Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass

Abstract

SummaryOrchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an ~1.84‐Gb chromosome‐scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb and a super‐scaffold N50 of 252.52 Mb, which is the first chromosome‐scale assembled genome of a cool‐season forage grass. The genome includes 40 088 protein‐coding genes, and 69% of the assembled sequences are transposable elements, with long terminal repeats (LTRs) being the most abundant. The LTRretrotransposons may have been activated and expanded in the grass genome in response to environmental changes during the Pleistocene between 0 and 1 million years ago. Phylogenetic analysis reveals that orchardgrass diverged after rice but before three Triticeae species, and evolutionarily conserved chromosomes were detected by analysing ancient chromosome rearrangements in these grass species. We also resequenced the whole genome of 76 orchardgrass accessions and found that germplasm from Northern Europe and East Asia clustered together, likely due to the exchange of plants along the ‘Silk Road’ or other ancient trade routes connecting the East and West. Last, a combined transcriptome, quantitative genetic and bulk segregant analysis provided insights into the genetic network regulating flowering time in orchardgrass and revealed four main candidate genes controlling this trait. This chromosome‐scale genome and the online database of orchardgrass developed here will facilitate the discovery of genes controlling agronomically important traits, stimulate genetic improvement of and functional genetic research on orchardgrass and provide comparative genetic resources for other forage grasses.

Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureumSchum.)

“…By reference to the genome of its closely related species P. glaucum (AA, 2n=14), the sequences were assembled into A' and B sub-genomes each of which contained 7 pairs of collinear chromosomes. The quality of this assembly was significantly better than the recently published genome assemblies of orchard grass (Dactylis glomerata L.) 32 , pearl millet 18 , ryegrass (Lolium perenne L.), T. urartu and barley 41 . Our sequencing and assembly strategy integrated Nanopore ultra-long reads sequencing, BioNano for chromosome-scale scaffolding, and a modified Hi-C protocol, which may be readily applicable to other complex genome sequencing and assembly 26 .…”

“…The allotetraploid elephant grass with A'A'BB genome was originated about 15 MYA. It was perhaps caused by the grazing pressure while herbivores outbreak in the Miocene era of Africa 18,32 .…”

Revealing the full-length transcriptome of caucasian clover rhizome development

“…The number of sequences containing more than one SSR was 13,856, and the number of SSRs present in compound form was 10,041. In addition, most are mononucleotides (33,533), dinucleotides (8,610) and trinucleotides (14,026).…”

“…Based on the GO analysis, 57,583 transcripts were enriched in the three ontologies ( Fig.2d) "biological process", "molecular function" and "cellular component". Transcripts involved in biological processes mainly included "metabolic process" (39,010), "cellular process" (33,383), and "singleorganism process" (26,933). In molecular function, transcripts were mainly enriched in "binding" (32,350), "catalytic activity" (32,206), and "transporter activity" (3,404).…”

“…It does not require assembly and can completely retain the entire sequence from the 3' to 5' ends of an RNA, but with a higher error rate; moreover, the second-generation stepwise approach can correct mistakes [28][29][30][31]. PacBio has been utilized to detect more than 42,280 different splicing isoforms and a large number of AS events were found to be associated with the rhizome system and assist genome annotation in orchardgrass [32,33]. The results indicate that posttranscriptional regulation plays an important role in the rhizome system.…”