Download 2015-16 NBAF Annual Report - NERC Biomolecular Analysis Facility

SERVICES & FACILITIES ANNUAL REPORT - FY April 2015 to March 2016
SERVICE
FUNDING
AGREEMENT
ESTABLISHED as S&F
TERM
NERC Biomolecular
Analysis Facility,
NBAF
PAYG & Block
F14/G6/48
(NBAF–B:
R8/H10/61)
1998 (NBAF–S)
2005 (NBAF–E & NBAF–L)
2009 (NBAF–B)
N/A
TYPE OF SERVICE PROVIDED:
NBAF provides fully-supported access to a wide range of advanced molecular genetic, genomic, metabolomic and
bioinformatic technologies to the UK environmental science community in order to address ecological or evolutionary
questions. Service is provided at four nodes: Birmingham (NBAF–B: metabolomics), Edinburgh (NBAF–E:
sequencing and bioinformatics), Liverpool (NBAF–L: microarraying, sequencing and bioinformatics) and Sheffield
(NBAF–S: genotyping and population genetics). Access to the Facility is organised centrally through competitive peerreviewed proposals that are assessed by the independent members of the Steering Committee (application form at
http://www.nbaf.nerc.ac.uk) to ensure that (i) only the best science is supported, (ii) access to more than one node is
coordinated, and (iii) projects are followed through to dissemination of the results. Each node is embedded in a wellequipped and vigorous research environment that, together with continuing developments in equipment and training,
makes ‘state-of-the-art’ services available to the NERC community. NBAF provides access to high-level capability,
and the associated training, that are rarely available elsewhere. NBAF–S, and to a limited extent NBAF–B, are
equipped to train and supervise researchers in undertaking their own analyses at the bench. NBAF–B supports
metabolomic analyses using both mass spectrometry and NMR methods. At NBAF–S most studies require the
development and implementation of highly polymorphic genetic markers, such as microsatellites and single nucleotide
polymorphisms (SNPs). These and other polymorphisms (such as major histocompatibility loci) are then genotyped in
large-scale studies using capillary and high-throughput Illumina sequencer, SNP typing or qPCR platforms. NBAF–E
offers experimental design consultancy, data generation and analysis based on high-throughput sequencing. NBAF–E
uses ABI 3730 instruments for capillary sequencing and next-generation HiSeqX, HiSeq 4000, HiSeq2500 and MiSeq
instruments for whole-genome, transcriptome and reduced-representation sequencing, including targeted resequencing,
amplicon sequencing and genotyping-by-sequencing, at any scale (from viruses to polyploid animals and plants).
NBAF–L offers sequencing, gene expression and bioinformatic services, particularly for environmental diversity
through amplicon sequencing on long-read platforms, targeted resequencing of exons and reduced genomic regions,
and gene expression analysis on microarray- and short-read (Illumina and Agilent) platforms. Building on dedicated
bioinformatic expertise, NBAF–L provides an integrated experimental design and assay service, including statistical
and network-based interpretation of results. Access to NBAF–E and NBAF–L is PAYG. NBAF collectively offers a
wide menu of training courses in genomics and metabolomics, and also offers project-focussed wet lab and
bioinformatics training.
ANNUAL TARGETS AND PROGRESS TOWARDS THEM
Capacity is defined by the availability of staff time, and all four nodes make >85% of funded staff time available to
users, with any remainder allocated to R&D. Almost all projects this year have been accommodated according to the
agreed schedule, with most slippage arising from delays in the arrival of users or their samples.
SCORES AT LAST REVIEW (each out of 5)
Need
Uniqueness
5
4.5
CAPACIT
Y of
HOST
ENTITY
FUNDED
by S&F
%
Quality of Service
5
Date of Last Review:
Quality of Science & Training
5
Staff & Status
Staff (grade, fte): NBAF–S: DA Dawson (G7 100%), G Horsburgh (G7 100%), H
Hipperson (G7 100%), C Pagnier (G5 80%), R Tucker (G6 20%); NBAF–B: U
Sommer (G7 100%), C Heude (G7 100%), J Engel (G7 100%); NBAF–E: K Gharbi
(UOE8 20%), H Gunter (UOE7 40%), S Wardlow (UOE5 100%), J Risse (UOE06
45%100%), Y Fang (Res 7, 75%), C Hertz-Fowler (Res 9, 20%), L Parsons (Cler 5
30%)); NBAF–L: M Hughes (Res 8 50%) R Gregory (Res 7 50%), L Olohan (Res 7
FINANCIAL DETAILS: CURRENT FY
Total Resource
Unit Cost £k
Allocation
Unit 1
Unit 2
Unit 3
£k 1,900.38
Variable
FINANCIAL COMMITMENT (by year until end of current agreement) £k
2015-16
2016-17
STEERING COMMITTEE
NBAFSC
Independent Members
Chair +7
Meetings per annum
1-2
2011
Average
4.88
Next
Review
(March)
Contract
Ends
(31 March)
TBC
2017
Capital
Expend £k
4.94
Income
£k
Full Cash
Cost £k
2,027.77
Other S&F Overseen
None (one SC for 4 nodes)
1
APPLICATIONS: DISTRIBUTION OF GRADES (current FY — 2015/16)
Pilot
10
9
8
7
6
5
4
3
2
1
0
R*
NERC Grant projects*
1
5
4
4
0
0
0
0
0
0
0
0
0
Other academic
0
1
3
3
0
0
0
0
0
0
0
0
0
Students
0
1
3
2
2
1
0
0
0
0
0
1
0
1
7
10
9
2
1
0
0
0
0
0
1
0
TOTAL = 31
APPLICATIONS: DISTRIBUTION OF GRADES (per annum average previous 3 financial years —2012/2013, 2013/2014 & 2014/2015)
NERC Grant projects*
Other academic
Students
TOTAL
10
1.3
0
0
1.3
9
6
2.7
3.3
12.0
8
15
3
3.3
21.3
7
4.7
8
6
18.7
6
0.3
3.3
3.7
7.3
PROJECTS COMPLETED (current FY – 2015/16)
10
9
7
8 (4)
(5)
NERC Grant projects*
6
20
37
5
Other Academic
0
7
6
5
Students
0
8
11
9
5
0
0
1
1
4
0
0
0.3
0.3
6 (3)
5 (2)
0
0
8
0
0
0
8
7.5
19.5
1
0
0
0
1 (β)
2
0
0
0
Other
NERC
Grant*
7
60
0
0
0.3
0
0.3
0
0
0
0
3 (1)
0
0
0
1
2
0
0
0
0
4
Project Funding Type (current FY – 2015/16) (select one category for each project)
Infrastructure
Grand
PhD Students
NERC
Total
Supplement to NERC Grant *
NERC Other Centre
122
3
0
0
0
0
0
0
0
PAYG
PhD Students
NERC Other
2.5
7.5
Project Funding Type (per annum average previous 3 financial years - 2012/2013, 2013/2014 & 2014/2015)
Infrastructure
PAYG
Grand
PhD Students
PhD Student
NERC
NERC
Total
Supplement to NERC Grant *
Other
Grant* NERC Other
NERC Other Centre
146
10.7
13.5
19.7
2.3
6.2
57
4.5
10.7
User type (current FY – 2015/16) (include each person named on application form)
Academic
NERC Centre
NERC Fellows
PhD Students
253
4
15
40
User type (per annum average previous 3 financial years - 2012/2013, 2013/2014 & 2014/2015)
Academic
NERC Centre
NERC Fellows
PhD Students
274.3
14
21.3
59.3
R*
0.3
0.3
1
1.7
Pilot
0
29.7
13.7
43.3
0
(Reject)
0
0
0
Pilot
0
9
6
NERC
Centre
Other
0
9
NERC
Centre
Other
1.3
20.2
Commercial
1
Commercial
1.7
OUTPUT & PERFORMANCE MEASURES (current year)
Publications (by science area & type) (calendar year 2015)
SBA
ES
MS
AS
TFS
EO
Polar
Grand Total
Refereed
Non-Ref/ Conf Proc
0
0
28
0
103
0
3
134
82
31
Distribution of Projects (by science areas) (FY 2015/16)
Grand Total
SBA
ES
MS
AS
TFS
EO
PhD Theses
21
122
2
0
2.8
28
1.8
87.3
0
OUTPUT & PERFORMANCE MEASURES (per annum average previous 3 years)
Publications (by science area & type) (Calendar years 2012, 2013 & 2014)
SBA
ES
MS
AS
TFS
EO
Polar
Grand Total
Refereed
Non-Ref/ Conf Proc
0
0.7
21.3
0
85
0
0.7
107.7
69.7
14
Distribution of Projects (by science areas) (FY 2012/2013, 2013/2014 & 2014/2015)
Grand Total
SBA
ES
MS
AS
TFS
EO
146
1
3
28
0.3
105.3
0
Polar
PhD Theses
24
Polar
8.3
Distribution of Projects by NERC strategic priority (current FY 2015/16)
Grand
Total
Climate System
Biodiversity
Earth System
Science
Sustainable Use of
Natural Resources
Natural Hazards
Environment,
Pollution &
Human Health
Technologies
122
5.9
93.4
3.5
6.9
3
8.2
1
2
OVERVIEW & ACTIVITIES IN FINANCIAL YEAR (2015/16):
NBAF-B upgraded its direct infusion mass spectrometry (Thermo Q Exactive) metabolomics pipeline following the
decommissioning of the decade-old Thermo LTQ FT Ultra mass spectrometer in 2015. This included the re-optimisation
of the “SIM stitching” approach, new software development and integration into the recently published Galaxy-M
workflow to faciliate transparency and sharing of the analysis methods. Training was also expanded considerably through
the launch of the Birmingham Metabolomics Training Centre, via delivery of the 2-day “Introduction to Metabolomics
for the Environmental Scientist” and week-long “NERC-MDIBL Environmental Genomics and Metabolomics” course,
with all available places being filled, and a further computational course being written.
NBAF-E, as a part of Edinburgh Genomics, has undergone major reorganisation through the year, focussing its genome
science activities and whole-mammalian genome resequencing activities. The Edinburgh Genomics facility has purchased
and installed six HiSeqX instruments, illumina’s latest high-throughput sequencer. These are available to NERC science
for genome sequencing and resequencing at very favourable costs. Edinburgh genomics also installed a HiSeq 4000
instrument. Based on the same technology as the HiSeqX, this instrument is ideal for RNA-Seq and other counting-bysequencing applications, custom genome and transcriptome sequencing library processing, and similar applications. The
facility now has the largest capacity of any open-access genomics facility in the UK. We also developed our robotics and
library preparation capacity, installing Illumina robotics and developing standard protocols for high-throughput
processing of, for example, double-digest RAD-Seq and multiplexed targeted selection sequencing. NBAF-E ran over 20
short courses in various aspects of genomics and bioinformatics technologies, reaching over 360 scientists.
NBAF-L built a single-cell genomics laboratory within dedicated, refurbished space. This offers the potential to examine
transcriptomes from single cells, to genome sequence organisms from very low starting material of tissue, and to examine
ecological interations between microbiola species at the microscopic scale. Facilities include: PALM laser dissection
microscope, Sony cell sorter, Fluidigm C1 station, Mosquito nano-pipettor and a clean room. NABF-L have also invested
heavily in synthetic biology, which offers the potential to test specific hypotheses by re-engineering pathways and to
exploit novel environmental genes within industrial processes. NBAF-L ran short courses in gene analysis and
metagenomic analysis of communities, which were well received and over-subscribed.
NBAF-S installed a major new SNP typing platform, the LGC SNPline, to support flexible KASP-based typing of
samples from small and medium-scale projects of the scale often required by the NERC community. The system is
suitable for typing hundred of SNPs in thousands of individuals. It is more flexible than its predecessor BeadXpress in
that it is also very convenient to run both small numbers of SNPs and small numbers of samples, as is often required for
following up, for example, candidate genes identified in genome-wide scans. NBAF-S ran four courses this year on
population genetic and parentage analyses, eDNA and metabarcoding, data validation techniques, and covering data
analysis on the HPC grid at Sheffield. NBAF-S’s population genomics course was hugely over-subscribed, with 140
applicants applying for the 30 available places, and was very positively received by those who could be accommodated.
In previous years NBAF has run a very successful pilot grants competition to enable new users, in particular (including
PhD projects) to gain access to NBAF-E and NBAF-L, which are otherwise only accessible via PAYG. Unfortunately, no
funding was available in 2015/16 to support this competition.
SCIENCE HIGHLIGHTS
A few examples of publications arising from work supported by the four NBAF nodes, often in collaboration, are
described below.
Adaptation to novel environments: Genome-wide DNA methylation patterns in two morphotypes of threespine
stickleback (Gasterosteus aculeatus) (Smith G et al 2015 Molecular Biology and Evolution 32, 888-895; JIF: 9.10)
Saltwater and freshwater present extremely different environments, yet
populations of marine three-spined stickleback (Gasterosteus
aculeatus) have repeatedly invaded freshwater habitats. There are
known to be major morphological and physiological changes
associated with these invasions. Here, Smith et al examined
differences in the patterns of DNA methylation that might regulate the
activity of genes undelying these changes. Working with NBAFLiverpool to develop new methodology, they discovered a number of
genes that showed differences in methylation between freshwater and
marine forms, with functions including cardiovascular function and
growth. These results provide a fresh perspective on vertebrate
development that could not be gained from human and mouse studies.
[Supported by NBAF-L]
3
Photosynthetic innovation broadens the niche within a single species (Lundgren
et al 2015 Ecology Letters 18, 1021-1029; JIF: 10.7)
C4 photosynthesis, a combination of anatomical and biochemical novelties, is the
focus of current research because it is more
efficient than non-C4 photosynthesis in warm
and arid conditions, and it may be possible to
engineer crop plants (e.g. rice) to increase
yields and improve food security. Multiple
plant
lineages
have
evolved
C4
photosynthesis. This study inferred the
dispersal history across geographical and
environmental space in the only known species with both C4 and non-C4
genotypes, the grass Alloteropsis semialata. While non-C4 individuals remained
confined to a limited geographical area and restricted ecological conditions, C4
individuals dispersed across three continents and into an expanded range of
environments, encompassing the ancestral one. This first intraspecific investigation
of C4 evolutionary ecology showed that, in otherwise similar plants, C4
photosynthesis does not shift the ecological niche, but broadens it, allowing
dispersal into diverse conditions and over long distances. Over macroevolutionary timescales, this immediate effect can
be blurred by subsequent specialisation towards more extreme niches. [DNA extraction and Sanger sequencing was
supported at NBAF-S and Illumina sequencing at NBAF-E.]
The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines. (Williams et al
2015 Molecular Ecology 24, 3316–3328; JIF: 6.5)
Understanding the distribution of genetic diversity in exploited species is
fundamental to successful conservation. Genetic structure and the degree of
gene flow among populations must be assessed to design appropriate
strategies to prevent the loss of distinct populations. The cephalopod
Nautilus pompilius is fished unsustainably in the Philippines for the
ornamental shell trade and has limited legislative protection, despite the
species' recent dramatic decline in the region. This study used 14
microsatellite markers to evaluate the population structure of N. pompilius
around Australia and the Philippines. Despite their relative geographical
proximity, Great Barrier Reef individuals were found to be genetically
isolated from Osprey Reef and Shark Reef in the Coral Sea. Conversely,
despite the larger geographical distances between the Philippines and west Australian reefs, samples displayed only a
small degree of genetic structure. Demographic scenarios modelled using approximate Bayesian computation analysis
indicated that this limited divergence was not due to contemporary gene flow between the Philippines and west Australia.
Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large
average effective population sizes that persisted at both locations following their separation. The lack of connectivity
among populations suggests that immigrants from west Australia would not facilitate natural recolonization if the
Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species'
biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate
sustainable harvesting, thereby preserving the diversity of genetically distinct stocks. [DNA extraction, marker
development, genotyping and data analyses were supported by NBAF-S.]
The metabolic response of marine copepods to environmental warming and ocean acidification in the absence of
food (Mayor et al 2015 Sci. Rep. 5, 13690; JIF: 5.58)
Calanus spp. numbers in the North Sea have declined by about 70% since the 1960s.
This study investigated the influence of predicted climate-change driven ocean
acidification, temperature change and food deprivation on the metabolic profiles of
copepods. It was discovered that the biochemical effects of food deprivation greatly
exceeded the other factors.
A novel class of taurine lipids and essential
polyunsaturated fatty acids was found to change its levels significantly. NBAF-B
performed the high-resolution mass spectrometry-based metabolomics analyses and
lipid identification. (Picture: C. finmarchicus, by Dan Mayor.) [Supported by NBAF-B]
Impacts of local adaptation of forest trees on associations with herbivorous insects: Implications for adaptive
forest management. (Sinclair et al 2015 Evolutionary Applications 8, 972-987; JIF: 3.9)
Disruption of species interactions is a key issue in climate change biology. Interactions involving forest trees may be
particularly vulnerable due to evolutionary rate limitations imposed by long generation times. One mitigation strategy for
4
such impacts is climate matching – the augmentation of local native tree populations by input
from nonlocal populations currently experiencing predicted future climates. This strategy is
controversial because of potential cascading impacts on locally-adapted animal communities. We
explored these impacts using abundance data for local native gallwasp herbivores sampled from
20 provenances of sessile oak (Quercus petraea) planted in a common garden trial. We
hypothesized that non-native provenances would show (i) declining growth performance with
increasing distance between provenance origin and trial site, and (ii) phenological differences to
local oaks that increased with latitudinal differences between origin and trial site. Under a local
adaptation hypothesis, we predicted declining gallwasp abundance with increasing phenological
mismatch between native and climate-matched trees. Both hypotheses for oaks were supported.
Provenance explained significant variation in gallwasp abundance, but no gall type showed the
relationship between abundance and phenological mismatch predicted by a local adaptation
hypothesis. Our results show that climate matching would have complex and variable impacts on oak gall communities.
[Supported by NBAF-E]
Comparative transcriptomics in European pine species (Wachowiak et al 2015
BMC Genomics 16, 1444; JIF: 4.3)
Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related, but
phenotypically and ecologically very distinct, European pine species providing an
excellent study system for the analysis of the genetic basis of adaptive variation and
speciation. For comparative genomic analysis of the species, transcriptome sequence
was generated for 17 samples collected across the European distribution range using
Illumina paired-end sequencing technology. De novo transcriptome assembly of a
reference sample of P. sylvestris contained 40,968 unigenes, of which fewer than
0.5% were identified as putative retrotransposon sequences. Based on gene
annotation approaches, 19,659 contigs were identified and assigned to unique genes
covering a broad range of gene ontology categories. About 80% of the reads from
each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms
were identified in 22,041–24,096 of the unigenes, so providing a set of ~220–262k identified SNPs for each species. Very
similar levels of nucleotide polymorphism were observed across species and the highest pairwise nucleotide divergence
was found between P. mugo and P. sylvestris at a common set of unigenes. The study provided whole-transcriptome
sequence and a large set of SNPs to advance population and association genetic studies in pines. The study demonstrated
that transcriptome sequencing can be a very useful approach for the development of novel genomic resources in species
with large and complex genomes. [Supported by NBAF-E]
Sexual selection drives asymmetric introgression in wall lizards (While et al 2015 Ecology Letters 18, 1366-1375;
JIF: 10.7)
Hybridisation is increasingly recognised as an important cause of
diversification and adaptation. This study showed how divergence in male
secondary sexual characters between two lineages of the common wall
lizard (Podarcis muralis) gives rise to strong asymmetries in male
competitive ability and mating success, resulting in asymmetric
hybridisation upon secondary contact. Combined with no negative effects of hybridisation on survival or reproductive
characters in F1-hybrids, these results suggest that introgression should be asymmetric, resulting in the displacement of
sexual characters of the sub-dominant lineage. This prediction was confirmed in two types of secondary contact, across a
natural contact zone and in two introduced populations. The study illustrates how divergence in sexually selected traits
via male competition can determine the direction and extent of introgression, contributing to geographical patterns of
genetic and phenotypic diversity. [New markers were identified and genotyped at NBAF-S.]
NBAF-Birmingham is at the forefront of metabolomics technology development via its partnership with two multinational instrument developers and manufacturers. These partnerships focus on collaborative scientific innovation to
develop tools for more rapid and more information rich metabolomics analyses of environmental samples. First, this
includes a formal Technology Alliance Partnership (TAP) between the University of Birmingham and Thermo Fisher
Scientific, led by Professor Viant. The TAP currently comprises 5 PhD CASE studentships and significant loaned
instrumentation, with scientific objectives such as novel tools for deep annotation of model species metabolomes, and
higher throughput methods for mass spectrometry screening. Second, the University of Birmingham has a formal
Technology Collaboration with Beckman Coulter, also including significant loaned instrumentation. This collaboration is
focused on developing a robotic system to extract metabolites from small tissue samples. Collectively, these companies
co-fund our research in environmental metabolomics while, in return, benefit from the refinement of the products that
they are developing and marketing, as well as access to key opinion leaders in metabolomics.
NBAF-Sheffield has been developing its expertise in eDNA by both supporting new research projects and transferring its
5
expertise to practical applications. This has enabled the Sheffield Molecular Ecology Laboratory to support an eDNA
service for the survey of great crested newts (Triturus cristatus), a protected species that can be difficult and costly to
detect using conventional methods and in a narrow time window (the newt breeding season). The Laboratory has
therefore been able to support environmental consultancies in undertaking this important work efficiently.
FUTURE DEVELOPMENTS/STRATEGIC FORWARD LOOK
Metabolomics: Expanding metabolomics training provision remains a top priority to facilitate a greater and more
informed uptake of metabolomics by the UK enviornmental sciences community. This includes the more frequent
delivery of existing courses, as well as the launch of a new course ‘Computational Metabolomics for the Environmental
Scientist’. NBAF-B will also pursue the development of higher sensitivity nano-LC-MS techniques to address the needs
of a new project in 2016. Furthermore, the capability to identify selected metabolites will be increased through the
development of chromatographic fractionation, followed by characterisation by mass spectrometry and NMR
spectroscopy.
New-generation sequencing: The capability available in NBAF for long-read sequencing is to be augmented. The current
platform provided by the PacBio RSII at NBAF-L will be replaced in August 2016 with a PacBio Sequel, which offers 5x
the data datageneration at a similar cost. Edinburgh Genomics, the home of NBAF-E, is also aiming to install a Sequel
instrument in 2016-17. These new platforms, coupled with new assembly algorithms, offer the potential for high-quality
de novo sequencing of genomes for most species. This is a significant boon to the environmental genomics community,
who tend to work on ‘non-model’ species, where important biological questions can be answered within an ecological or
evolutionary context. NBAF-E continues to work on the Oxford Nanopore MinION system, a long-read platform that has
benefits of size and adaptability, particularly to detection of non-canonical bases (such as methylations). This technology
is still in beta test phase but is maturing rapidly. Additional long-range sequencing technologies that leverage short-read
sequencers, based on single-molecule libraries and three-dimensional DNA conformation to deliver kilobase to hundreds
of kilobase contiguity are promising, and the facilities are exploring their utility for NERC science.
Gene expression profiling and chromatin modification assessment: Expression profiling and various methods of
assessment of genome or chromatin modification can be achieved by using the ultrahigh throughput sequencers as
“counting instruments”. For all the various approaches to differential expression, differential epigenetic modification and
differential binding of regulatory factors to DNA and RNA, the new sequencers at NBAF-E and -L (the HiSeq4000 and
HiSeqX) are step changes in value for money. The facilities will continue to develop new standard assays for single-cell
transcriptome and chromatin immunoprecipitation assays, for whole-genome DNA methylation sequencing and related
approaches. In particular, we are interested in performing several assays on the same samples from the same organisms
and tissues, requiring development of nanogram-scale techniques for library preparation. The bioinformatic landscape for
expression and chromatin mark analyses continues to develop rapidly, and NBAF-E in particular has been collaborating
to develop best practice methods for analysis, and exploring the parameters of replicate numbers and other experimental
design parameters that will maximise access to biological insight.
eDNA and metabarcoding: NBAF-S has a relatively long history of using mitochondrial DNA sequencing (barcoding) to
detect the presence and identity of parasites (such as malaria strains) and in diet analysis (e.g. moth predation by bats,
used to describe habitat use), initially using capillary sequencers. The host lab has also been providing an eDNA service
to environmental consultants for the detection of protected species, and this experience has improved NBAF-S’s ability to
support research using these techniques. The advent of NGS, especially longer reads on the MiSeq, has made these kinds
of studies ever more feasible, and several NBAF projects are already in progress or scheduled. The advent of eDNA
analyses has greatly extended the importance of molecular methods to ecologists, but is not as yet an “off the shelf”
technique, with very specific support required by each user. We expect continuing rapid innovation in this area.
Population genomics: At NBAF-E, installation of the HiSeqX and its extension to non-human genome sequencing and
resequencing brings true population genomics within the reach of NERC science. Similarly, the HiSeq4000 offers
radically reduced per-gigabase sequencing costs. We are continuing to develop new applications on these exciting new
instruments. NBAF-S is progressively transferring all its sequencing needs to Illumina platforms, especially the MiSeq as
it provides read-lengths of up to 600 bp, so matching the read-length on the ABI platforms used previously. Almost all
genotyping (except SNP and telomere analysis) is currently conducted on this platform, and it is hoped that microsatellite
analyses will also transfer from the ABI3730 capillary sequencer to the MiSeq during the coming year. We expect that
the use of multiplexed tags within single sequencing libraries should make this feasible.
Pilot grants scheme: The Facility hopes that this funding can be revived in 2016/17, as it is the only means through which
non-grantholders are able to access the Edinburgh and Liverpool nodes, and a key avenue to both educating our research
community and trialling novel and potentially disruptive technological advances. The cost is relatively small, so that it
would, as before, represent excellent value for money.
6