On the Order of Gene Distribution on Chromosomes Across the Animal Kingdom

SummaryBackgroundThe large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered manner across the animal kingdom.ResultsTwenty-one animal genomes reported in the NCBI database were examined. Numerically, there was a trend towards increasing overall gene content with increasing size of the genome as reflected by the chromosomal complement. Gene frequency on individual chromosomes in each animal genome was analyzed and demonstrated uniformity of proportions within each animal with respect to both average gene frequency on individual chromosomes and gene distribution across the unique genomes. Further, average gene distribution across animal species followed a relationship whereby it was, approximately, inversely proportional to the square root of the number of chromosomes in the unique animal genomes, consistent with the notion that there is an ordered increase in gene dispersion as the complexity of the genome increased. To further corroborate these findings a derived measure, termed gene spacing on chromosomes correlated with gene frequency and gene distribution.ConclusionAs animal species have evolved, the distribution of their genes on individual chromosomes and within their genomes, when viewed on a large scale is not random, but follows a mathematically ordered process, such that as the complexity of the organism increases, the genes become less densely distributed on the chromosomes and more dispersed across the genome.

Single cell RNA-seq denoising using a deep count autoencoder

Single-cell RNA sequencing (scRNA-seq) has enabled researchers to study gene expression at a cellular resolution. However, noise due to amplification and dropout may obstruct analyses, so scalable denoising methods for increasingly large but sparse scRNAseq data are needed. We propose a deep count autoencoder network (DCA) to denoise scRNA-seq datasets. DCA takes the count distribution, overdispersion and sparsity of the data into account using a zero-inflated negative binomial noise model, and nonlinear gene-gene or gene-dispersion interactions are captured. Our method scales linearly with the number of cells and can therefore be applied to datasets of millions of cells. We demonstrate that DCA denoising improves a diverse set of typical scRNA-seq data analyses using simulated and real datasets. DCA outperforms existing methods for data imputation in quality and speed, enhancing biological discovery.

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. This chordate subphylum contains a particularly diverse range of reproductive methods, regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of chordate traits. To gain further insights into the evolution of the tunicate phylum, we have sequenced the genome of the colonial Stolidobranchian Botrylloides leachii.We have produced a high-quality (90 % BUSCO genes) 159 Mb assembly, containing 82 % of the predicted total 194 Mb genomic content. The B. leachii genome is much smaller than that of Botryllus schlosseri (725 Mb), but comparable to those of Ciona robusta and Molgula oculata (both 160 Mb). We performed an orthologous clustering between five tunicate genomes that highlights sets of genes specific to some species, including a large group unique to colonial ascidians with gene ontology terms including cell communication and immune response.By analysing the structure and composition of the conserved gene clusters, we identified many examples of multiple cluster breaks and gene dispersion, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. In addition, we investigate lineage-specific gene gain and loss within the Wnt, Notch and retinoic acid pathways. Such examples of genetic change within these highly evolutionary conserved pathways commonly associated with regeneration and development may underlie some of the diverse regenerative abilities observed in the tunicate subphylum. These results supports the widely held view that tunicate genomes are evolving particularly rapidly.

Linked digenic epistasis in the inheritance of tillering and yielding ability in a cross of wheat

The nature of genetic variation in an intervarietal cross ('WG 377' × 'Sonalika') of bread wheat (Triticum aestivum L. em Thell.) was determined for grain yield and tillers per plant by analyzing 21 generation means and 36 family variances. For both traits, duplicate epistasis of linked loci in the pairs and gene dispersion was observed through the analysis of 21 generation means. The analysis of generation variances further suggested repulsion phase linkages for the gene pairs. The additive genetic component was significant for both traits in each of the analyses. Prevalence of gene dispersion suggested the possibility of high transgressive segregation. However, the task of exploiting additive genetic variation would be difficult because of duplicate epistasis and repulsion phase linkages. Considering these results a breeding procedure like biparental mating among a large number of superior F2 plants which encourages crossing-over is suggested.Key words: Triticum, linked epistasis, quantitative traits, additive effects, tillering.