The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica

The complete chloroplast genome of the monotypic genus of Bulleyia Schltr. (Orchidaceae)

Bulleyia Schltr. is monotypic and represented only by Bulleyia yunnanensis Schltr., native to the Yunnan of China, Bhutan, and northeast India. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of B. yunnanensis. The cp genome sequence of B. yunnanensis was 159,581 bp in length and presented a typical quadripartite structure consisting of one large single-copy region (LSC, 87,563 bp), one small single-copy region (SSC, 18,714 bp), and two inverted repeat regions (IR, 26,652 bp). Besides, the cp genome encoded 132 genes, including 113 unique genes (79 protein-coding genes, 30 tRNA genes, and four rRNA genes). The phylogenetic analysis suggested that B. yunnanensis be closely related to Pholidota in tribe Arethuseae.

Population Genomics of Transitions to Selfing in Brassicaceae Model Systems

Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory, and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.

Comparative Analysis of the Chloroplast Genomic Information of Cunninghamia lanceolata (Lamb.) Hook with Sibling Species from the Genera Cryptomeria D. Don, Taiwania Hayata, and Calocedrus Kurz

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an important coniferous tree species for timber production, which accounts for ~40% of log supply from plantations in southern China. Chloroplast genetic engineering is an exciting field to engineer several valuable tree traits. In this study, we revisited the published complete Chinese fir (NC_021437) and four other coniferous species chloroplast genome sequence in Taxodiaceae. Comparison of their chloroplast genomes revealed three unique inversions found in the downstream of the gene clusters and evolutionary divergence were found, although overall the chloroplast genomic structure of the Cupressaceae linage was conserved. We also investigated the phylogenetic position of Chinese fir among conifers by examining gene functions, selection forces, substitution rates, and the full chloroplast genome sequence. Consistent with previous molecular systematics analysis, the results provided a well-supported phylogeny framework for the Cupressaceae that strongly confirms the “basal” position of Cunninghamia lanceolata. The structure of the Cunninghamia lanceolata chloroplast genome showed a partial lack of one IR copy, rearrangements clearly occurred and slight evolutionary divergence appeared among the cp genome of C. lanceolata, Taiwania cryptomerioides, Taiwania flousiana, Calocedrus formosana and Cryptomeria japonica. The information from sequence divergence and length variation of genes could be further considered for bioengineering research.

The complete chloroplast genome sequence of Cunninghamia lanceolata

We determined the complete chloroplast genome sequence of Cunninghamia lanceolata (GenBank accession: NC_021437.1) in this study. The total length of the chloroplast genome is 135 334 bp. The GC content is 35%. A total of 119 genes are successfully annotated, including 35 tRNA (20 tRNA species), 3 rRNA (3 rRNA species) and 81 protein-coding genes (81 PCG species). Twelve protein-coding genes (rps16, ycf3, rpoC1, atpF, rps12, ndhB, rpl2, rpl16, petD, petB, ndhA, rps15) contain one or two introns. A maximum likelihood phylogenetic analysis showed that this newly characterized Cunninghamia lanceolata chloroplast genome will provide essential data for further study on phylogenetic resolution, biodiversity for the genus Cunninghamia and Taxodiacea.

The complete chloroplast genome sequence of Dendrobium officinale

The complete chloroplast sequence of Dendrobium officinale, an endangered and economically important traditional Chinese medicine, was reported and characterized. The genome size is 152,018 bp, with 37.5% GC content. A pair of inverted repeats (IRs) of 26,284 bp are separated by a large single-copy region (LSC, 84,944 bp) and a small single-copy region (SSC, 14,506 bp). The complete cp DNA contains 83 protein-coding genes, 39 tRNA genes and 8 rRNA genes. Fourteen genes contained one or two introns.

The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure

The origin of Cardamine flexuosa (Wavy Bittercress) has been a conundrum for more than six decades. Here we identify its parental species, analyse its genome structure in comparison to parental genomes and describe intergenomic structural variations in C. flexuosa. Genomic in situ hybridization (GISH) and comparative chromosome painting (CCP) uncovered the parental genomes and the chromosome composition of C. flexuosa and its presumed diploid progenitors. Cardamine flexuosa is an allotetraploid (2n = 4x = 32), originating from two diploid species, Cardamine amara and Cardamine hirsuta (2n = 2x = 16). The two parental species display almost perfectly conserved chromosomal collinearity for seven out of the eight chromosomes. A 13 Mb pericentric inversion distinguishes chromosome CA1 from CH1. A comparative cytomolecular map was established for C. flexuosa by CCP/GISH. Whereas conserved chromosome collinearity between the C. amara and C. hirsuta subgenomes might have promoted intergenomic rearrangements through homeologous recombination, only one reciprocal translocation between two homeologues has occurred since the origin of C. flexuosa. The genome of C. flexuosa demonstrates that allopolyploids can maintain remarkably stable subgenomes over 10(4) -10(5)  yr throughout a wide distribution range. By contrast, the rRNA genes underwent genome-specific elimination towards a diploid-like number of loci.

The genetic structure of Arabidopsis thaliana in the south-western Mediterranean range reveals a shared history between North Africa and southern Europe

BACKGROUND

Deciphering the genetic structure of Arabidopsis thaliana diversity across its geographic range provides the bases for elucidating the demographic history of this model plant. Despite the unique A. thaliana genomic resources currently available, its history in North Africa, the extreme southern limit in the biodiversity hotspot of the Mediterranean Basin, remains virtually unknown.

RESULTS

To approach A. thaliana evolutionary history in North Africa, we have analysed the genetic diversity and structure of 151 individuals collected from 20 populations distributed across Morocco. Genotyping of 249 genome-wide SNPs indicated that Morocco contains substantially lower diversity than most analyzed world regions. However, IBD, STRUCTURE and PCA clustering analyses showed that genetic variation is strongly geographically structured. We also determined the genetic relationships between Morocco and the closest European region, the Iberian Peninsula, by analyses of 201 populations from both regions genotyped with the same SNPs. These analyses detected four genetic groups, but all Moroccan accessions belonged to a common Iberian/Moroccan cluster that appeared highly differentiated from the remaining groups. Thus, we identified a genetic lineage with an isolated demographic history in the south-western Mediterranean region. The existence of this lineage was further supported by the study of several flowering genes and traits, which also found Moroccan accessions similar to the same Iberian group. Nevertheless, genetic diversity for neutral SNPs and flowering genes was higher in Moroccan than in Iberian populations of this lineage. Furthermore, we analyzed the genetic relationships between Morocco and other world regions by joint analyses of a worldwide collection of 337 accessions, which detected an additional weak relationship between North Africa and Asia.

CONCLUSIONS

The patterns of genetic diversity and structure of A. thaliana in Morocco show that North Africa is part of the species native range and support the occurrence of a glacial refugium in the Atlas Mountains. In addition, the identification of a genetic lineage specific of Morocco and the Iberian Peninsula indicates that the Strait of Gibraltar has been an A. thaliana migration route between Europe and Africa. Finally, the genetic relationship between Morocco and Asia suggests another migration route connecting north-western Africa and Asia.

The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids

The chloroplast genome of Phalaenopsis equestris was determined and compared to those of Phalaenopsis aphrodite and Oncidium Gower Ramsey in Orchidaceae. The chloroplast genome of P. equestris is 148,959 bp, and a pair of inverted repeats (25,846 bp) separates the genome into large single-copy (85,967 bp) and small single-copy (11,300 bp) regions. The genome encodes 109 genes, including 4 rRNA, 30 tRNA and 75 protein-coding genes, but loses four ndh genes (ndhA, E, F and H) and seven other ndh genes are pseudogenes. The rate of inter-species variation between the two moth orchids was 0.74% (1107 sites) for single nucleotide substitution and 0.24% for insertions (161 sites; 1388 bp) and deletions (189 sites; 1393 bp). The IR regions have a lower rate of nucleotide substitution (3.5-5.8-fold) and indels (4.3-7.1-fold) than single-copy regions. The intergenic spacers are the most divergent, and based on the length variation of the three intergenic spacers, 11 native Phalaenopsis orchids could be successfully distinguished. The coding genes, IR junction and RNA editing sites are relatively more conserved between the two moth orchids than between those of Phalaenopsis and Oncidium spp.

Signals of speciation within Arabidopsis thaliana in comparison with its relatives

The species within the now well-defined Arabidopsis genus provide biological materials suitable to investigate speciation and the development of reproductive isolation barriers between related species. Even within the model species A. thaliana, genetic differentiation between populations due to environmental adaptation or demographic history can lead to cases where hybrids between accessions are non-viable. Experimental evidence supports the importance of genome duplications and genetic epistatic interactions in the occurrence of reproductive isolation. Other examples of adaptation to specific environments can be found in Arabidopsis relatives where hybridization and chromosome doubling lead to new amphidiploid species. Molecular signals of speciation found in the Arabidopsis genus should provide a better understanding of speciation processes in plants from a genetic, molecular and evolutionary perspective.

Cytoplasmic phylogeny and evidence of cyto-nuclear co-adaptation in Arabidopsis thaliana

In recent years Arabidopsis thaliana has become a model species for genomic variability and adaptation studies. Although impressive quantities of data have been gathered on the nuclear genomic diversity of this species, little has been published regarding its cytoplasmic diversity. We analyzed the diversity of plastid (pt) and mitochondrial (mt) genomes among 95 accessions, covering most Arabidopsis geographic origins. Four intergenic regions of the pt genome were sequenced, and a total of 68 polymorphisms and 65 pt haplotypes were identified. Several strategies were developed to identify mt polymorphisms among a subset of 14 accessions. Fifteen polymorphisms were further developed as PCR-based markers and used to analyze the whole set of 95 accessions. Using statistical parsimony, we built pt and mt phylogenetic networks of haplotype groups. To root the pt network, the pt intergenic regions of two related Arabidopsis species, Arabidopsis lyrata and Arabidopsis arenosa, were also sequenced. The mt and pt phylogenies are highly congruent and could be combined into a single cytoplasmic phylogeny. To estimate whether co-adaptation between nuclear and cytoplasmic genomes exists in A. thaliana, we tested the germination capacity in challenging conditions of 27 pairs of reciprocal F(2) families. We found that the cytoplasm donor had a significant effect on the germination capacity of some F(2) families.

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Organellar DNA sequences are widely used in evolutionary and population genetic studies, however, the conservative nature of chloroplast gene and genome evolution often limits phylogenetic resolution and statistical power. To gain maximal access to the historical record contained within chloroplast genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) to simultaneously sequence multiple genomes using the Illumina Genome Analyzer. We PCR-amplified approximately 120 kb plastomes from eight species (seven Pinus, one Picea) in 35 reactions. Pooled products were ligated to modified adapters that included 3 bp indexing tags and samples were multiplexed at four genomes per lane. Tagged microreads were assembled by de novo and reference-guided assembly methods, using previously published Pinus plastomes as surrogate references. Assemblies for these eight genomes are estimated at 88-94% complete, with an average sequence depth of 55x to 186x. Mononucleotide repeats interrupt contig assembly with increasing repeat length, and we estimate that the limit for their assembly is 16 bp. Comparisons to 37 kb of Sanger sequence show a validated error rate of 0.056%, and conspicuous errors are evident from the assembly process. This efficient sequencing approach yields high-quality draft genomes and should have immediate applicability to genomes with comparable complexity.

Effective population size and tests of neutrality at cytoplasmic genes inArabidopsis

Cytoplasmic genomes typically lack recombination, implying that genetic hitch-hiking could be a predominant force structuring nucleotide polymorphism in the chloroplast and mitochondria. We test this hypothesis by analysing nucleotide polymorphism data at 28 loci across the chloroplast and mitochondria of the outcrossing plantArabidopsis lyrata, and compare patterns with multiple nuclear loci, and the highly selfingArabidopsis thaliana. The maximum likelihood estimate of the ratio of effective population size at cytoplasmic relative to nuclear genes inA. lyratadoes not depart from the neutral expectation of 0·5. Similarly, the ratio of effective size inA. thalianais close to unity, the neutral expectation for a highly selfing species. The results are thus consistent with neutral organelle polymorphism in these species or with comparable effects of hitch-hiking in both cytoplasmic and nuclear genes, in contrast to the results of recent studies on gynodioecious taxa. The four-gamete test and composite likelihood estimation provide evidence for very low levels of recombination in the organelles ofA. lyrata, although permutation tests do not suggest that adjacent polymorphic sites are more closely linked than more distant sites across the two genomes, suggesting that mutation hotspots or very low rates of gene conversion could explain the data.

Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana

The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated--such as the position of a locus within the chromosome, or imperfect repeats--appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.