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Chinese Plum Genome Offers Insights into Early Flowering, Scent

NEW YORK (GenomeWeb News) – In a paper that appeared online last week in Nature Communications, researchers led by BGI-Shenzen's Jun Wang presented their genome sequence and assembly of the Chinese plum, Prunus mume.

The approach the researchers took to generate the P. mume genome mirrored that used to produce the goat genome, which was reported earlier last week in Nature Biotechnology by a team that included some of the same researchers. In both instances, investigators combined a next-generation sequencing approach with optical mapping to produce a reference genome.

With the P. mume genome in hand, Wang and his colleagues examined the ancestral Rosaceae family genome and, combined with transcriptome data, explored P. mume's ability to flower in the cold and its signature scent.

"The P. mume genome lays a solid foundation for identification of important economic traits, and provides a valuable resource for P. mume breeding and other Rosaceae species studies," said Wenbin Chen, a project manager at BGI and co-first author of the paper, in a statement. "The work here also brings a new approach for further exploring the biosynthesis of floral scent and regulation mechanism of early blooming in endodormancy, and other comparative genomics studies on Rosaceae species."

Domesticated P. mume is often cultivated though grafting, leading it to be diverse, but also with a difficult-to-assemble genome, the researchers said. Instead of sequencing a cultivated plant, the researchers traced the origin of P. mume to a region in Tibet and collected wild samples from there.

They then sequenced that wild sample using the Illumina GAII, generating 50.4 gigabases of sequencing data. Using SOAPdenovo software, they assembled nearly 85 percent of the P. mume genome.

The investigators then turned to whole-genome mapping to refine their assembly. Using OpGen's Argus system, they generated whole-genome shotgun single-molecule restriction maps that they used in conjunction with the company's Genome Builder software to extend their scaffolds into 49 super scaffolds. Their assembled reference P. mume genome contains about 240 megabases.

Additionally, the investigators drew upon a segregating F1 population of 260 seedlings to develop, using a restriction-site-associated DNA marker approach, a linkage map that includes eight linkage groups. Having such a map, the researchers noted, "improves the quality of the reference and will be useful in molecular-marker assisted breeding and further map-based cloning."

Then, by generating 11.3 gigabases of RNA-seq data from a number of different tissue types — bud, fruit, leaf, root, and stem — Wang and his colleagues were able to annotate nearly 83 percent of the P. mume genome. They noted that it contains about 31,390 protein-coding genes, similar in number to that of the strawberry, Fragaria vesca, but fewer than that of the apple, Malus X domestica, both members of the Rosaceae family.

Further, by comparing the P. mume genome to other Rosaceae family members, the researchers uncover possible chromosomal changes that occurred during P. mume evolution. They reported resurrecting nine ancestral Rosaceae chromosomes, and said that 11 fission and 11 fusion events may have occurred in the P. mume genome since that nine-chromosome ancestor.

Transcriptome data also allowed the investigators to study certain traits, such as P. mume's ability to flower in the early spring, even at below-freezing temperatures. They examined genes previously associated with dormancy and release from dormancy, such as the dormancy-associated MADS-box transcription factor, or DAM, family and C-repeat-binding transcription factors, or CBFs, in P. mume. The researchers found six tandem DAM genes in P. mume that appeared to be serial duplications — duplications that are not found in F. vesca or M. X domestica. Additionally, they found 13 CBF orthologous genes and seven CBF regulons as well as putative CBF biding sites upstream of DAM genes.

"We suggest that these additional sites render P. mume more sensitive to cold and result in early blooming in spring," the researchers wrote.

P. mume fragrance had previously been linked to benzenoids and phenylpropanoids, and here researchers sniffed out an expansion of the benzyl alcohol acetyltransferase family, which catalyses benzyl acetate synthesis. A number of the BEAT genes were in tandem, which the researchers said suggests that they, too, derived from serial duplication events.

"The sequence of the P. mume genome is a valuable resource for biological research and breeding," Wang and his colleagues concluded.