| 1. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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| 2. |
- de La Torre, Amanda R, et al.
(författare)
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Insights into conifer giga-genomes
- 2014
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Ingår i: Plant Physiology. - : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 166:4, s. 1724-1732
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Tidskriftsartikel (refereegranskat)abstract
- Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.
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| 3. |
- O'Connell, Lisa M., et al.
(författare)
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Patterns of post-glacial colonization by western redcedar (Thuja plicata, Cupressaceae) as revealed by microsatellite markers
- 2008
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Ingår i: Botany - Botanique. - : Canadian Science Publishing. ; , s. 194-203
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Konferensbidrag (refereegranskat)abstract
- As knowledge of historical migration in response to climatic change allows insight into the dynamic nature of range shifts, patterns of post-glacial colonization were evaluated for the western redcedar (Thuja plicata Donn ex D. Don). We sampled and genotyped 620 trees from 23 populations across its range, including disjunct coastal and interior mesic sites. Genetic variation at eight microsatellite loci (mean alleles/locus = 10.30, mean expected heterozygosity = 0.755) was much higher than previous studies involving other markers, and inbreeding coefficients were predominantly positive (mean = 0.110). The two southernmost populations showed greatest genetic distances, while remaining populations clustered into three distinct geographic groups, comprising northern-coastal, central, and southern-interior populations, respectively. Genetic diversity decreased with latitude, while genetic and geographic distances were strongly correlated (r = 0.788). Our findings are consistent with independent routes of relatively recent colonization from one major refugium, located south of the glacial maximum, rather than ancient vicariant events. Regional bottlenecks, detected in the south of the range, may have resulted from local extinctions as the range of western redcedar advanced northward. Combined with inbreeding and the evolution of inbreeding tolerance, this may have promoted homozygosity for most classes of genetic markers as observed in other studies of this species.
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| 4. |
- Thompson, Stacey Lee, et al.
(författare)
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A novel mating system analysis for modes of self-oriented mating applied to diploid and polyploid arctic Easter daisies (Townsendia hookeri).
- 2006
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Ingår i: Heredity. - : Nature Publishing Group. - 0018-067X .- 1365-2540. ; 97:2, s. 119-126
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a new model for mating system analysis, which attempts to distinguish among alternative modes of self-oriented mating within populations. This model jointly estimates the rates of outcrossing, selfing, automixis and apomixis, through the use of information in the family structure given by dominant genetic marker data. The method is presented, its statistical properties evaluated, and is applied to three arctic Easter daisy populations, one consisting of diploids, the other two of tetraploids. The tetraploids are predominantly male sterile and reported to be apomictic while the diploids are male fertile. In each Easter daisy population, 10 maternal arrays of six progeny were assayed for amplified fragment length polymorphism markers. Estimates, confirmed with likelihood ratio tests of mating hypotheses, showed apomixis to be predominant in all populations (ca. 70%), but selfing or automixis was moderate (ca. 25%) in tetraploids. It was difficult to distinguish selfing from automixis, and simulations confirm that with even very large sample sizes, the estimates have a very strong negative statistical correlation, for example, they are not independent. No selfing or automixis was apparent in the diploid population, instead, moderate levels of outcrossing were detected (23%). Low but significant levels of outcrossing (2-4%) seemed to occur in the male-sterile tetraploid populations; this may be due to genotyping error of this level. Overall, this study shows apomixis can be partial, and provides evidence for higher levels of inbreeding in polyploids compared to diploids and for significant levels of apomixis in a diploid plant population.
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| 5. |
- Thompson, Stacey Lee, et al.
(författare)
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Cryptic sex within male-sterile polyploid populations of the Easter daisy, Townsendia hookeri
- 2008
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Ingår i: International journal of plant sciences. - : University of Chicago Press. - 1058-5893 .- 1537-5315. ; 169:1, s. 183-193
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Tidskriftsartikel (refereegranskat)abstract
- After a transition from sexuality to asexuality, the evolutionary dynamics in apomictic lineages will largely depend on the frequency of recombination. We evaluated the presence and extent of asexuality and recombination within populations of the Easter daisy, Townsendia hookeri, from the Yukon Territory, Canada. Amplified fragment-length polymorphism (AFLP) fingerprints were used to genotype 78 individuals from four populations. Multilocus AFLP genotypes from each population were subjected to four tests for deviations from free recombination among loci, and the long-term frequency of sexuality was estimated for each population with a novel procedure. In addition, a sample of individuals was surveyed for genome size using flow cytometry, and pollen was assayed for male fertility. One male-fertile, diploid population showed evidence of rampant recombination. Two male-sterile populations (i.e., with aborted anthers) were tetraploid and asexual. The remaining population was male-sterile and included both triploids and tetraploids. Evidence of both sexuality and asexuality was uncovered in this mixed-ploidy population, at an equilibrium rate of approximately three sexual events every two generations. The presence and extent of sexuality differed with ploidy, while cryptic sex was uncovered within a morphologically asexual population, thus reinforcing the power of genome surveys to assess reproductive dynamics at the limit of a plant's geographical range.
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| 6. |
- Thompson, Stacey Lee, et al.
(författare)
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Three-gene identity coefficients demonstrate that clonal reproduction promotes inbreeding and spatial relatedness in yellow-cedar, Callitropsis nootkatensis
- 2008
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Ingår i: Evolution. - : John Wiley & Sons. - 0014-3820 .- 1558-5646. ; 62:10, s. 2570-2579
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Tidskriftsartikel (refereegranskat)abstract
- Asexual reproduction has the potential to promote population structuring through matings between clones as well as through limited dispersal of related progeny. Here we present an application of three-gene identity coefficients that tests whether clonal reproduction promotes inbreeding and spatial relatedness within populations. With this method, the first two genes are sampled to estimate pairwise relatedness or inbreeding, whereas the third gene is sampled from either a clone or a sexually derived individual. If three-gene coefficients are significantly greater for clones than nonclones, then clonality contributes excessively to genetic structure. First, we describe an estimator of three-gene identity and briefly evaluate its properties. We then use this estimator to test the effect of clonality on the genetic structure within populations of yellow-cedar (Callitropsis nootkatensis) using a molecular marker survey. Five microsatellite loci were genotyped for 485 trees sampled from nine populations. Our three-gene analyses show that clonal ramets promote inbreeding and spatial structure in most populations. Among-population correlations between clonal extent and genetic structure generally support these trends, yet with less statistical significance. Clones appear to contribute to genetic structure through the limited dispersal of offspring from replicated ramets of the same clonal genet, whereas this structure is likely maintained by mating among these relatives.
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