Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genome-wide dissection of co-selected UV-B responsive pathways in the UV-B adaptation of qingke

Qingke (Tibetan hulless barley) has long been cultivated and exposed to long-term and strong UV-B radiation on the Tibetan Plateau, which renders it an ideal target for elucidating novel UV-B responsive mechanisms. Here we report a comprehensive metabolite profiling and metabolite-based genome-wide association study using 196 diverse qingke and barley accessions. Our results demonstrated both constitutive and induced accumulation, and common genetic regulation, of metabolites of the different phenylpropanoid branches in UV-B protection. A total of 90 significant mGWAS loci for these metabolites were located in the barley-qingke differentiation regions and a number of high-level metabolite trait alleles were found to be significantly enriched in qingke, suggesting co-selection of various phenylpropanoids. Upon dissecting the entire phenylpropanoid pathway, we identified a number of determinants controlling natural variation of phenylpropanoid contents, including three novel proteins, a flavone C-pentosyltransferase, a tyramine hydroxycinnamoyl acyltransferase and a MYB transcription factor. Our study, furthermore, demonstrated co-selection of both constitutive and induced phenylpropanoids for UV-B protection in this species

Transhumance, livestock mobility and mutual benefits between crop and livestock production

Grazing-based livestock production, named pastoralism, is classified into nomadism, transhumance and agro-pastoralism. Transhumance is characterised by the seasonal and recurring movement of livestock whereby seasonal grazing areas and routes for livestock movement are fixed. All grazing based livestock production systems including transhumance are constrained globally for a variety of reasons. The major threats to the system are globalisation, nationalisation or privatisation of rangelands, national parks and community forestry policies restricting free grazing and shortage of labour. The collapse or decline of such social-ecological systems (SESs), which have existed for over 1000s years, often induces adverse impacts on societies and ecosystems. Here we review the literature on transhumance, and discuss reasons for transhumance, and the associated advantages and disadvantages of livestock movement in transhumance. Our review also focuses on how the integration of crop and livestock production in transhumance derives mutual benefits. The review indicates that the seasonal movement of livestock is an ecological necessity in areas with harsh climates and low pasture production. Transhumance is also a herders’ adaptive management to adjust to variable grazing resources and environmental conditions. The disadvantages of seasonal movement of livestock such as greater herding labour required and expenditure of more energy for livestock, are far outweighed by the ecological advantages. Some of these are: to minimise grazing competition and to protect rangeland pastures from being overgrazed. Our review also indicates that the integration of crop and livestock production derives mutual benefits and contributes for their enhanced sustainability

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species