Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome "obesity" in conifers and white pines. Comparative analysis of P. lambertiana and P. taeda L. reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines, the principal pathogen of P. lambertiana is white pine blister rust (Cronartium ribicola J.C. Fischer ex Raben.). Identification of candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1. We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population, and associated with Cr1 in unrelated sugar pine individuals sampled throughout the species' range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response.KEYWORDS conifer genome; transposable elements; white pine blister rust T HE gymnosperm genus Pinus is diverse and ubiquitous in temperate zones (Critchfield and Little 1966;Farjon and Filer 2013). Pines are often the keystone trees of terrestrial ecosystems (Richardson and Rundel 1998;Keane et al. 2012, and citations therein). Typical of conifers, pines have megagenomes that vary greatly in size among species, yet their karyotype is highly conserved. Pinus is divided into two large, ancient monophyletic subgenera, Strobus and Pinus, "white pines" and "yellow pines," respectively (Critchfield and Little 1966;Gernandt et al. 2005). The first Pinus genome sequence (22 Gbp) was recently reported for Pinus taeda L. ), a yellow pine commonly known as loblolly pine. The genomes of white pines are larger and more variable in size (Tomback 1982). Fossils allied with Strobus are known from the early Tertiary and late Cretaceous (Millar 1998) et al. 2006), the discovery of the underlying genes, and of markers serviceable for genetic improvement in reforestation, may be greatly accelerated by the genome sequence itself. P. lambertiana, commonly known as sugar pine, is a white pine native to western North America that is distributed from northern Oregon to Baja California at a wide span of altitudes. It is currently the tallest pine species, with heights reaching 76 m. The female cones of sugar pine are also gigan...

Follow this and additional works at: http://digitalcommons.uconn.edu/eeb_articles Recommended Citation Sezen, Uzay U.; Chazdon, Robin L.; and Holsinger, Kent E., "Genetic consequences of tropical second-growth forest regeneration" (2005). EEB Articles. 2.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.

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Iriartea deltoidea (Arecaceae) is an abundant canopy palm with a wide geographic distribution in Neotropical wet forests. We analyzed the genetic profile across three generations of Iriartea within a 43-ha area encompassing two areas of second-growth and adjoining old-growth forest at La Selva Biological Field Station in northeastern Costa Rica. A total of 311 reproductively mature trees, 99 large saplings, 207 small saplings, and 601 seedlings were genotyped using 141 AFLP loci. Parentage analysis revealed high dispersal distances, both for seed (over 2.3 km) and pollen (over 3.8 km), indicating a large genetic neighborhood within La Selva Biological Station. In a 20-ha area of second growth, the founding palm population was dominated by a small number of parental trees located in the adjacent old-growth forest; two old-growth trees contributed 48% of the second-growth genes. The genetic diversity of reproductively mature trees in this second-growth forest was significantly reduced compared to adjacent old-growth forest. Within 400 m of the border with old-growth forest, we observed a similar reduction of genetic diversity in saplings, and an even greater loss of genetic diversity in the second generation of seedlings. Nearly half of these seedlings were offspring of local parents. In contrast, in the distant portion of second-growth forest (400-800 m from the old-growth border), parentage analysis showed that 40% of seedlings originated from outside the study area and only 10% were offspring of local parents. These high levels of gene flow maintained genetic diversity in saplings and seedlings similar to levels observed in old-growth forest. Our findings highlight the importance of gene flow from diverse seed and pollen sources for sustaining levels of genetic diversity of tree populations in second-growth forests.