Spinach Genome Sequenced

An international team of researchers from Cornell University’s Boyce Thompson Institute and Shanghai Normal University has produced the first high-quality genomic sequence for spinach (Spinacia oleracea). Additionally, the team has sequenced the transcriptomes (all the RNA) of 120 cultivated and wild spinach plants.

Spinach (Spinacia oleracea). Image credit: George Hodan.

Spinach (Spinacia oleracea). Image credit: George Hodan.

Spinach is an annual or biennial plant in the amaranth family Amaranthaceae, which is composed of about 180 genera and 2,500 species including important crops such as beets and quinoa.

It is native to central Asia and thought to have originated in Persia (Iran).

Spinach is an important and nutritious green leafy vegetable and a rich source of carotenoids, folate, vitamin C, calcium and iron.

It is commonly used as a salad, a cooked vegetable or as an ingredient in fresh or cooked meat and vegetable dishes.

Spinach is increasing in popularity and is cultivated in more than 60 countries with production increased nearly tenfold in the past four decades.

Since spinach was first domesticated, gardeners and breeders have improved many agronomically important traits, such as leaf quality and nutrition, and over time these improvements have re-shaped the spinach genome.

In turn, breeders today can use genomic information to speed up improvements, which is especially important for combating significant diseases, like downy mildew.

“The spinach genome sequence and transcriptome variants developed in this study provide a wealth of valuable information that can be used to breed spinach with better disease-resistance, higher yield and better quality,” said lead co-author Dr. Zhangjun Fei, of Boyce Thompson Institute and Shanghai Normal University.

Plant material from a Chinese spinach cultivar, Sp75, was used for developing the spinach genome sequence.

“The spinach genome contains 25,495 protein-coding genes and is highly repetitive, with 74.4% of its content in the form of transposable elements,” Dr. Fei and co-authors said.

Armed with a better understanding of the spinach genome, they identified several genes that may confer resistance to the downy mildew pathogen.

Once identified in a resistant variety of spinach, such genes could be quickly transferred to other, possibly more nutritious varieties, boosting their immune systems to fight this disease while still maintaining marketable traits.

Spinach genome landscape: (a) ideogram of the six spinach pseudochromosomes (in Mb scale); (b) gene density represented as number of genes per Mb; (c) percentage of coverage of repeat sequences per Mb; (d) transcription state. The transcription level was estimated by read counts per million mapped reads in 1-Mb windows; (e) GC content in 1-Mb windows. The six spinach pseudochromosomes represented 47% of the genome assembly. Image credit: Xu et al, doi: 10.1038/ncomms15275.

Spinach genome landscape: (a) ideogram of the six spinach pseudochromosomes (in Mb scale); (b) gene density represented as number of genes per Mb; (c) percentage of coverage of repeat sequences per Mb; (d) transcription state. The transcription level was estimated by read counts per million mapped reads in 1-Mb windows; (e) GC content in 1-Mb windows. The six spinach pseudochromosomes represented 47% of the genome assembly. Image credit: Xu et al, doi: 10.1038/ncomms15275.

Of particular interest to the team is the discovery that the genomes of cultivated spinach varieties are not too different from their wild progenitors.

“When a plant is domesticated, its genome will evolve over centuries of selection. In many cases, it gets forced through a bottleneck of genetic changes necessary for cultivation, creating a very different plant from that which was first brought out of the wild,” the authors said.

“A great example is the comparison of maize to its ancestor, teosinte.”

“By analyzing transcriptome variants of a large collection of cultivated and wild spinach accessions, we found that unlike other vegetable crops such as tomato and cucumber, spinach has a weak domestication bottleneck,” said lead co-author Dr. Chen Jiao, of Boyce Thompson Institute.

“This was great news because it means there is still much room for spinach improvement, but it also made it tougher to pinpoint genomic markers that could speed up the breeding process.”

“Nonetheless, we identified many regions in the genome directly attributable to the domestication process, that could be possibly linked to valuable traits, such as bolting, leaf number, and stem length.”

The research was published in the online edition of the journal Nature Communications.

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Chenxi Xu et al. 2017. Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nature Communications 8, article number: 15275; doi: 10.1038/ncomms15275

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