NEW YORK, March 22 - It's not everyday you hear about the shrew, but four researchers at the Laboratory of Developmental Genetics at the Institute of Cytology and Genetics in Novosibirsk, Russia, are busy trying to make genomic sense of this insectivore.
By studying the shrew, the lab hopes to help researchers around the world to uncover answers to questions about evolutionary genetics. The project, which receives less than $3,500 a year, is headed by well-known mammalian genome researcher Oleg Serov.
Denis Larkin, a 26-year-old Russian researcher working on the shrew, recently corresponded with GenomeWeb about the work his lab is conducting.
GW: Why is the shrew of interest?
DL: Shrews, including Sorex araneus , are representative of insectivores. Sorex araneus is the only species from this order currently involved in gene mapping. So, the gene map of the shrew is of special interest for attempts to reconstruct ancestral genome of placental mammals. Moreover, according to morphological data, insectivores are close to primitive ancestral mammals and their genome may be close to the ancestral ones. But insectivores are almost certainly of polyphyletic lineage. Our data are best considered representative of the Soricidae , rather than insectivores in general. For more precise pictures of the insectivore genome, other distinctive insectivores, such as hedgehogs and tenrecs, should be studied. Sorex araneus has one of the most labile karyotypes among all mammalian species.
More than 100 chromosomal races of Sorex araneus have been found. Most of them are formed by Robertson rearrangements of chromosomal arms. Because of its very labile karyotype, the common shrew became a model organism for studying species-formation processes. Often if two chromosomal races (those that have different types of chromosomal arm combinations) inhabit close to each other (for example on two banks of a narrow brook a hybrid zone can be formatted. In these cases of special interest we try to study if there is a gene flow from one race to another and chromosome arm transfer. To solve these problems effectively we also need chromosomal markers.
GW: If the shrew is not considered a model organism, what is the importance of mapping it to the human?
DL: Sorex araneus cannot be considered a model organism like mouse or rat. But for mapping we use markers common with human and other mammals. We use the human genome as the basic genome as we try to reveal the gene synteny between different groups, such as the common shrew and other mammalian species.
GW: Is your team also sequencing the shrew?
DL: No, we don't have enough money for that. The project only has about 100,000 rubles ($3,479) a year, which comes from the Russian Foundation for Basic Research.
GW: What technique are you using to map the shrew?
DL: Currently for mapping we use the somatic cell hybrid panel established in our lab by Drs. Svetlana Pack and Ludmila Matyakhina, which is suitable for discriminating all of the metacentric chromosomes of Novosibisk race. For mapping we use PCR primers designed for mapping genomes of distinct species (CATS-primers (Lyons et al, 1997), bovine primers (Yang and Womack, 1995, 1998) cat primers (Murphy et al, 2000), and porcine primers (Larkin et al., 2001). Some of these primers we obtained from laboratories where they were developed. We test them to find those that work well in shrews and can be used for mapping of homologous genes. Surely, the sequencing of PCR products should be done to confirm significant gene homology. In some cases we sequence sorted PCR products to reveal homology with human and other species genes.
GW: What instruments and computers are you using?
DL: We use PCR analysis and some computer programs to construct gene-specific primers.
GW: Where can the information on the shrew genome be found?
DL: Complete information about shrew genome mapping can be found at Sorex araneus Genome Database http://shrewbase.da.ru . Information about population analysis and chromosomal races is available from the International Sorex araneus Cytogenetics Committee Newsletter at http://meiosis.bionet.nsc.ru/ISACC/Isacc.htm .
GW: What other genomics projects are researchers working on at the Laboratory of Developmental Genetics in Novosibirsk?
Other genomic projects in our lab include the mapping of the American mink genome using somatic cell hybrid panel established in our institution by Nikolai Rubtsov. We also analyze conservative gene groups of several porcine chromosomes. The leader or this work is Natalia Zhdanova and the investigation includes cytogenetic and RH mapping of porcine chromosomes 12 and 2. For the RH mapping of pig chromosome 12 we use the whole genome INRA-University of Minnesota Porcine Radiation Hybrid panel obtained from France's Lab of Cellular Genetics. And, for the mapping of pig chromosome 2, we use the RH panel specific for the chromosome developed in our laboratory by Natalia Zhdanova and Elena Ivanova. These projects are also funded from the Russian Foundation for Basic Research.
GW: Is your lab or any other lab conducting population studies on the Russian population?
DL: Our laboratory does not perform such analysis but I know that our institution has laboratories performing analysis of this type. From what I know it includes population analysis of the aboriginal people of Siberia and Altai.
GW: What role do you see for your lab in the context of genomics efforts worldwide?
DL: It depends on the funding situation here in Russia. If the situation improves our lab could contribute to the mapping of mammals which are of low practical use for people (such as shrew or mink), but whose genomes are significant for understanding the principles of mammalian genome evolution.