Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin

Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics

BACKGROUND

Sweet yellow clover (Melilotus officinalis) is a diploid plant (2n = 16) that is native to Europe. It is an excellent legume forage. It can both fix nitrogen and serve as a medicine. A genome assembly of Melilotus officinalis that was collected from Best corporation in Beijing is available based on Nanopore sequencing. The genome of Melilotus officinalis was sequenced, assembled, and annotated.

RESULTS

The latest PacBio third generation HiFi assembly and sequencing strategies were used to produce a Melilotus officinalis genome assembly size of 1,066 Mbp, contig N50 = 5 Mbp, scaffold N50 = 130 Mbp, and complete benchmarking universal single-copy orthologs (BUSCOs) = 96.4%. This annotation produced 47,873 high-confidence gene models, which will substantially aid in our research on molecular breeding. A collinear analysis showed that Melilotus officinalis and Medicago truncatula shared conserved synteny. The expansion and contraction of gene families showed that Melilotus officinalis expanded by 565 gene families and shrank by 56 gene families. The contacted gene families were associated with response to stimulus, nucleotide binding, and small molecule binding. Thus, it is related to a family of genes associated with peptidase activity, which could lead to better stress tolerance in plants.

CONCLUSIONS

In this study, the latest PacBio technology was used to assemble and sequence the genome of the Melilotus officinalis and annotate its protein-coding genes. These results will expand the genomic resources available for Melilotus officinalis and should assist in subsequent research on sweet yellow clover plants.

Revisiting the amalgaviral landscapes in plant transcriptomes expands the host range of plant amalgaviruses

Plant amalgaviruses are monopartite, double-stranded RNA viruses, capable of vertical transmission through seeds. An attempt to revisit plant transcriptome-assembled contigs for amalgaviral sequences identified 40 putative novel amalgaviruses in 35 plant species, nearly doubling the number of plant amalgaviruses. Of the 35 plant species, 33 are reported to host amalgaviruses for the first time, including a pteridophytic and two gymnospermic species. Coding-complete genomes of all identified viruses were recovered and the putative +1 programmed ribosomal frameshift (PRF) sites were determined. Genomes of 35 identified amalgaviruses contained the conserved +1 PRF motif 'UUU_CGN', while variant versions were predicted in five genomes. Phylogenetic analysis grouped pteridophyte- and gymnosperm-infecting amalgaviruses together in divergent sub-clades while few of the related angiosperm-infecting amalgaviruses infect members of the same plant family, reiterating the co-evolution of plant amalgaviruses and their hosts. The current study paves way for further studies on understanding biological properties of identified viruses.

Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses

The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared with dichorhaviruses, is a bi-segmented genome. Before 2017, a sole varicosavirus was known and characterized, and then two more varicosaviruses were identified through high-throughput sequencing in 2017 and 2018. More recently, the number of known varicosaviruses has substantially increased in concert with the extensive use of high-throughput sequencing platforms and data mining approaches. The novel varicosaviruses have revealed not only sequence diversity, but also plasticity in terms of genome architecture, including a virus with a tentatively unsegmented genome. Here, we report the discovery of 45 novel varicosavirus genomes which were identified in publicly available metatranscriptomic data. The identification, assembly, and curation of the raw Sequence Read Archive reads has resulted in 39 viral genome sequences with full-length coding regions and 6 with nearly complete coding regions. The highlights of the obtained sequences include eight varicosaviruses with unsegmented genomes, which are linked to a phylogenetic clade associated with gymnosperms. These findings have resulted in the most complete phylogeny of varicosaviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant rhabdoviruses. Thus, the extensive use of sequence data mining for virus discovery has allowed us to unlock of the hidden genetic diversity of varicosaviruses, the largely neglected plant rhabdoviruses.