Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines

Abstract

Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations and closely related taxa, through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast-level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world's rarest pines - Torrey pine (Pinus torreyana) - due to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90% ( approximately 105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/ approximately 21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population-level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants.

Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads

“…This result is consistent with previous studies showing low within-population diversity in addition to limited gene flow among populations in C. debaoensis 1011. Whittall et al 49 found a comparable level of intraspecific divergence in pines, irrespective of the rarity of the considered species. However, in the pest species Jacobaea vulgaris (Asteraceae), the intraspecific divergence was four times higher50, perhaps due to it’s short generation times as opposed to those prevailing in slow growing and long-lived trees.…”

Chloroplast Genome Differences between Asian and American Equisetum arvense (Equisetaceae) and the Origin of the Hypervariable trnY-trnE Intergenic Spacer

“…The cp genomes of Panicum virgatum , which has different ecotypes in upland and lowland regions, contained 116 SNPs and 46 indels [10], and high variability in indel (3–278) and SNP (6–1000) numbers was noted in the cp genomes of 13 Gossypium species [11]. Finally, comparison of intraspecific variation in rare and widespread pines indicated low levels of divergence [8]. These data improved our understanding of cp genome evolution and divergence times of closely related taxa.…”

An Evaluation of Putative Sympatric Speciation within Limnanthes (Limnanthaceae)

“…A total of 10 pmol was used for 76 cycles of paired-end sequencing in a single lane of an Illumina GAI in the Central Service Laboratory of the Oregon State University Center for Genome Research and Biocomputing. Assembly of the microreads followed a modified protocol of Whittall et al [26]. Microreads, after tag removal, were assembled into contigs with the de novo assembler Velvet v. 0.7 [27].…”