Download Genome 10K: A Proposition to Obtain Whole Genome Sequence For

LGDMSNO09700
June 15, 2009
Journal of Heredity
Genome 10K: A Proposition to Obtain Whole Genome Sequence
For 10,000 Vertebrate Species
Genome 10K Community of Scientists
Table of Contents
Table of Contents ............................................................ Error! Bookmark not defined.
Abstract ........................................................................................................................... 3
Introduction ..................................................................................................................... 4
Proposal .......................................................................................................................... 7
Mammals......................................................................................................................... 9
Birds .............................................................................................................................. 10
Reptiles ......................................................................................................................... 11
Amphibians ................................................................................................................... 12
Fish ............................................................................................................................... 13
Discussion ..................................................................................................................... 14
Methods: ....................................................................................................................... 17
Appendix 1: Policy issues.............................................................................................. 19
Appendix 2: Detailed table of classes, orders, families, genera and species ................ 20
Appendix 3: Technological issues ................................................................................. 24
Authors: ......................................................................................................................... 25
References: ................................................................................................................... 26
Table 1: Vertebrate taxa ................................................................................................ 30
Table 2: List of collections and participating institutions (Fill this in) .............................. 31
Figure legends (need these) (Fill in references) ............................................................ 34
Figure 1: A phylogenetic view of the vertebrate subclass.............................................. 35
Figure 2: The mammalian radiations ............................................................................. 36
Figure 3: The birds of the world ..................................................................................... 37
Figure 4: The reptiles of today ....................................................................................... 38
Figure 5: The amphibians’ phylogeny............................................................................ 39
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Abstract
The completion of the human genome project was recently complemented by
whole genome assessment of 32 mammals and 24 non-mammal vertebrate species
suitable for comparative genomic analyses. Here, we anticipate a precipitous drop in
sequencing costs and increase in sequencing efficiency, with concomitant development
of greater annotation technology by proposing to create a collection of tissue and DNA
specimens for 10,000 vertebrate species specifically designated for whole genome
sequencing in the very near future. For this purpose we, the G10K Community of
Scientists, assemble and allocate a collection of some 16,000 representative vertebrate
species spanning evolutionary diversity across living mammals, birds, reptiles,
amphibians and fishes (circa 60,000 living species).
With this resource, the biological science community for genome sequence
assessment may now pursue the opportunity to unfold a new era of investigation in the
biological sciences; embark upon the most comprehensive study of biological evolution
ever attempted; and invigorate genomic inference into nearly every aspect of vertebrate
biological enquiry.
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Introduction
The bold insight behind the success of the human genome project (HUGO) was
that, while vast, the roughly three billion bits of digital information specifying the total
genetic heritage of an individual is finite and might, with dedicated resolve, be brought
within the reach of our technology [1] [2] [3]. The number of living species is similarly
vast, estimated to be between 106 and 108 for all phyla, and approximately 5 x 104 for
the subphylum vertebrata, including humans and other mammals. With that same unity
of purpose, we can now contemplate reading the genetic heritage of all species,
beginning with the vertebrates. The feasibility of a “Genome 10K” project to catalog the
diversity of vertebrate genomes requires but one more order of magnitude reduction in
the cost of DNA sequencing, following the four orders of magnitude reduction we have
seen in the last 10 years (Mardis 2008, Shendure 2008, Eid 2009). It is time to prepare
for this undertaking.
Living vertebrate species derive from a common ancestor that lived roughly 500
million years ago, near the time of the Cambrian explosion of animal life. Because a
core repertoire of about 10,000 genes in a genome of about a billion bases is seen in
multiple, deeply-branching vertebrates and close deuterostome out-groups, we may
surmise that the haploid genome of the common vertebrate ancestor was already highly
sophisticated; consisting of 108 - 109 bases specifying a body plan that includes
segmented muscles derived from somites, a notochord and dorsal hollow neural tube
differentiating into primitive forbrain, midbrain, hindbrain and spinal chord structures,
basic endocrine functions encoded in distant precursors to the thyroid, pancreas and
other vertebrate organs, and a highly sophisticated innate immune system[4-8] [9] [10],
and associated physiological capacity to survive extreme environmental change. In the
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descent of the living vertebrates, the roughly 108 bases in the functional DNA segments
that specify these sophisticated features, along with more fundamental biological
processes, encountered on average more than 30 substitutions per nucleotide site, the
outcome of trillions of natural evolutionary experiments. These and other genetic
changes, including rearrangements, duplications and losses, spawned the diversity of
vertebrate forms that inhabit the planet today. A Genome 10K project explicitly detailing
these genetic changes will provide an essential reference resource for an emerging new
synthesis of molecular, organismic, developmental and evolutionary biology to explore
the forms of life, just as the human genome project has provided an essential reference
resource for a new biomedicine.
Beyond elaborations of ancient biochemical and developmental pathways,
vertebrate evolution is characterized by stunning innovations, including adaptive
immunity, physiological resilience to environmental perturbation, multi-chambered
hearts, cartilage, bones and teeth, and specialized endocrine organs such as the
pancreas, thyroid, thymus, pituitary, adrenal and pineal glands[11]. At the cellular level,
the neural crest, sometimes referred to as a fourth germ layer, is unique to vertebrates
and gives rise to a great variety of structures, including some skeletal elements;
tendons and smooth muscle; neurons and glia of the autonomic nervous system and
aspects of the sensory systems; melanocytes in the skin; dentin in the teeth; parts of
endocrine system organs; and connective tissue in the heart [12, 13]. Sophisticated
vertebrate sensory, neuroanatomical and behavioral elaborations coupled with often
dramatic anatomical and physiological changes allowed exploitation of oceanic,
terrestrial, and atmospheric ecological niches. Anticipated details of expansions and
losses of specific gene families revealed by the Genome 10K project will provide
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profound insights into the molecular mechanisms behind these extraordinary
innovations.
Understanding the genetic basis of recent and rapid adaptive changes within
species (and between closely related species) will also be facilitated by Genome 10k.
Contemporary evolution studies are exciting and increasingly important (e.g., Stockwell
et al. 2003; Bell et al. 2003), especially considering the urgent need for predicting
species’ responses to climate change, pollution, emerging diseases, and invasive
species; such understanding could help curb the accelerating extinction crisis and slow
the loss of biodiversity world wide. Recent whole genome studies and comparisons
have facilitated discovery and mapped many adaptive molecular variations within
species (e.g. Voigt et al. 2007). Genome sequences from a given reference species
could enable genome-wide studies in many species important for biodiversity
conservation (Kohn et al. 2006) and understanding contemporary evolution (Thomas et
al. 2009).
Adaptive changes in non-coding regulatory DNA also play a fundamental role in
vertebrate evolution and its understanding represents an even greater challenge
(citations?; Hoekstra and Coyne 2007; Stranger et al. 2008). Almost no part of the noncoding vertebrate gene regulatory apparatus bears any discernable resemblance at the
DNA level to analogous systems in our deuterostome distant cousins, yet the apparatus
occupies the majority of the bases we find to be under selection in vertebrate genomes,
and is hypothesized to be the major source of evolutionary innovation within vertebrate
subclades [14] [15] [6] [16]. The origins and evolutionary trajectory of the subset of noncoding functional elements under the strongest stabilizing selection can be traced deep
into the vertebrate tree [17], in many cases to its very root, while other non-coding
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functional elements have uniquely arisen at the base of a particular class, order or
family of vertebrate species. Within vertebrate clades that evolved from a common
ancestor in the last 108 million years, such as mammals (5000 species), modern birds
(10,000 species), Neobatrachia (5,000 frog and toad species), Acanthomorpha (16,000
fish species), snakes (3000 species), geckos (1000 species) and skinks (1300 species),
evolutionary coalescence to a common ancestral DNA segment can be reliably
determined even for segments of neutrally evolving DNA. This enables detailed studies
of base-by-base evolutionary changes throughout the genome, in both coding and noncoding DNA [14]. With an estimated neutral branch length of about 20 substitutions per
site within such clades, the Genome 10K project provides enormous depth of genomewide sequence variation to address critical hypotheses concerning the origin and
evolution of functional non-coding DNA segments and their role in molding physiological
and developmental definitions of living animal species.
Proposal
To this end, we propose to assemble a “virtual collection” of frozen or otherwise
suitably preserved tissues or DNA samples representing on the order of 10,000 extant
vertebrate species as well as some recently extinct species that are amenable to
genomic sequencing (Table 1). This collection represents combined specimen materials
from at least 15 participating institutions (Table 2). In most cases, we collected both
male and female samples, and for certain species, several samples reflecting
geographic diversity and/or diversity within localized populations.
Tissues in genetic resources collection have been stored with different methods,
which yield varying results with regard to DNA quality [18]. Many tissues that are
sampled from the field may be left at ambient temperatures for several hours before
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they are finally frozen in liquid nitrogen and subsequently stored there or at -80°C.
Nonetheless, many of these tissues still yield high quality DNA [19] In other cases, non–
cryogenic field buffers [20] are used, although with varying results. In addition to DNA
quality, permit and species validation are also important issues (Appendix 1). We follow
four general guidelines for Genome 10K sample collection.

We seek 10μg of genomic DNA or about 0.5g of frozen tissue for each target
species.

Tissues may be field preserved in liquid nitrogen, ethanol, or DMSO. Initial
preservation in liquid nitrogen is strongly recommended for new acquisitions when field
conditions permit. Transport in liquid nitrogen or dry ice is encouraged. Tissues should
be stored in -80ºC freezers or in liquid nitrogen.

Tissues should be documented with voucher specimens linked to institutional
accession codes when feasible. Preserved carcasses are preferred; photo vouchers
acceptable and DNA Barcode information will be collected for all (DNA barcode
reference). In the case of rare or endangered species, a tissue sample, locality, ID by
competent biologist and DNA-barcode confirmation or listing in the International Species
Information System is nominally acceptable.

All specimens used in the G10K project will be obtained and transported in
accord with local and international statutes regulating the collection, use, and transport
of biological specimens.
In addition to samples for DNA extraction, we included 1,006 cryopreserved
fibroblast cell lines derived from 602 different vertebrate species, primarily mammals,
but include representatives of 300 taxa comprising 42 families of non-mammalian
amniotes and one amphibian species, which provides an additional window into the
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unique cell biology of these species. With the recent development of transformation
techniques to create induced pluripotent stem (iPS) cells from fibroblast lines [21, 22]
[23] [24], the potential of cell line studies is greatly expanded. While it is still unclear how
well current cell line generation methods can be extended to all vertebrate clades [25]
[26], we propose to initiate primary fibroblast cell cultures for as many species as
possible, with a target of at least 2,000 diverse species, as corollary to the Genome 10K
project. These cell cultures, along with cDNA derived from primary tissues, will provide
direct access to gene expression and regulation in the vertebrate species we catalog
and provide a renewable experimental resource to complement the Genome 10K
genome sequences. For at least one species of each vertebrate order, we propose to
assemble additional genomic resources, including physical maps and a BAC library, cell
lines, and primary tissues for transcriptome analysis. For these species, we will also
sequence multiple individuals to assess within-species diversity, including members of
both sexes to assess sex chromosome differences. A resource of this magnitude would
help catalyze a much-needed extension of experimental molecular biology beyond the
very limited set of model organisms it currently explores.
The Genome 10K species collection will include tissue/DNA specimens from five
major taxonomic groups: mammals, birds, amphibians, reptiles and fishes (Table 1).
Mammals
Mammals contain a morphologically and behaviorally diverse assemblage of
approximately 5,400 species from 1200-1300 genera distributed in three major lineages:
monotremes (platypus and echidnas—5 species), marsupials (~330 species, including
the koala, kangaroos, opossums, etc.), and the speciose eutherian, or placental
mammals (~5,000 species).
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The Genome 10K collections contain exemplars of all 139 families and we have
access to ~90% of non-muroid and non-sciurid rodent genera and non-vespertilionid bat
genera (Appendix 2, mammals). Ultimately, we will target all 1,200-1,300 genera.
Additional sampling will be applied to deeply divergent, and especially
endangered, or EDGE (Evolutionary Distinct and Endangered) species, including all
Zaglossus (echidna) species, Cuban and Hispaniolan solenodon, saddle-baked tapir,
aardvark, etc. For fundamental biological investigation, it is a high priority to sequence
“extremophiles”, such as deep sea divers, long-lived spcies (e.g. bowhead whales), high
elevation species, aquatic versus terrestrial taxa, species spanning the range of brain
size, body size, and morphological convergence as well as aquatic species, gliders,
lifespan extremes, nocturnal/diurnals, species with distinct sensory modalities, such as
echolocation, and social versus solitary species. We will also sample some closely
related domestic and wild mammal species that have undergone extraordinarily recent
and rapid evolution, following environmental change (e.g. temperature, disease
exposure) or domestication.
Capturing wide ecological diversity holds great potential in identifying the
genomic changes underlying the major mammalian anatomical and behavioral
transformations. Determining the genomic intrastructure for extreme physiological
responses also provides a unique opportunity for understanding the limits of mammalian
tissues from resistance to disease to environmental disturbance. We project
approximately 3,000 of the 5,400 living mammal species.
Birds
Like eutherian mammals, modern birds (Neornithes) arose in the Late
Cretaceous and diversified soon after the KT extinction event, 65 million years ago.
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Since then, birds have dispersed across the globe and now occupy a panoply of Earth's
habitats and diverse ecosystems representing a wide array of functional lifestyles. At
this time, we know very little about the genetic and developmental underpinnings of this
biological diversity, but we expect that many key questions can and will be addressed
as whole genome sequences are accumulated and interpreted.
During recent decades, the avian systematic community built large frozen tissue
collections that house high quality samples of a substantial portion of avian diversity.
These collections provide an essential resource for future genomic analyses of avian
structural, functional, and behavioral diversity. With representation from 15 natural
history collections distributed globally, the Genome 10K collection includes specimens
from 100% of the 27 orders, 87% of the 205 families, 71% of the 2,172 genera and 50%
of the 9,723 species of birds (Appendix 2, birds). Every order is represented in multiple
collections, as are all but 5 families and all but 104 genera, which is important for
ensuring at least one sample of high quality. We plan to sequence both sexes for many
lineages, especially the ratite birds, many of which have apparently monomorphic or
near-monomorphic sex chromosomes. Sampling each genus may result in
oversampling of some avian orders and families (such as the extremely diverse
passerines or hummingbirds), but we will strive to capture maximal phylogenetic
coverage across all bird species.
Reptiles
Non-avian reptile diversity includes snakes, lizards, turtles, crocodiles, and two
species of tuatara. Because the traditional view of interfamilial relationships (based on
morphology) differs appreciably with recent molecular phylogenies and the molecular
phylogenies with one another, major issues such as the origin of snakes (which are
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clearly nested within lizards) remain controversial (references). Despite these
uncertainties, the content of the major groups of reptiles (i.e., the families) are quite
stable. Following online databases and Townsend et al. (2004) [27], reptile diversity is
distributed among the following groupings: Snakes are divided among 19 families, 477
genera, and 3048 species. Lizards are comprised 33 families, 490 genera, and 5,057
species. Turtle diversity is divided among 13 families, 91 genera, and 313 species.
Crocodiles include 23 species divided among 7 genera in 3 taxonomic families. The
tuatara is the only extant member of the formerly diverse and widespread
Rhyncocephalians. Total reptile diversity therefore includes 69 families, 1,066 genera,
and 8,442 species. The Genome 10K collection has 67%, 34% and 10% of these,
respectively (Appendix 2, reptiles).
Amphibians
The Class Amphibia is divided into three orders: Anura (frogs), Caudata
(salamanders) and Gymnophiona (caecilians), derived from a common ancestor
approximately 370MYA and representing the only three surviving lineages from a much
greater diversity that existed before the Permian extinction 250MYA [28]. These major
clades contain 5,532 frog species, 552 salamander species, and 176 caecilian species,
respectively. Amphibian taxonomy is currently in a state of flux, if not disarray, with
competing groups of systematists making frequent and conflicting changes. Although
controversial, we summarize amphibian diversity and tissue holdings (Appendix 2,
amphibians) largely following the work of Frost et al. (2006) [29] because this schema
tends to split groups, adding more families and genera, which helps us label the major
lineages using the standard ranks of Linnean classification. This taxonomy contains 61
families of amphibians shared among the three orders, containing a total of 510 genera
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and 6,260 species. The Genome 10K collection contains a total of 394 species (6%),
144 genera (28%), and 45 families (74%).
Collectively, amphibians are of global conservation concern, most recently
because of pathogenic affects of a chytrid fungus, Batrachochytrium dendrobatidis [30].
Habitat loss, pollutants, pesticides, herbicides, fertilizers and climatic changes further
contribute to their rapid demise.
Fish
“Fishes” include all non-tetrapod vertebrates comprising (i) jawless vertebrates
(hagfishes and lampreys, 108 species), (ii) chondrichthyans (sharks, rays, chimeras,
970 species), (iii) actinopterygians (ray-fin fishes, 26,950 species), and (iv) piscine
sarcopterygians (coelacanths, lungfishes, 8 species). Total described diversity
comprises approximately 28,036 species [31], but actual diversity is probably greater
than 50,000 species. A broad outline of the evolution of these most deeply coalescing of
the vertebrate clades is provided by Stiassny et al. (2004) [32].
In keeping with their very ancient origins, fishes account for nearly 50% of all
living species of vertebrates, exhibiting a vast diversity in their morphology, physiology,
behavior and ecological adaptations, and providing an exceptional opportunity to study
basic vertebrate biology.
Fishes are also a commercially important group of vertebrates as a food crop
totaling about US $51 billion in trade per year, increasingly driven by the aquaculture
industry [33]. Some 16% of all protein consumed is fish protein, and about one billion
people depend on fishes as their major source of protein. Because of the great demand,
many groups of fishes are over-exploited. Molecular data for commercially important
species of fishes, especially those that are currently endangered and those raised by
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aquaculture will be valuable in designing strategies for maintaining sustainable stocks
and combating disease and other threats.
Fish tissues for the Genome 10K project reside in a number of institutions and
are usually curated as parts of formal institutional collections. The total number of
species represented by tissue samples is not known, but 6,400 species have been
DNA-barcoded and collections of new species continue to be added. Fresh material
from many commonly available species can be obtained easily from fishing boats and
the pet-trade industry for both genome and other molecular projects. The Genome 10K
project has in hand suitable samples from 60/62 orders (97%), 382/492 families (78%),
1,270 of about 3,006 genera (42%) and 2,667 of about 11,430 species (23%),
(Appendix 2, fish).
The largest known animal genome is that of the marbled lungfish, Protopterus
aethiopicus, with a haploid size of 133 pg (about 130Gb), followed by the salamanders
Necturus lewisi and Necturus punctatus at 120pg (about 117Gb) [10]. The genomes are
bloated through the activity of transposons which, combined with their enormous size,
make genome sequencing and assembly extremely challenging. While RNAsequencing is one avenue by which we may get direct access to interesting biology in
these species, we recommend that full genome sequencing projects for selected largegenome species be undertaken nonetheless. There are important questions pertaining
to gene regulation, genome structure and genome evolution that cannot be answered
from analysis of transcribed RNA alone.
Discussion
Careful observations of the morphological and functional adaptations in
vertebrates have formed the basis of biological studies for a millennium, but it is only
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very recently that we are able to observe the action of evolution directly at the genetic
level. It is not known whether convergent adaptations in independent lineages are often
governed by analogous changes in a small number of orthologous genome loci or if
macro-evolutionary events in separate lineages usually result from entirely idiosyncratic
combinations of mutations. Evidence from several recent studies point toward the
former hypothesis (Nachman et al. 2003, still need to get the best cites). For example,
adaptive hind limb reduction occurred independently many times in different lineages
and even within the same species, just as sticklebacks in different lakes adapted from
an ocean to a freshwater environment [34]. These stickleback adaptations are all traced
to independent deletions of the same distal enhancer of the PITX2 development gene,
demonstrating remarkable convergent evolution at the genomic level [35]. By cataloging
the footprints of adaptive evolution in every genomic locus on every vertebrate lineage,
the Genome 10K project will provide the power to thoroughly test the “same adaptation,
same loci” hypothesis, along with other fundamental questions about molecular
adaptive mechanisms.
In the course of this investigation, we will discover the genetic loci governing
fundamental vertebrate processes. The study of the evolution of viviparity is an
outstanding example. Birds, crocodiles and turtles all lay eggs, while apart from
monotremes, mammals are all live-bearers. Thus, we found one fundamental transition
from oviparity to viviparity in these amniotes, which caused a fundamental
reorganization in the developmental program and large-scale change in gene
interactions that we are only just beginning to understand.
Remarkably however, reptiles have an estimated 108 independent origins of the
evolution of viviparity. Fish have an equally spectacular variety of such transitions, along
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with some amphibians, such as the frog genus Gastrotheca, which includes species
with placental-like structures. These many independent instances of the evolution of
viviparity afford an extraordinary opportunity to explore the genomics behind this
reproductive strategy. The architecture of sex determination in vertebrates is similarly
diverse, with examples of XY, ZW and temperature sensitive determination methods.
This provides an equally exciting opportunity. In fact, many vertebrate species have
abandoned sex altogether. What happens when an asexual genome descends from an
ancestral sexual genome, as has occurred repeatedly in Cnemidophorus lizard
lineages? Are the independent parthenogenetic genomes parallel in any way? In one
group of lizards, the formation of unisexual species is phylogenetically constrained, yet
in others it is not. Many species of lizards and snakes are also known to have facultative
parthenogenesis: unmated females produce viable eggs and offspring. Unisexuality also
occurs in amphibians and fish by gynogenesis, hybridogenesis, and in amphibians by
kleptogenesis. Do these parallel convergent changes involve the same genes? By
identifying the genomic loci that support different evolutionary innovations, such
analyses will drive fundamental progress in molecular and developmental biology, as
have discoveries of the molecular basis for human diseases. The evolution of longevity
remains another question of great interest. What mechanisms are responsible for the
two orders of magnitude differences among vertebrates and what sets the limits for
long-lived species found in each of the vertebrate clades?
The symphony of vertebrate species that cohabit on our planet attests to
underlying life processes with remarkable potential. Genomics reveals a unity behind
these life processes that is unrivaled by any other avenue of investigation, exposing an
undeniable molecular relatedness and common origin among species. By revealing
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genetic vulnerabilities in endangered species and tracking host-pathogen interactions,
genomics plays an increasing role in sustaining biodiversity and tracking emerging
infectious diseases. Access to the information contained in the genomes of threatened
and endangered species is an important component of the Genome 10K project and
provides crucial information for comparative vertebrate genomics, while generating
information that will assist in many conservation efforts [36] [37] Kohn et al. 2006,
Schwartz et al. 2009. In studying the genomes of recently extinct species as well,
molecular aspects of species vulnerability are revealed and vital gaps in the vertebrate
record restored. In all these ways, the Genome 10K project will re-engage the public in
the quest for the scientific basis of animal diversity and in the application of the
knowledge we gain to improve animal health and species conservation.
As Guttenberg altered the course of human history with the publication of the first
book, so did the human genome project forever change the course of the life sciences
with the publication of the first full vertebrate genome sequence. When Guttenberg’s
success was followed by the publication of other books, libraries naturally emerged to
hold the fruits of this new technology for the benefit of all who sought to imbibe the vast
knowledge made available by the new print medium. We must now follow the human
genome project with a library of vertebrate genomes; a genomic ark for thriving and
threatened species alike; and a permanent digital recording of countless molecular
triumphs and stumbles across some 500 million years of evolutionary episodes that
forged the “endless forms most beautiful” on our living world.
Methods:
[Add something about anticipated advanced in third-generation sequencing?]
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Branch length estimates:
[Add something about anticipated advanced in third-generation sequencing?]
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Appendix 1: Policy issues

The Genome 10K consortium members recognize this endeavor to be a [open
access?] noncommercial research program without “reach-through” IP agreements.

All individual(s)/institute(s) contributing biomaterials for sequencing thus comply
with the above mentioned noncommercial policy and acknowledge that contributed
samples have been collected and distributed in accordance with applicable national and
international laws and regulations.

The reference materials used for genome sequencing should be clearly
identified, accessible and where possible, adhere to best practices for biodiversity
repositories (particularly concerning taxonomic identification of voucher
specimens/tissues and genome size estimation [38]). Reference documentation should
include digital images/CT scans of the morphological voucher specimens, geospatial
coordinates of the specimen collection site [39] and other emerging metadata standards
proposed for genome sequences [40].

Deposition and publication will follow the Ft Lauderdale agreement (citation) in
accord with prior best practices in genomic research, including release of primary
sequence data to the international databases within 24 hours and release of the full
genome assemblies as soon as quality assurance is complete.

Consortium is committed to building programs for training of highly qualified
personnel, particularly in developing nations.
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Appendix 2: Detailed table of classes, orders, families, genera and species
Group
Orders
Mammals
Afrosoricida
Mammals
Families
Genera
Species
2/2 - 100%
12/17 - 36%
7/51 - 13%
Cetartiodactyla
10/10 - 100%
81/89 - 91%
156/240 - 65%
Mammals
Carnivora
15/15 - 100%
82/126 - 65%
131/287 - 45%
Mammals
Cetacea
11/11 - 100%
38/40 - 95%
80/84 - 95%
Mammals
Chiroptera
13/18 - 72%
74/203 - 36%
162/1116 - 14%
Mammals
Cingulata
1/1 - 100%
3/9 - 33%
4/21 - 19%
Mammals
Dasyuromorphia
2/3 - 66%
3/23 - 13%
3/71 - 4%
Mammals
Dermoptera
1/1 - 100%
1/2 - 50%
1/2 - 50%
Mammals
Didelphimorphia
1/1 - 100%
6/17 - 35%
8/87 - 9%
Mammals
Diprotodontia
11/11 - 100%
19/39 - 48%
27/143 - 18%
Mammals
Erinaceomorpha
1/1 - 100%
4/10 - 40%
6/24 - 25%
Mammals
Hyracoidea
1/1 - 100%
3/3 - 100%
4/4 - 100%
Mammals
Lagomorpha
2/3 - 66%
7/13 - 53%
16/92 - 17%
Mammals
Macroscelidea
1/1 - 100%
3/4 - 75%
3/15 - 20%
Mammals
Microbiotheria
1/1 - 100%
1/1 - 100%
1/1 - 100%
Mammals
Monotremata
2/2 - 100%
2/3 - 66%
2/5 - 40%
Mammals
Notoryctemorphia
1/1 - 100%
1/1 - 100%
1/2 - 50%
Mammals
Paucituberculata
1/1 - 100%
3/3 - 100%
3/6 - 50%
Mammals
Peramelemorphia
2/3 - 66%
3/8 - 37%
3/21 - 14%
Mammals
Perissodactyla
3/3 - 100%
6/6 - 100%
16/17 - 94%
Mammals
Pholidota
1/1 - 100%
1/1 - 100%
6/8 - 75%
Mammals
Pilosa
4/4 - 100%
5/5 - 100%
7/10 - 70%
Mammals
Primates
14/15 - 93%
54/69 - 78%
145/376 - 38%
Mammals
Proboscidea
1/1 - 100%
2/2 - 100%
3/3 - 100%
Mammals
Rodentia
29/33 - 87%
118/481 - 24%
274/2277 - 12%
Mammals
Scandentia
2/2 - 100%
3/5 - 60%
9/20 - 45%
Mammals
Sirenia
2/2 - 100%
2/3 - 66%
2/5 - 40%
Mammals
Soricomorpha
3/4 - 75%
19/45 - 42%
26/428 - 6%
Mammals
Tubulidentata
1/1 - 100%
1/1 - 100%
1/1 - 100%
Birds
Anseriformes
3/3 - 100%
41/52 - 78%
129/162 - 79%
Birds
Apodiformes
2/3 - 66%
97/125 - 77%
238/429 - 55%
Birds
Caprimulgiformes
5/5 - 100%
17/22 - 77%
47/118 - 39%
Birds
Charadriiformes
14/18 - 77%
66/90 - 73%
208/383 - 54%
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Group
Orders
Birds
Ciconiiformes
3/3 - 100%
32/39 - 82%
69/116 - 59%
Birds
Coliiformes
1/1 - 100%
2/2 - 100%
5/6 - 83%
Birds
Columbiformes
1/2 - 50%
31/44 - 70%
129/311 - 41%
Birds
Coraciiformes
9/11 - 81%
34/51 - 66%
96/209 - 45%
Birds
Cuculiformes
1/1 - 100%
22/36 - 61%
53/138 - 38%
Birds
Falconiformes
3/3 - 100%
60/83 - 72%
145/304 - 47%
Birds
Galliformes
5/5 - 100%
56/80 - 70%
131/290 - 45%
Birds
Gaviiformes
1/1 - 100%
1/1 - 100%
3/5 - 60%
Birds
Gruiformes
9/10 - 90%
32/59 - 54%
73/196 - 37%
Birds
Musophagiformes
1/1 - 100%
5/6 - 83%
16/23 - 69%
Birds
Opisthicomiformes
1/1 - 100%
1/1 - 100%
1/1 - 100%
Birds
Passeriformes
90/107 - 84%
838/1226 - 68%
2796/5756 - 48%
Birds
Pelecaniformes
7/7 - 100%
8/9 - 88%
30/62 - 48%
Birds
Phaethontiformes
1/1 - 100%
1/1 - 100%
3/3 - 100%
Birds
Phoenicopteriformes
1/1 - 100%
3/3 - 100%
4/5 - 80%
Birds
Piciformes
5/5 - 100%
53/68 - 77%
255/398 - 64%
Birds
Podicipediformes
1/1 - 100%
5/6 - 83%
11/22 - 50%
Birds
Procellariiformes
4/4 - 100%
19/27 - 70%
52/112 - 46%
Birds
Psittaciformes
1/1 - 100%
67/85 - 78%
186/364 - 51%
Birds
Sphenisciformes
1/1 - 100%
6/6 - 100%
13/17 - 76%
Birds
Strigiformes
2/2 - 100%
21/29 - 72%
64/195 - 32%
Birds
Struthioniformes
6/6 - 100%
14/15 - 93%
37/59 - 62%
Birds
Trogoniformes
1/1 - 100%
5/6 - 83%
25/39 - 64%
Amphibians
Anura
32/48 - 66%
107/411 - 26%
302/5532 - 5%
Amphibians
Caudata
10/10 - 100%
32/66 - 48%
86/552 - 15%
Amphibians
Gymnophiona
3/3 - 100%
5/33 - 15%
6/176 - 3%
Reptiles
Testudines
10/14 - 71%
43/98 - 43%
60/295 20%
Reptiles
Sphenodontia
0/1 - 0%
0/1 - 0%
0/1 0%
Reptiles
Squamata
35/41 - 85%
309/758 - 40%
735/3996 18%
1/1 - 100%
8/9 - 89%
21/25 - 84%
Reptiles
Families
Genera
Species
Fishes
Petromyzontiformes
1/1 - 100%
2/10 - 20%
2/38 - 5%
Fishes
Myxiniformes
1/1 - 100%
2/6 - 33%
3/24 - 12%
Fishes
Rajiformes
1/1 - 100%
8/16 - 50%
25/107 - 23%
Fishes
Torpediniformes
2/4 - 50%
2/5 - 40%
5/15 - 33%
Fishes
Heterodontiformes
1/1 - 100%
1/1 - 100%
3/5 - 60%
Page 21
Group
Orders
Families
Genera
Species
Fishes
Squaliformes
1/1 - 100%
2/2 - 100%
14/19 - 73%
Fishes
Orectolobiformes
5/5 - 100%
7/8 - 87%
13/17 - 76%
Fishes
Carcharhiniformes
6/8 - 75%
27/37 - 72%
70/140 - 50%
Fishes
Echinorhiniformes
1/1 - 100%
1/1 - 100%
1/1 - 100%
Fishes
Lamniformes
5/5 - 100%
8/10 - 80%
11/14 - 78%
Fishes
Hexanchiformes
3/3 - 100%
4/4 - 100%
5/6 - 83%
Fishes
Chimaeriformes
3/3 - 100%
4/4 - 100%
9/18 - 50%
Fishes
Lepidosireniformes
2/2 - 100%
2/2 - 100%
2/8 - 25%
Fishes
Ceratodontiformes
0/1 - 0%
0/1 - 0%
0/1 - 0%
Fishes
Coelacanthiformes
1/1 - 100%
1/1 - 100%
1/2 - 50%
Fishes
Acipenseriformes
2/2 - 100%
3/7 - 42%
5/38 - 13%
Fishes
Semionotiformes
1/1 - 100%
2/2 - 100%
4/7 - 57%
Fishes
Amiiformes
1/1 - 100%
1/1 - 100%
1/1 - 100%
Fishes
Elopiformes
2/2 - 100%
2/2 - 100%
5/7 - 71%
Fishes
Anguilliformes
14/15 - 93%
27/70 - 38%
52/159 - 32%
Fishes
Clupeiformes
4/6 - 66%
20/53 - 37%
38/142 - 26%
Fishes
Cypriniformes
4/5 - 80%
43/327 - 13%
92/1588 - 5%
Fishes
Characiformes
10/13 - 76%
44/104 - 42%
78/325 - 24%
Fishes
Siluriformes
14/37 - 37%
45/282 - 15%
71/929 - 7%
Fishes
Gymnotiformes
4/7 - 57%
5/21 - 23%
5/45 - 11%
Fishes
Esociformes
2/2 - 100%
4/4 - 100%
7/11 - 63%
Fishes
Salmoniformes
4/4 - 100%
17/36 - 47%
27/188 - 14%
Fishes
Gadiformes
9/11 - 81%
31/52 - 59%
54/132 - 40%
Fishes
Batrachoidiformes
1/1 - 100%
4/9 - 44%
7/16 - 43%
Fishes
Lophiiformes
10/12 - 83%
16/24 - 66%
21/45 - 46%
Fishes
Cyprinodontiformes
8/9 - 88%
29/109 - 26%
87/626 - 13%
Fishes
Beloniformes
5/5 - 100%
17/31 - 54%
36/97 - 37%
Fishes
Scorpaeniformes
20/32 - 62%
63/130 - 48%
149/465 - 32%
Fishes
Perciformes
114/151 - 75%
492/1108 - 44%
1213/4698 - 25%
Fishes
Pleuronectiformes
11/11 - 100%
64/95 - 67%
91/213 - 42%
Fishes
Osteoglossiformes
6/6 - 100%
9/28 - 32%
10/142 - 7%
Fishes
Polypteriformes
0/1 - 0%
0/2 - 0%
0/9 - 0%
Fishes
Gonorynchiformes
2/4 - 50%
2/7 - 28%
2/10 - 20%
Fishes
Mugiliformes
1/1 - 100%
5/8 - 62%
6/26 - 23%
Fishes
Tetraodontiformes
10/10 - 100%
51/69 - 73%
92/181 - 50%
Page 22
Group
Orders
Fishes
Myliobatiformes
6/7 - 85%
18/22 - 81%
57/112 - 50%
Fishes
Atheriniformes
6/8 - 75%
13/33 - 39%
19/174 - 10%
Fishes
Synbranchiformes
2/2 - 100%
5/6 - 83%
6/19 - 31%
Fishes
Beryciformes
7/7 - 100%
12/18 - 66%
30/49 - 61%
Fishes
Stomiiformes
6/7 - 85%
18/21 - 85%
30/52 - 57%
Fishes
Albuliformes
1/1 - 100%
1/2 - 50%
2/14 - 14%
Fishes
Pristiformes
1/1 - 100%
2/2 - 100%
4/5 - 80%
Fishes
Zeiformes
4/5 - 80%
8/11 - 72%
12/17 - 70%
Fishes
Gasterosteiformes
7/10 - 70%
21/37 - 56%
31/98 - 31%
Fishes
Myctophiformes
2/2 - 100%
18/32 - 56%
28/90 - 31%
Fishes
Aulopiformes
12/14 - 85%
24/32 - 75%
36/68 - 52%
Fishes
Lampridiformes
6/6 - 100%
8/9 - 88%
10/15 - 66%
Fishes
Percopsiformes
2/3 - 66%
2/3 - 66%
2/4 - 50%
Fishes
Polymixiiformes
1/1 - 100%
1/1 - 100%
3/4 - 75%
Fishes
Stephanoberyciformes
5/7 - 71%
9/17 - 52%
10/49 - 20%
Fishes
Dactylopteriformes
1/1 - 100%
2/2 - 100%
3/4 - 75%
Fishes
Ophidiiformes
3/3 - 100%
12/18 - 66%
14/24 - 58%
Fishes
Argentiniformes
4/6 - 66%
8/21 - 38%
13/32 - 40%
Fishes
Ateleopodiformes
1/1 - 100%
1/2 - 50%
1/3 - 33%
Fishes
Notacanthiformes
2/2 - 100%
4/4 - 100%
6/7 - 85%
Fishes
Rhiniformes
1/1 - 100%
1/1 - 100%
1/1 - 100%
9/10 - 90%
15/24 - 62%
32/74 - 43%
Fishes
Families
Genera
Species
Page 23
Appendix 3: Technological issues
(To be provided)
Page 24
Authors:
Coordinators: David Haussler, Stephen J. O’Brien, Oliver Ryder
Mammals Group Members: Scott Baker, James Estes, Philippe Gaubert, Jennifer
Graves, Alexander Graphodatsky, Kristofer M. Helgen, *Warren E. Johnson, Harris
Lewin, Gordon Luikart, Lorry I. Lokey, *William Murphy, Steve O’Brien, Oliver Ryder,
Mark Springer, Emma Teeling, Robert Wayne, Terrie Williams, Nathan Wolfe, YaPing
Zhang
Birds Group Members: *Keith Barker, Joel Cracraft, Scott Edwards, Olivier Hanotte,
*Fred Sheldon
Amphibians and Reptiles Group Members: *Andrew Crawford, Matthew LeBreton,
Paolo Martelli, *Jim McGuire, *Robert Murphy, Brad Shaffer, *Barry Sinervo
Fishes Group Members: Fred Allendorf, Giacomo Bernardi, Guillamo Orti, David
Rawson, *Byrappa Venkatesh, Robert Vrijenhoek, Robert Ward, *Ed Wiley
General Policy Group Members: Scott Baker, *Adam Felsenfeld, Eric Green, *Robert
Hanner, *Olivier Hanotte, David Haussler, Paul Hebert, Steve O'Brien, Oliver Ryder,
Hector Seuanez, YaPing Zhang
Analysis Group Members: *Michele Clamp, Mark Diekhans, David Haussler, Bailey
Kessing, David Kingsley, *Webb Miller, Ngan Nguyen, Brian Pike, Stephan Schuster,
Josh Stuart, Steve Turner
*Chairs
Page 25
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Page 29
Please chairs proof these numbers; they are the meat of the White paper
Add column for coalescence date time for each group also chairs??
Table 1: Vertebrate taxa [41]
Group
Orders
Families
Genera
Species
Mammals
29/29
100%
152/153
99%
656/1231
53%
1107/5417
20%
Birds
27/27
100%
179/205
87%
1537/2172
71%
4819/9723
50%
Amphibians
3/3
100%
45/61
74%
144/510
28%
394/6260
6%
Reptiles
3/4
75%
46/69
67%
360/1066
34%
816/8442
10%
60/62
97%
382/515
74%
1270/4494
28%
Fishes
2667/27977 10%
Extant of the current Genome 10K collection is tabulated as (number of species in collection) / (total
number of species) and percentage with similar summaries for genera, families and orders. The total
numbers are computed using the NCBI taxonomy (www. ncbi.nlm.nih.gov), but substituted the Wilson
and Reeder [42] tree for the mammals and the Howard and Moore [43] tree for birds.
Page 30
Table 2: List of collections and participating institutions (Fill this in)
Institutions
Steward(s)
Academy of Natural Sciences, Philadelphia
NEED TABLE OF SAMPLES
Web address
http://research.amnh.org/ornithology/personnel/jlc.h
tm
American Museum of Natural History
Joel Cracraft
Australian National University
NEED TABLE OF SAMPLES
Biodiversity Research Institute, University of Kansas
Edward Wiley
Burke Museum, University of Washington
NEED TABLE OF SAMPLES
Círculo Herpetológico de Panamá
NEED TABLE OF SAMPLES
CSIRO Marine and Atmospheric Research
Robert Ward
http://www.cmar.csiro.au/anfc/
CTR for Reproduction of Endangered Species-San Diego
Zoo
Oliver Ryder
http://www.sandiegozoo.org/conservation/about/ad
ministrators/oliver_ryder_ph.d/
Hong Kong Zoological Gardens
Paolo Martelli
http://www.lcsd.gov.hk/parks/hkzbg/en/index.php
Institute of Cytology and Genetics, Russian Academy,
Siberian Branch
Alexander Graphodatsky
http://www.bionet.nsc.ru/indexEngl.html
Institute of Molecular and Cell Biology, Singapore
NEED TABLE OF SAMPLES
Kunming Institute of Zoology, Chinese Academy of Sciences
NEED TABLE OF SAMPLES
LIRANS Institute, University of Bedfordshire, UK,
David Rawson
Louisiana State University Museum of Zoology
NEED TABLE OF SAMPLES
LSU Museum of Natural Science
Fred Sheldon
http://appl003.lsu.edu/natsci/lmns.nsf/$Content/Sh
eldon?OpenDocument
Marine Mammal Institute, Oregon State University
Scott Baker
http://mmi.oregonstate.edu/
http://www.nhm.ku.edu/fishes/
http://www.beds.ac.uk/research/lirans/personnel/ra
wson_d
Page 31
Institutions
Steward(s)
Monterey Bay Aquarium Research Institute
NEED TABLE OF SAMPLES
Museum of Comparative Zoology, Harvard*
NEED TABLE OF SAMPLES
Museum of Vertebrate Zoology (MVZ)
NEED TABLE OF SAMPLES
Museum of Vertebrate Zoology, UC Berkeley
NEED TABLE OF SAMPLES
Museum Victoria, Australia
NEED TABLE OF SAMPLES
National Cancer Institute Lab of Genomic Diversity
Stephen O’Brien
Natural History Museum of Los Angeles County
NEED TABLE OF SAMPLES
Royal Ontario Museum (ROM)
Robert Murphy
Smithsonian Institution, National Museum of Natural History
NEED TABLE OF SAMPLES
Smithsonian Tropical Research Institute
Andrew Crawford
Swedish Museum of Natural History
NEED TABLE OF SAMPLES
Texas A&M University
William Murphy
The Field Museum, Chicago
NEED TABLE OF SAMPLES
UCLA, Institute of the Environment
Matthew LeBreton
University College-Dublin
NEED TABLE OF SAMPLES
University of California, Riverside
NEED TABLE OF SAMPLES
University of California, Santa Cruz
NEED TABLE OF SAMPLES
University of Montana
NEED TABLE OF SAMPLES
Web address
http://home.ncifcrf.gov/ccr/lgd/
http://labs.eeb.utoronto.ca/murphy/
http://www.stri.org/
http://gene.tamu.edu/faculty_pages/faculty_Murphy
W.php
http://www.ioe.ucla.edu/ctr/staff/LeBreton_Matthew
.html
Page 32
Institutions
Steward(s)
Web address
University of Nebraska, Lincoln
Guillermo Orti
http://golab.unl.edu/index.html
University of Nevada, Las Vegas
NEED TABLE OF SAMPLES
Zoological Museum of Copenhagen, Denmark
University of Montana
Gordon Luikart
NEED TABLE OF SAMPLES
http://dbs.umt.edu/research_labs/allendorflab/
CIBIO, University of Porto, Portugal
Albano Beja-Pereira
http://cibio.up.pt/
Alexander Graphodatsky, Department of Molecular and Cell Biology, Institute of Chemical Biology and Fundamental Medicine of the
Russian Academy of Sciences
Lorry I. Lokey Visiting Professor , Stanford University, Human Biology
•
Founder and Director, The Global Viral Forecasting Initiative
Page 33
Figure legends (need these) (Fill in references)
Legend(s) here
Page 34
Figure 1: A phylogenetic view of the vertebrate subclass
Page 35
Figure 2: The mammalian radiations
Page 36
Figure 3: The birds of the world
Page 37
Figure 4: The reptiles of today
Page 38
Figure 5: The amphibians’ phylogeny
Page 39