Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology 6:R23. 2005
Salzberg, S. L., Dunning Hotopp, J. C., Delcher, A. L., Pop M., Smith,
D. R., Eisen, M. B. and W. C. Nelson.
The Trace Archive is a repository for the raw,
unanalyzed data generated by large-scale genome sequencing projects.
The existence of this data offers scientists the possibility of
discovering additional genomic sequences beyond those originally
sequenced. In particular, if the source DNA for a sequencing project
came from a species that was colonized by another organism, then the
project may yield substantial amounts of genomic DNA, including
near-complete genomes, from the symbiotic or parasitic organism.
By searching the publicly available repository of
DNA sequencing trace data, we discovered three new species of the
bacterial endosymbiont Wolbachia pipientis in three different species
of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We
extracted all sequences with partial matches to a previously sequenced
Wolbachia strain and assembled those sequences using customized
software. For one of the three new species, the data recovered were
sufficient to produce an assembly that covers more than 95% of the
genome; for a second species the data produce the equivalent of a
'light shotgun' sampling of the genome, covering an estimated 75-80% of
the genome; and for the third species the data cover approximately 6-7%
of the genome.
The results of this study reveal an unexpected
benefit of depositing raw data in a central genome sequence repository:
new species can be discovered within this data. The differences between
these three new Wolbachia genomes and the previously sequenced strain
revealed numerous rearrangements and insertions within each lineage and
hundreds of novel genes. The three new genomes, with annotation, have
been deposited in GenBank.
Host Genotype Determines Cytoplasmic Incompatibility Type in the Haplodiploid Genus Nasonia
Seth R. Bordenstein, Julieanne J. Uy and John H. Werren
ABSTRACT
In haplodiploid species, Wolbachia-induced
cytoplasmic incompatibility (CI) can be expressed in one of two ways:
as a “conversion” of diploid fertilized eggs into haploid
males or as embryonic mortality. Here we describe CI-type variation
within the parasitic wasp genus Nasonia and genetically analyze the
basis of this variation. We reach four main conclusions: (i) CI is
expressed primarily as conversion in N. vitripennis, but as embryonic
mortality in the sibling species N. giraulti and N. longicornis; (ii)
the difference in CI type between N. giraulti (mortality) and N.
vitripennis (conversion) is determined by host nuclear genotype rather
than by Wolbachia differences; (iii) N. vitripennis “conversion
genes” are recessive in hybrid females; and (iv) a difference in
CI level between the sibling species N. giraulti and N. longicornis is
due to the different Wolbachia infections in the species rather than to
the host genotype. These results show that host nuclear genes can
influence the type of CI present in a species. On the basis of these
findings, we propose a model for how different CI types evolve in
haplodiploids due to selection on nuclear genes modifying CI.
Wolbachia and genetic variability in the birdnest blowfly Protocalliphora sialia
E. BAUDRY, J. BARTOS, K. EMERSON, T. WHITWORTH and J . H. WERREN
Abstract
Wolbachia
are widespread cytoplasmically inherited bacteria
that induce various reproductive alterations in host arthropods,
including cytoplasmic incompatibility (CI), an incompatibility between
sperm and egg that typically results in embryonic death. CI has been
invoked as a possible mechanism for reproductive isolation and
speciation in arthropods, by restricting gene flow and promoting
maintenance (and evolution) of genetic divergence between populations.
Here we investigate patterns of Wolbachia infection and nuclear and
mitochondrial differentiation in geographical populations of the
birdnest blowfly Protocalliphorasialia. Blowflies in western North
America are infected with two A-groupWolbachia, with some individuals
singly and others doubly infected. Individuals in eastern North America
mostly show single infections with a B-group Wolbachia. Populations in
the Midwest are polymorphic for infections and show A- or B-group
infection. There is a low level of mitochondrial divergence and perfect
concordance of mitochondrial haplotype with infection type, suggesting
that two Wolbachia-associated selective sweeps of the mitochondrion
have occurred in this species. Amplified fragment length polymorphism
analysis of nuclear genetic variation shows genetic differentiation
between the eastern–Midwestern and western populations. Both
Midwestern and eastern flies infected with A-Wolbachia show eastern
nuclear genetic profiles. Current results therefore suggest that
Wolbachia has not acted as a major barrier to gene flow between western
and eastern–Midwestern populations, although some genetic
differentiation between A-Wolbachia infected and B-Wolbachia infected
individuals in eastern–Midwestern populations cannot be ruled out.
SEX DETERMINATION, SEX RATIOS, AND GENETIC CONFLICT
John H. Werren
ABSTRACT
Genetic mechanisms of sex determination are
unexpectedly diverse and change rapidly during evolution. We review the
role of genetic conflict as the driving force behind this diversity and
turnover. Genetic conflict occurs when different components of a
genetic system are subject to selection in opposite directions.
Conflict may occur between genomes (including paternal-maternal and
parentalzygotic conflicts) or within genomes (between cytoplasmic and
nuclear genes or sex chromosomes and autosomes). The sex-determining
system consists of parental sex-ratio genes, parental-effect sex
determiners, and zygotic sex determiners, which are subject to
different selection pressures because of differences in their modes of
inheritance and expression. Genetic conflict theory is used to explain
the evolution of several sex-determining mechanisms, including sex
chromosome drive, cytoplasmic sex-ratio distortion, and cytoplasmic
male sterility in plants. Although still limited, there is growing
evidence that genetic conflict could be important in the evolution of
sex-determining mechanisms.
OBTAINING, STORING AND ARCHIVING SPECIMENS AND TISSUE SAMPLES FOR USE IN MOLECULAR STUDIES. In
Techniques in Molecular Systematics and Evolution. R. DeSalle, Gonzalo
Giribet, Ward Wheeler. Basel, Boston, Berlin, Birkhauser Verlag:
176-248. 2002
Lorenzo Prendini, Robert Hanner and Rob DeSalle.
The obvious first step in any systematic or
population genetics study is to focus on a group of organisms or a
level of interest. We assume that these issues are self-explanatory and
the reader is referred to the second section of this book for examples
of the application of molecular techniques to a wide range of
questions, and a summary of the problems that can arise in the course
of such studies. Equally important in the initial stages of systematic
analysis are sampling strategy, collection, storage, vouchering and
archiving.These last two points are especially important for
molecular studies since no standard protocol currently exists for the
disposition of tissue or DNA vouchers to scientifically validate the
results of the study, although this situation is changing as a number
of museums and research universities establish biorepositories for the
long term storage of genetic resources.
There are several ways in which tissues can be
obtained for analysis, each with its own peculiarities, nuances and
requirements. The purpose of this chapter is not to give an exhaustive
account of collecting and sampling techniques, but rather to focus on
the most important aspects of collection and storage for successful
systematic analysis. Other publications have reviewed the plethora of
field collection techniques that exist for organisms as diverse as
plants, fungi, vertebrates and invertebrates, and the reader is advised
to consult literature relevant to the taxa of interest for specific
details about collecting these organisms. In this chapter we will focus
on five aspects of collection and storage: 1) storage of
freshly-collected tissues in the field; 2) obtaining tissues from other
sources, e.g. museum collections, stock centers and commercial supply
companies; 3) transportation, long-term storage and archiving of tissue
samples and voucher specimens; 4) selection of appropriate tissues for
protein or nucleotide extraction; and 5) legal and ethical issues
involved in the collection and storage of tissues.
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