genomics of ferns and lycophytes. chapter 6: structure and evolution of fern plastid genomes paul g....
TRANSCRIPT
Genomics of Ferns and Lycophytes
Chapter 6: Structure and evolution of fern plastid genomes
Paul G. Wolf and Jessie M. Roper
Marchantia cp genome
• ca. 150 kb, circular molecule• large and small single copy regions separated by inverted repeat• gene number and order +/- conserved across land plants
Question:
What is the inheritance of the chloroplast genome in ferns?
Generally in land plants: maternal (via the egg, excluded via sperm)
• maternal with some biparental in Angiosperms• paternal in Gymnosperms• ferns?
Phyllitis (Aspleniaceae) – biparentalOsmunda (Osmundaceae) – maternalPolystichum (Drypoteridaceae) – maternalPteridium Dennstaedtiaceae) – maternalPellaea (Pteridaceae) – maternal
“During insemination in Ceratopteris richardii [Pteridaceae], the sperm cytoskeleton and flagella rearrange, and the coils of the cell extend while entering the neck canal. . . . All cellular components, except plastids, enter the egg cytoplasm”
Lopez-Smith and Renzagalia, 2008 (Sexual Plant Reproduction)
Marchantia cp genome
• ca. 150 kb• large and small single copy regions separated by inverted repeat• gene number and order +/- conserved across land plants
1992
Marchantia
tobacco
30kb inversion
Lycopodium
Equisetum
Psilotum
Osmunda
Lycopodium = Marchantia order
ferns = tobacco order
1992
30kb inversion
Fern and lycophyte total chloroplast genomes sequenced
• Huperzia• Isoetes• Selaginella
• Equisetum (basal fern)• Psilotum (basal fern)• Angiopteris (basal fern)• Adiantum (polypod)• Alsophila (polypod - 2009 paper)*
Gao et al. (2009) Complete chloroplast genome sequence of a tree fern Alsophila spinulosa
Fern and lycophyte total chloroplast genomes sequenced
• few advanced ferns sequenced
• but, Fern Tree of Life project will do many more
Rearrangements in fern chloroplast genomes
1. loss of some tRNA and other protein coding genes Gao et al. 2009
Rearrangements in fern chloroplast genomes
1. loss of some tRNA and other protein coding genes
1. 2 inversions in the Inverted Repeat (IR) of some ferns
Gao et al. 2009
Rearrangements in fern chloroplast genomes
1. loss of some tRNA and other protein coding genes
1. 2 inversions in the Inverted Repeat (IR) of some ferns
30kb inversion
IR inversion 1
IR inversion 2
?
[also using PCR assays for these inversions in other genera]
Chapter 7: Evolution of the nuclear genome of ferns and lycophytes
Takuya Nakazato, Michael S. Barker, Loren H. Rieseberg, and Gerald J. Gastony
Unfurling fern biology in the genomics age (BioScience, 2010)
Michael S. Barker and Paul G. Wolf
Academic family tree of Gerald J. Gastony
Rolla and Alice Tryon 1950s and 1990s
Is there an “Alice Tryon Women in Science” bequest for Botany Department?
Academic family tree of Gerald J. Gastony
Rieseberg
Nakazato
Barker
The neglected fern and lycophyte nuclear genomes
1. 1 genetic linkage map - Ceratopteris
1. 4 EST libraries – Selaginella (2), Ceratopteris, Adiantum
2. 3 BAC libraries - Selaginella (2), Ceratopteris
3. 1 nuclear genome sequencing project in the works - Selaginella
- or the “crying ferns”
The neglected fern and lycophyte nuclear genomes
Why?
- or the “crying ferns”
1. large genome size (>2X)
1. lack of funding for low economically important plants
The neglected fern and lycophyte nuclear genomes
Why?
- or the “crying ferns”
1. large genome size (>2X)
1. lack of funding for low economically important plants
But !
1. 2nd largest land plant group
2. sister to seed plants
3. diverse land plant lineages need to be compared
4. homologs of important seed plant genes occur in ferns
A short history of the study of the fern genome
Haploid chromosome number
• 57 in ferns vs. 16 in angiosperms [ > 14 = polyploid (Grant, 1981) ]
Ophioglossum (adder’s-tongue fern) - 2n = 1440 (96 ploid) in O. reticulatum
A short history of the study of the fern genome
Haploid chromosome number
• 57 in ferns vs. 16 in angiosperms [ > 14 = polyploid (Grant, 1981) ]
Questions:
How does this fern choreograph meiosis with an n > 600? Has it ever been observed? Do large n's lead to more aborted or nonviable spores?
A short history of the study of the fern genome
Haploid chromosome number
• 57 in ferns vs. 16 in angiosperms [ > 14 = polyploid (Grant, 1981) ]
• 13.6 in heterosporous ferns is exception
• heterosporous lycophytes << homosporous lycophytes
• heterosporous seed plants << homosporous ferns & allies
Therefore, homosporous ferns acquire high chromosome number to select for increased heterozygosity via polyploidy
Hypothesis of Klekowski & Baker (1966)
A short history of the study of the fern genome
Therefore, homosporous ferns acquire high chromosome number to select for increased heterozygosity via polyploidy
Hypothesis of Klekowski & Baker (1966)
Two lines of evidence did not support this hypothesis
1. Isozyme analysis indicated widespread silencings of genes – diploid numbers of copies
1. nn2. Most homosporous ferns are
outcrossing
A short history of the study of the fern genome
Homosporous ferns acquired high chromosome numbers with diploid gene expression via repeated cycles of polyploidization and subsequent gene silencing without chromosome loss
Hypothesis of Chris Haufler (1987)
A short history of the study of the fern genome
Many lines of evidence support this as the working hypothesis in ferns
1. Pseudogenes in nuclear genes in Polystichum
1. FISH detection of multiple dispersed chromosomal locations of rDNA in Ceratopteris
1. +/- Genetic linkage map analysis in Ceratopteris
Homosporous ferns acquired high chromosome numbers with diploid gene expression via repeated cycles of polyploidization and subsequent gene silencing without chromosome loss
Hypothesis of Chris Haufler (1987)
The future of fern genomics?
Ceratopteris has emerged as the “model” organism for fern genomics
Study of the origin of polyploidy (neo- and paleo-)
Correlating genomic changes to speciation and development
Two examples using Ceratopteris
1. Nakazato et al. (2006) genetic linkage analysis
1. Barker (2010) EST analysis
The future of fern genomics?
Ceratopteris genetic linkage analysis
• 700 genetic markers
• 85% multiple copies
• 24% single copy – low!
• large numbers of duplicate genes on different chromosomes
The future of fern genomics?
Ceratopteris genetic linkage analysis surprises!
• Expect clusters of linked duplicate genes on different chromosomes in recent (neo-) polyploids
Maize linkage map
Oxford plot of polyploid cotton’s A & D genomes
Rong et al. 2004
• Expect clusters of linked duplicate genes on different chromosomes in recent (neo-) polyploids
Duplicated gene copies are hyper-dispersed across the genome of Ceratopteris
• Expect clusters of linked duplicate genes on different chromosomes in recent polyploids
Indicates ancient polyploid event and many subsequent chromosomal changes
The future of fern genomics?
Ceratopteris EST analysis
• expressed sequence tags
• examines transcriptome
• mRNA is extracted
The future of fern genomics?
Ceratopteris EST analysis
• cDNA is made with reverse transcriptase
• ds cDNA is cloned into vector – library formed
• cDNA sequenced from 5’ and 3’ ends (= Tags)
• 400-800 bp ESTs can be contiged
The future of fern genomics?
Ceratopteris EST analysis
• synonymous substitution (silent) rate – Ks – obtained for duplicate genes
• most duplications young and placed in ‘zero’ class
• peak in duplications at 0.96 – 1.84 Ks or showing paleopolyploidy
The future of fern genomics?
Ceratopteris EST analysis
• synonymous substitution (silent) rate – Ks – obtained for duplicate genes
• most duplications young and placed in ‘zero’ class
• peak in duplications at 0.96 – 1.84 Ks or showing paleopolyploidy
• using molecular clocks and phylogenetic trees, paleopolyploidy linked to early polypod diversification
Question Set 1
1. Ferns and fern allies are diverse and old; is it really appropriate to expect that all have their nuclear genomes evolving by same “rules”?
1. You have been given a blank check to sequence the fern genome of yourchoice. Which would you choose and why? What methods would you use?
2. Why is the fate of most duplicate genes to eventually become silenced? Could mutations accumulate in both copies at the same rate causing subfunctionalization, where mutations cause the two copies to functionally be diminished to one over time?
3. If you are really interested in understanding the process of speciation, would ferns be the better choice relative to angiosperms?
1. What are the justifications for selecting Ceratopteris richardii as a model organism for ferns? Do the “idiosyncratic” features of its genome affect generalization to ferns?
2. Could maintaining large amounts of physical genetic material be disadvantageous for fern evolution? Could it be related to slow speciation rates, compared to angiosperms? Or, on the other hand, could the silenced genes hold the key to the long history of fern evolution?
1. Can high chromosome numbers in ferns and lycophytes simply be an outcome of the ‘stringent bivalent pairing’ that is known in the group? How might that idea be further examined or tested?
Question Set 2