We are in the early stage of a revolution in the field of comparative genomics. Within the past five years, thousands of animal, plant, and fungal genomes have been sequenced and assembled to high quality. There is even serious discussion around sequencing the genomes of every eukaryotic species on earth. Here, I explain why this genomic revolution is happening and discuss the feasibility of sequencing genomes on a massive scale. Having a very wide diversity of genome sequences will accelerate applied research in biomedicine, biotechnology, aquaculture, agriculture, and conservation, and facilitate fundamental research in areas such as ecology, physiology, developmental biology, and evolutionary biology. In this article, I explore new findings and new questions in evolutionary biology emerging from animal genome analyses. Examples are drawn from marine animals such as polychaetes, bivalves, cephalopods, fish, and bryozoans, plus unusual terrestrial groups such as gerbils, moths, and bee-flies. I highlight patterns of mutation, the dynamics of gene families, and chromosomal organisation of genomes as areas ripe for further research. An even wider diversity of genome sequences will be needed to fill the knowledge gaps or investigate emerging puzzles, and a case is made for sequencing the genomes of over 100,000 species.

Bitter gourd is a highly nutritious vegetable and important medicinal plant of economic importance. The present study is focused on cytogenetical characterization of 12 accessions of bitter gourd from different parts of India, aiming to differentiate their karyotypes and outline diagnostic features of the chromosomes within each accession's haploid complement. All the accessions possess 2n = 22 numbers of chromosomes. The chromosomes mainly were metacentric (16‒22 chromosomes), and the presence or absence of sub-metacentric (0‒6 chromosomes) chromosomes. The length of the chromosomes varied from 0.83 to 1.93 μm among the accessions studied. Significant differences were obtained for the seven intra-chromosomal indices and four inter-chromosomal indices among the accessions. Principal component analysis and unweighted pair group method with arithmetic mean study revealed relatively distant positioning of individuals that advocated intraspecific phylogenetic relationships and higher karyoevolutionary affinity in bitter gourd accessions. In the meiotic study, regular meiotic behaviour indicates genetic stability and a stable sexual cycle in different accessions. The percentage of pollen viability of all the studied accessions was very high (89.41–94.11%), and these accessions can be considered to be good pollinators. The results obtained will guide characterizing the elite genotypes, genotypes management and designing effective breeding programmes and crop improvement programmes.

The aim was to study the effect of the threshold number on the accuracy of genomic evaluation of the threshold traits using support vector machine (SVM), genomic best linear unbiased prediction (GBLUP) and Bayesian method B (BayesB). For this purpose, a genome consisting of three chromosomes was simulated for 1000 individuals on which 3000 bi-allelic single nucleotide polymorphism markers were evenly distributed. Genomic breeding values were predicted in different scenarios of threshold number (1–6 thresholds), QTL number (30 and 300 QTLs) and heritability level (0.1, 0.3 and 0.5). By increasing the number of thresholds from 1 to 6 thresholds, especially at higher levels of heritability, the accuracy of genomic evaluation increased; however, the increase in accuracy was not linear so that it was much more noticeable when the number of thresholds increased from 1 to 2 thresholds. In the most studied scenarios, SVM showed a very poor performance compared to other methods. BayesB ranked first regarding prediction accuracy, though in some cases the observed differences with GBLUP was not significant. While increase in heritability increased the accuracy of genomic evaluation, change in the QTL number had a slight effect on the prediction accuracy. According to the results, the SVM is not recommended for genomic evaluation of threshold traits, especially those which have only one threshold and instead, use of GBLUP and BayesB is recommended. For traits with more than one threshold, fortunately we can achieve accuracy similar to continuous traits by applying traditional genomic evaluation methods.

Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform. The hypothesis was tested using a case study of a set of dizygotic X-chromosome monosomy 53,X sheep twins. Genome-wide SNP data were available from the Illumina platform (11 082 autosomal and 191 X-chromosome SNPs) on 1848 male and 8954 female sheep and available from the AxiomTM platform (11 128 autosomal and 68 X-chromosome SNPs) on 383 female sheep. Genotype allele intensity values, either as their original raw values or transformed to logarithm intensity ratio (LRR), were used to accurately diagnose two dizygotic (i.e. fraternal) twin 53,X sheep, both of which received their single X chromosome from their sire. This is the first reported case of 53,X dizygotic twins in any species. Relative to the X-chromosome SNP genotype mean allele intensity values of normal females, the mean allele intensity value of SNP genotypes on the X chromosome of the two females monosomic for the X chromosome was 7.45 to 12.4 standard deviations less, and were easily detectable using either the AxiomTM or Illumina genotype platform; the next lowest mean allele intensity value of a female was 4.71 or 3.3 standard deviations less than the population mean depending on the platform used. Both 53,X females could also be detected based on the genotype LRR although this was more easily detectable when comparing the mean LRR of the X chromosome of each female to the mean LRR of their respective autosomes. On autopsy, the ovaries of the two sheep were small for their age and evidence of prior ovulation was not appreciated. In both sheep, the density of primordial follicles in the ovarian cortex was lower than normally found in ovine ovaries and primary follicle development was not observed. Mammary gland development was very limited. Results substantiate previous studies in other species that aneuploidy can be readily detected using SNP genotype allele intensity values generally already available, and the approach proposed in the present study was agnostic to genotype platform.

Genome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a parasite's pathogenicity, host–pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases.

We determined the relationship between aortic arch anatomy in tetralogy of Fallot with pulmonary stenosis and chromosomal or genetic abnormality, by performing analysis of 257 consecutive patients undergoing surgical repair from January, 2003 to March, 2011. Chromosomal or genetic abnormality was identified in 49 of the 257 (19%) patients. These included trisomy 21 (n = 14); chromosome 22q11.2 deletion (n = 16); other chromosomal abnormalities (n = 9); CHARGE (n = 2); Pierre Robin (n = 2); and Kabuki, Alagille, Holt–Oram, Kaufman McKusick, Goldenhar, and PHACE (n = 1 each). Aortic anatomy was classified as left arch with normal branching, right arch with mirror image branching, left arch with aberrant right subclavian artery, or right arch with aberrant left subclavian artery. Associated syndromes occurred in 33 of 203 (16%) patients with left arch and normal branching (odds ratio 1); three of 36 (8%) patients with right arch and mirror image branching (odds ratio 0.4, 95% confidence interval 0.1–1.6); seven of eight (88%) patients with left arch and aberrant right subclavian artery (odds ratio 36, 95% confidence interval 4–302); and six of 10 (60%) patients with right arch and aberrant left subclavian artery (odds ratio 8, 95% confidence interval 2–26). Syndromes were present in 13 of 18 (72%) patients with either right or left aberrant subclavian artery (odds ratio 15, 95% confidence interval 4–45). Syndromes in patients with an aberrant subclavian artery included trisomy 21 (n = 4); chromosome 22q11.2 deletion (n = 5); and Holt–Oram, PHACE, CHARGE, and chromosome 18p deletion (n = 1 each). Aberrant right or left subclavian artery in tetralogy of Fallot with pulmonary stenosis is associated with an increased incidence of chromosomal or genetic abnormality, whereas right aortic arch with mirror image branching is not. The assessment of aortic arch anatomy at prenatal diagnosis can assist counselling.

The F1 hybrid offspring of the distant hybridization between Cichlasoma trimaculatum (male) and Heros managuense (female) were successfully obtained through artificial fertilization, and the chromosome specimen of kidney cells of the two parents and their offspring were prepared using a low colchicine concentration air drying method, Howell and Black's (1980)silver–nucleolar organizer region (Ag–NOR) staining method and Sumner's (1972)C-band staining method. The karyotypes, Ag–NORs and C-bands of C. trimaculatum, H. managuense and their offspring were observed. The results showed that the diploid numbers of the two parents and the F1 hybrid offspring were all 2n=48. For C. trimaculatum, the karyotype formula was 2n=2m+8sm+26st+12t, NF=58. Two Ag–NORs were seen on the tips of the short arm of chromosome st7, and the entire chromosomes of st9 and st13 and the centromeres of the other chromosomes had positive C-bands. For H. managuense, the karyotype formula was 2n=2m+6sm+28st+12t, NF=56. Two Ag–NORs were located on the tips of the short arm of chromosome sm2 and positive C-bands were found in the centromere of all chromosomes. In the F1 hybrid offspring, the chromosome formula was 2n=2m+8sm+30st+8t, NF=58. Two Ag–NORs were seen on the tips of the short arm of chromosome sm2; all chromosomes presented positive C-bands in the centromere. No heteromorphic sex chromosome was found. After comparison with the two parents, the F1 hybrid offspring was suggested to be the filial generation of the two hybrid parents rather than the gynogenesis of H. managuense induced by heterogeneous sperm of C. trimaculatum.