We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html.

Plants flower in response to many varied cues, such as temperature, photoperiod, and age. The floral transition of Cardamine flexuosa, a herbaceous biennial-to-perennial plant, requires exposure to cold temperature, a treatment known as vernalization. C. flexuosa younger than 5 weeks old are not fully responsive to cold treatment. We demonstrate that the levels of two age-regulated microRNAs, miR156 and miR172, regulate the timing of sensitivity in response to vernalization. Age and vernalization pathways coordinately regulate flowering through modulating the expression of CfSOC1, a flower-promoting MADS-box gene. The related annual Arabidopsis thaliana, which has both vernalization and age pathways, does not possess an age-dependent vernalization response. Thus, the recruitment of age cue in response to environmental signals contributes to the evolution of life cycle in plants.

The Tarim Craton, located in the center of Asia, was involved in the assembly and breakup of the Rodinia supercontinent during the Neoproterozoic and the subduction-accretion of the Central Asian Orogenic Belt (CAOB) during the Paleozoic. However, its tectonic evolution during these events is controversial, and a link between the Neoproterozoic and Paleozoic tectonic processes is missing. Here we present zircon U-Pb ages, Hf isotopes, and whole-rock geochemical data for the extensive granitoids in the western Kuruktag area, northeastern Tarim Craton. Three distinct periods of granitoid magmatism are evident: circa 830-820 Ma, 660-630 Ma, and 420-400 Ma. The magma sources, melting conditions (pressure, temperature, and water availability), and tectonic settings of various granitoids from each period are determined. Based on our results and the geological, geochronological, geochemical, and isotopic data from adjacent areas, a long-lived accretionary orogenic model is proposed. This model involves an early phase (circa 950-780 Ma) of southward advancing accretion from the Tianshan to northern Tarim and a late phase (circa 780-600 Ma) of northward retreating accretion, followed by back-arc opening and subsequent bidirectional subduction (circa 460-400 Ma) of a composite back-arc basin (i.e., the South Tianshan Ocean). Our model highlights a long-lived accretionary history of the southwestern CAOB, which may have initiated as part of the circum-Rodinia subduction zone and was comparable with events occurring at the southern margin of the Siberian Craton, thus challenging the traditional southward migrating accretionary models for the CAOB.

The flowering plant genus Oenothera is uniquely suited for studying molecular mechanisms of speciation. It assembles an intriguing combination of genetic features, including permanent translocation heterozygosity, biparental transmission of plastids, and a general interfertility of well-defined species. This allows an exchange of plastids and nuclei between species often resulting in plastome–genome incompatibility. For evaluation of its molecular determinants we present the complete nucleotide sequences of the five basic, genetically distinguishable plastid chromosomes of subsection Oenothera (=Euoenothera) of the genus, which are associated in distinct combinations with six basic genomes. Sizes of the chromosomes range from 163 365 bp (plastome IV) to 165 728 bp (plastome I), display between 96.3% and 98.6% sequence similarity and encode a total of 113 unique genes. Plastome diversification is caused by an abundance of nucleotide substitutions, small insertions, deletions and repetitions. The five plastomes deviate from the general ancestral design of plastid chromosomes of vascular plants by a subsection-specific 56 kb inversion within the large single-copy segment. This inversion disrupted operon structures and predates the divergence of the subsection presumably 1 My ago. Phylogenetic relationships suggest plastomes I–III in one clade, while plastome IV appears to be closest to the common ancestor.