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Silkworm Resequencing Study Hints At Domestication History

NEW YORK (GenomeWeb News) – An international team of scientists, led by researchers at the Beijing Genomics Institute, has used re-sequencing to develop a genetic variation map for the silkworm, Bombyx mori, that's offering hints about the organism's domestication. The work appeared in today's advanced, online edition of Science.

The team sequenced the genomes of 40 different worms — representing 11 wild and 29 domestic silkworm lines — to about three times coverage. In so doing, they identified nearly 16 million SNPs, more than 300,000 small insertions and deletions, and upwards of 35,000 structural variants in the silkworm genomes.

"We systematically identified the genetic variants among these varieties," senior author Jun Wang, deputy director of BGI-Shenzhen, told GenomeWeb Daily News by e-mail. "Our strategy here provides a nearly complete genome level variation map, which gives more reliable information on genetic polymorphisms in a population."

Domestic B. mori silkworm strains that depend on humans have evolved from the wild silkworm, B. mandarina, over roughly 5,000 years, the researchers noted. This domestication has led to improvements in economically valuable traits such as cocoon size, growth rate, and digestion efficiency, Wang explained.

But there is still debate about how this domestication occurred. Some researchers have suggested silkworms originally showed mono-voltinism, producing one generation a year, and then evolved into strains that produced two or more generations a year. Others posit that it was actually the other way around. It is also unclear whether domestic worms arose once or several times.

"These theories are conflicting likely because they were derived from incomplete genetic information," Wang explained, noting that "geographic systems and voltinism have been central to previous studies of silkworm origin."

Researchers completed the draft version of the roughly 432 million base silkworm genome in 2004. The International Silkworm Genome Consortium published a more complete assembly four years later.

For the latest paper, Wang and his colleagues used the Illumina Genome Analyzer II to re-sequence the genomes of 40 different silkworm strains, including 29 inbred, domesticated silkworm strains and 11 wild strains.

The researchers made single and paired-end libraries for each line before sequencing the silkworm genomes to about three times coverage each. When they analyzed these genomes, comparing them to the silkworm reference, the team found 15,986,559 SNPs, 311,608 small insertions and deletions, and 35,093 structural variants.

In contrast to other domesticated organisms such as rice or wheat, which have dramatically less genetic variation than their wild counterparts, researchers found that domestic silkworms have about 83 percent of the genetic variation found in wild strains. That is a surprisingly high number given the population bottleneck and strong selective pressures associated with domestication, Wang noted.

"[O]ur study unexpectedly shows that these factors (bottleneck at domestication and strong artificial selection) have not been as drastic during silkworm domestication as seen in other domesticated organisms," he said.

Based on their findings, the researchers suspect domestic silkworms arose just once. And in light of the level of genetic variation that remains in domestic strains, he and his team suggest that either many individuals were selected during the original domestication process or that this domestication process occurred in several places at once.

By comparing the silkworm genomes with one another, the researchers also identified more than 1,000 regions dubbed "genomic regions of selective signals," or GROSS. These regions occur over nearly three percent of the silkworm genome and contain 354 protein-coding genes. Because these seem to be under strong artificial selection, the team speculated that GROSS genes are good candidates for domestication-specific genes.

Indeed, the team found that 159 genes in GROSS parts of the genome were differentially expressed in tissues under selective pressure during domestication, such as the silk gland, midgut, and testis.

By cataloging and characterizing potential domestication genes, the researchers hope to gain a clearer understanding of the genes behind economically important traits. That, in turn, may prove useful for commercial applications of silkworms, including their use as bioreactors for synthesizing proteins.

Wang said the team is currently conducting gene expression studies aimed at understanding candidate domestication-related genes. "These will add to our understanding of the domestication processes and help us get more information about the domestication history," he said, adding that genetic markers found in such studies should prove useful for detecting mutated genes and improving the silkworm's economic potential.

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