Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

ultivated peanut or groundnut (A. hypogaea L.) is among the most important oil and food legumes, grown on 25 million ha between latitudes 40° N and 40° S with annual production of ~46 million tons (http://www.fao.org/faostat/en/#home). It presumably was domesticated in South America ~6,000 years ago and then was widely distributed in post-Columbian times 1. Combining richness in seed oil (~46-58%) and protein (~22-32%), peanut is important in fighting malnutrition and ensuring food security.

The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.

No abstract

Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms 1-3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms. Many water lily species, particularly from Nymphaea (Nymphaeaceae), have large and showy flowers and belong to the angiosperms (also called flowering plants). Their aesthetic beauty has captivated notable artists such as the French impressionist Claude Monet. Water lily flowers have limited differentiation in perianths (outer floral organs), but they possess both male and female organs and have diverse scents and colours, similar to many mesangiosperms (core angiosperms, including eudicots, monocots, and magnoliids) (Supplementary Note 1). In addition, some water lilies have short life cycles and enormous numbers of seeds 4 , which increase their potential as a model plant to represent the ANA-grade of angiosperms and to study early evolutionary events within the angiosperms. In particular, N. colorata Peter has a relatively small genome size (2n = 28 and approximately 400 Mb) and blue petals that make it popular in breeding programs (Supplementary Note 1). We report here the genome sequence of N. colorata, obtained using PacBio RSII single-molecule real-time (SMRT) sequencing technology. The genome was assembled into 1,429 contigs (with a contig N50 of 2.1 Mb) and total length of 409 Mb with 804 scaffolds, 770 of which were anchored onto 14 pseudo-chromosomes (Extended Data Fig. 1 and Extended Data Table 1). Genome completeness was estimated to be 94.4% (Supplementary Note 2). We annotated 31,580 protein-coding genes and predicted repetitive elements with a collective length of 160.4 Mb, accounting for 39.2% of the genome (Supplementary Note 3). The N. colorata genome provides an opportuni...