GO‐FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO‐FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass‐roots organization formed to advance the annotation of newly assembled genomes of domesticated and non‐model organisms ( www.faang.org ). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org . In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO‐FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta‐data analysis standards were established.     

Highly specific micromethod for the enzymatic determination of radioactive [14C]lactate

By collecting released 14CO2 following the enzymatic decarboxylation of radiolabeled lactate, picomoles of the latter can be precisely, easily, and reproducibly measured in small biological fluids. This radioactive [14C]lactate microassay does not require a neutralization step, nor does it require chemical extractions and partioning procedures, ion exchange, or pyruvate derivatization. Under our specified conditions this simple reaction goes to completion in 90 min. Using this assay in porous adipose cells, with the cell number logarithmically less than that found in other literature methods, the measured glycolytic flux rates were consistent with those previously reported. In these studies, glycolysis was initiated with [U-14C]glucose 6-phosphate. This microradioactive lactate assay is useful when dealing with minute tissue samples and/or microliter aliquots of biological fluids.     

The phylogenetic content of flavonoid point scores

The history of flavonoid point scores is discussed and the advantages of each system are described. A variation of the Wagner Groundplan-divergence Method can be used to reveal the phylogenetic content of flavonoid point scores. Flavonoid features evolving on more than one occasion are readily detectable.     

Inventory control: cytochrome c oxidase assembly regulates mitochondrial translation

Mitochondria maintain genome and translation machinery to synthesize a small subset of subunits of the oxidative phosphorylation system. To build up functional enzymes, these organellar gene products must assemble with imported subunits that are encoded in the nucleus. New findings on the early steps of cytochrome c oxidase assembly reveal how the mitochondrial translation of its core component, cytochrome c oxidase subunit 1 (Cox1), is directly coupled to the assembly of this respiratory complex.     

Complete Genome Sequences of Elephant Endotheliotropic Herpesviruses 1A and 1B Determined Directly from Fatal Cases

A highly lethal hemorrhagic disease associated with infection by elephant endotheliotropic herpesvirus (EEHV) poses a severe threat to Asian elephant husbandry. We have used high-throughput methods to sequence the genomes of the two genotypes that are involved in most fatalities, namely, EEHV1A and EEHV1B (species Elephantid herpesvirus 1, genus Proboscivirus, subfamily Betaherpesvirinae, family Herpesviridae). The sequences were determined from postmortem tissue samples, despite the data containing tiny proportions of viral reads among reads from a host for which the genome sequence was not available. The EEHV1A genome is 180,421 bp in size and consists of a unique sequence (174,601 bp) flanked by a terminal direct repeat (2,910 bp). The genome contains 116 predicted protein-coding genes, of which six are fragmented, and seven paralogous gene families are present. The EEHV1B genome is very similar to that of EEHV1A in structure, size, and gene layout. Half of the EEHV1A genes lack orthologs in other members of subfamily Betaherpesvirinae, such as human cytomegalovirus (genus Cytomegalovirus) and human herpesvirus 6A (genus Roseolovirus). Notable among these are 23 genes encoding type 3 membrane proteins containing seven transmembrane domains (the 7TM family) and seven genes encoding related type 2 membrane proteins (the EE50 family). The EE50 family appears to be under intense evolutionary selection, as it is highly diverged between the two genotypes, exhibits evidence of sequence duplications or deletions, and contains several fragmented genes. The availability of the genome sequences will facilitate future research on the epidemiology, pathogenesis, diagnosis, and treatment of EEHV-associated disease.     

Evaluating ecosystem processes in willow short rotation coppice bioenergy plantations

Despite a growing body of research linking bioenergy cultivation to changing patterns of biodiversity, there has been remarkably little interest in how bioenergy plantations affect key ecosystem processes underpinning important ecosystem services. In this study, we compare how the processes of predation by ground arthropods and litter decomposition varied between Short Rotation Coppice (SRC) willow bioenergy plantations and alternative land‐uses: arable and set‐aside (agricultural land taken out of production). We deployed litter bags to measure variation in decomposition, and a prey removal assay coupled with pitfall traps and direct searches to investigate variation in predation pressure. Decomposition rate was higher in willow SRC and set‐aside than in cereal crops. Willow SRC had the highest abundance and diversity of ground‐dwelling arthropod predators, but land‐use had no detectable influence on predation of fly pupae or the combined activity‐density of the two principal Coleoptera families (carabids and staphylinids). Overall, our study demonstrates that the conversion of arable land to SRC may have implications for the rate of some, but not all, ecosystem processes, and highlights the need for further research in this area.     

The distribution and habitats of crossbills Loxia spp. in Britain, with special reference to the Scottish Crossbill Loxia scotica

A study was carried out, primarily in northern Scotland, to relate bill and wing measurements to diagnostic calls of crossbill species, and thereby use the calls to describe the distributions and habitats of the different species. Bill depth and wing length measurements from museum specimens and live‐trapped birds were used to describe the size categories. Almost all measurements of crossbills from England were similar to measurements of Common Crossbills from Fennoscandia. Museum specimens showed that crossbills in northern Scotland between 1822 and 1990 were a combination of Common Crossbills, birds which were intermediate between Common and Parrot Crossbills (Scottish Crossbills), and perhaps a few Parrot Crossbills. However, catches of crossbills between 1995 and 2000 showed that Parrot Crossbills (based on bill and wing measurements) were present at some sites in the Highlands. Recordings of flight calls and excitement calls of birds of known bill sizes allowed a classification of crossbills according to call types. Four different flight calls (referred to here as types 1–4) and five excitement calls (types A–E) were recognized. A sample of small‐billed birds, thereby identified as Common Crossbills, indicated that there were three groups of Common Crossbills: those giving type 1 flight calls and type A excitement calls (1A), type 2 flight calls and type B excitement calls (2B), and type 4 flight calls and type E excitement calls (4E). Large‐billed birds identified as Parrot Crossbills gave mainly type 2 flight calls and type D excitement calls. Birds with intermediate bill depths (Scottish Crossbills) gave type 3 flight calls and type C excitement calls. Distributions based on calls showed that 1A Common Crossbills were widespread in Scotland but the other types of Common Crossbill were rare. Parrot Crossbills were found in a few localities in the Highlands, and Scottish Crossbills (defined as those giving type 3 flight calls and type C excitement calls) were restricted to the northern and eastern Highlands. Scottish Crossbills and 1A Common Crossbills had overlapping distributions, and overlapped greatly in the types of forests they used between January and March when the Scots Pine cones were still closed. However, Scottish Crossbills were more frequently associated with stands containing Scots Pine compared with Common Crossbills.