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Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete 1-4. Here we report referencegrade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes 1,3 , these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement. Cotton represents the largest source of natural textile fibers in the world. Over 90% of annual fiber production comes from allotetraploid cotton (G. hirsutum and G. barbadense), which originated from an allopolyplodization event approximately 1-2 million year ago, followed by millennia of asymmetric subgenome selection 5,6. G. hirsutum is cultivated all over the world because of its high yield and G. barbadense is prized for its superior fiber quality. To cultivate G. hirsutum that produces longer, finer and stronger fibers, one approach is to introduce the superior fiber traits from G. barbadense into G. hirsutum. A genomics-enabled breeding strategy requires a detailed and robust understanding of genomic organization. Genomic feature G. hirsutum G. barbadense

BackgroundDNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species.ResultsBy analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species.ConclusionsThese results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1059-0) contains supplementary material, which is available to authorized users.

Background: Allopolyploid speciation requires rapid evolutionary reconciliation of two diverged genomes and gene regulatory networks. Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.).

Genetic maps of Brassica napus were constructed from four segregating populations of doubled haploid lines. Each mapping population had the same male parent and used the same set of RFLP probes, facilitating the construction of a consensus map. Chromosomal rearrangements were identified in each population by molecular marker analysis and were classified as de novo homeologous nonreciprocal transpositions (HNRTs), preexisting HNRTs, and homeologous reciprocal transpositions (HRTs). Ninety-nine de novo HNRTs were identified by the presence of a few lines having duplication of a chromosomal region and loss of the corresponding homeologous region. These de novo HNRTs were more prevalent in one population that had a resynthesized B. napus as a parent. Preexisting HNRTs were identified by fragment duplication or fragment loss in many DH lines due to the segregation of HNRTs preexisting in one of the parents. Nine preexisting HNRTs were identified in the three populations involving natural B. napus parents, which likely originated from previous homeologous exchanges. The male parent had a previously described HRT between N7 and N16, which segregated in each population. These data suggest that chromosomal rearrangements caused by homeologous recombination are widespread in B. napus. The effects of these rearrangements on allelic and phenotypic diversity are discussed.