100 genic) mapped in a segregating F2 population (Acala Maxxa × TX2094) using the Fluidigm EP1 system. A G. hirsutum genetic linkage map of 1,688 cM was constructed based entirely on these new SNP markers. Of the genic-based SNPs, we were able to identify within which genome (‘A’ or ‘D’) each SNP resided using diploid species sequence data. Genetic maps generated by these newly identified markers are being used to locate quantitative, economically important regions within the cotton genome

Effect of exercise and heat-induced hypohydration on brain volume

Purpose: The aim of the present study was to quantify changes in brain volume following exercise/heat-induced hypohydration in man. Methods: Eight active men completed intermittent exercise in a warm environment, until 2.9 ± 0.1 % of body mass was lost. Subjects remained hypohydrated for two hours following the end of exercise. Brain volume was measured before, immediately following, and 1h and 2h after exercise using MRI (Philips 3T Achieva). Measures of subjective feelings and core body temperature were also monitored. Blood samples were drawn to determine serum electrolyte concentrations and osmolality and to allow calculation of changes in blood and plasma volumes. Results: Brain volume was not influenced by hypohydration (0.2 ± 0.4 %; ES 0.2; P = 0.310). Reductions in ventricular (4.0 ± 1.8 %; ES 4.6; P < 0.001) and CSF (3.1 ± 1.9%; ES 3.3; P = 0.003) volumes were observed following exercise. Compared with pre-exercise levels, serum osmolality was elevated throughout the 2h post-exercise period (+10 ± 2 mosmol/kg; P < 0.001). Core temperature increased from 37.1 ± 0.3oC at rest to 39.3 ± 0.5oC at the end of exercise (P = 0.001). Conclusions: These data demonstrate that brain volume remains unchanged in response to moderate hypohydration and the presence of serum hyperosmolality, suggesting that mechanisms are in place to defend brain volume

Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification: Proof of Concept

Bacterial artificial chromosome (BAC) libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. Here we describe the utilization of the Fluidigm access array genotyping system in conjunction with KASPar genotyping technology to identify individual BAC clones corresponding to specific single-nucleotide polymorphisms (SNPs) from an Amplicon Express seven-plate super pooled Amaranthus hypochondriacus BAC library. Ninety-six SNP loci, spanning the length of A. hypochondriacus linkage groups 1, 2, and 15, were simultaneously tested for clone identification from four BAC super pools, corresponding to 28 384-well plates, using a single Fluidigm integrated fluidic chip (IFC). Forty-six percent of the SNPs were associated with a single unambiguous identified BAC clone. PCR amplification and next-generation sequencing of individual BAC clones confirmed the IFC clone identification. Utilization of the Fluidigm Dynamic array platform allowed for the simultaneous PCR screening of 10,752 BAC pools for 96 SNP tag sites in less than three hours at a cost of ~$0.05 per reaction

Outcomes of conduct problems in adolescence: 40 year follow-up of national cohort

Objective To describe long term outcomes associated with externalising behaviour in adolescence, defined in this study as conduct problems reported by a teacher, in a population based sample

A Chromosome-Scale Assembly of the Garden Orach (Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing

Atriplex hortensis (2n = 2x = 18, 1C genome size 1.1 gigabases), also known as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam. Chenopodioideae) that has spread in cultivation from its native primary domestication area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a highly complex but, as understood now, a monophyletic group of mainly halophytic and/or xerophytic plants, of which A. hortensis has been a vegetable of minor importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due primarily to its exceptional leaf and seed protein quantities (approaching 30%) and quality (high levels of lysine). Although there is some literature describing the taxonomy and production of A. hortensis, there is a general lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic positioning, and future potential of the species. Here, we report the assembly of the first high-quality, chromosome-scale reference genome for A. hortensis cv. “Golden.” Long-read data from Oxford Nanopore’s MinION DNA sequencer was assembled with the program Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325 scaffolds with a N50 of 98.9 Mb – with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy- (32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only 2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three distinct populations with little variation within subpopulations. These resources provide vital information to better understand A. hortensis and facilitate future study