Article
Biochemistry & Molecular Biology
Alex Makunin, Petra Korlevic, Naomi Park, Scott Goodwin, Robert M. Waterhouse, Katharina von Wyschetzki, Christopher G. Jacob, Robert Davies, Dominic Kwiatkowski, Brandyce St Laurent, Diego Ayala, Mara K. N. Lawniczak
Summary: The study developed a multilocus amplicon sequencing approach that can simultaneously identify mosquito species and detect the presence of malaria parasites. The method was shown to be effective in determining species identity and resolving population structure, and is characterized by its quick, inexpensive, high-throughput, and accurate nature.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Tomasz Suchan, Mariya A. Kusliy, Naveed Khan, Lorelei Chauvey, Laure Tonasso-Calviere, Stephanie Schiavinato, John Southon, Marcel Keller, Keiko Kitagawa, Johannes Krause, Alexander N. Bessudnov, Alexander A. Bessudnov, Alexander S. Graphodatsky, Silvia Valenzuela-Lamas, Jaroslaw Wilczynski, Sylwia Pospula, Krzysztof Tunia, Marek Nowak, Magdalena Moskal-delHoyo, Alexey A. Tishkin, Alexander J. E. Pryor, Alan K. Outram, Ludovic Orlando
Summary: DNA hybridization-capture techniques allow researchers to target specific genomic regions for sequencing, which is especially helpful for analyzing ancient DNA. HyRAD, a cost-effective alternative to commercial capture protocols, demonstrated its performance in obtaining authentic aDNA data from osseous remains, even in samples with low endogenous content. This approach utilizes double enzymatic restriction of DNA extracts to produce RNA probes that cover only a fraction of the genome, serving as baits for capturing homologous fragments from aDNA libraries.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Evolutionary Biology
Anna S. Molodtseva, Alexey Makunin, Valentina V. Salomashkina, Ilya G. Kichigin, Nadezhda V. Vorobieva, Sergey K. Vasiliev, Mikhail Shunkov, Alexey A. Tishkin, Sergey P. Grushin, Peeter Anijalg, Egle Tammeleht, Marju Keis, Gennady G. Boeskorov, Nikolai Mamaev, Innokenty M. Okhlopkov, Alexey P. Kryukov, Elena A. Lyapunova, Marina Kholodova, Ivan Seryodkin, Urmas Saarma, Vladimir A. Trifonov, Alexander S. Graphodatsky
Summary: The brown bear is an iconic carnivore in the Northern Hemisphere, with mitochondrial research showing South Siberia as a refuge for Eurasian brown bears, further confirming the hypothesis of multiple migration waves in the Pleistocene.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Svetlana A. Romanenko, Dmitry Yu Prokopov, Anastasia A. Proskuryakova, Guzel Davletshina, Alexey E. Tupikin, Fumio Kasai, Malcolm A. Ferguson-Smith, Vladimir A. Trifonov
Summary: Tandemly arranged and dispersed repetitive DNA sequences are important elements in vertebrate genomes. Through sequencing and analysis, we identified major tandem repetitive DNAs and LTR retrotransposons in the Nile crocodile genome. These repeats show variability in structure, organization, and distribution.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Anastasia A. Proskuryakova, Ekaterina S. Ivanova, Polina L. Perelman, Malcolm A. Ferguson-Smith, Fentang Yang, Innokentiy M. Okhlopkov, Alexander S. Graphodatsky
Summary: The family Cervidae, characterized by a wide range of diploid chromosome numbers, has been studied for chromosomal rearrangements using chromosome painting. This study focuses on building a chromosome map of a reindeer and a black muntjac and comparing it with other species' maps to understand the variability of Cervidae karyotypes. The findings suggest that intrachromosomal rearrangements in autosomes of Cervidae are more frequent than previously thought.
CYTOGENETIC AND GENOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Katerina V. Tishakova, Dmitry Yu. Prokopov, Guzel I. Davletshina, Alexander V. Rumyantsev, Patricia C. M. O'Brien, Malcolm A. Ferguson-Smith, Massimo Giovannotti, Artem P. Lisachov, Vladimir A. Trifonov
Summary: In this study, chromosome-specific DNA libraries of C. calyptratus were obtained through chromosome flow sorting, and these libraries were compared with the genomes of three other squamate reptiles. The ancestral syntenic regions in the C. calyptratus chromosomes were identified. PCR-assisted mapping indicated that chromosome 5 may be the sex chromosome pair in C. calyptratus. The comparative chromosome map generated in this study can be used as the basis for future genome assembly and evolutionary studies of chameleons.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Artem Lisachov, Alexander Rumyantsev, Dmitry Prokopov, Malcolm Ferguson-Smith, Vladimir Trifonov
Summary: In this study, we describe the satellite DNA families found in two snake species from different families. Contrary to common belief, we found high conservation of these satellites in terms of nucleotide sequences and chromosomal localizations. Satellite DNA sequences make up a large portion of animal genomes, and they are typically located in heterochromatin clusters near centromeres or telomeres. The function of these clusters is to maintain chromosome and nuclear structure, and regulate chromosome behavior during cell division. Understanding satellite DNA diversity is important for studying sex chromosome evolution, hybridization, and speciation. Through our research, we identified four satellite DNA families in two snake species and determined their chromosomal localization. We found that one family is localized in the centromeres of both species, while the others form clusters on specific chromosomes or subsets of chromosomes. Our results demonstrate the high conservation of satellite DNA in snakes and support the library model of satellite DNA evolution.
Article
Biochemistry & Molecular Biology
Tatyana V. Karamysheva, Tatyana A. Gayner, Eugeny A. Elisaphenko, Vladimir A. Trifonov, Elvira G. Zakirova, Konstantin E. Orishchenko, Mariya A. Prokhorovich, Maria E. Lopatkina, Nikolay A. Skryabin, Igor N. Lebedev, Nikolay B. Rubtsov
Summary: This study presents a comprehensive cytogenomic approach to identify the precise genomic mapping of balanced chromosomal abnormalities in patients. By utilizing several techniques, including multicolor banding and chromosome microdissection, the researchers were able to determine the length and position of the inverted region and rule out genetic imbalance. They also discussed the challenges associated with genetic counseling in regions rich in DNA repeats and high genomic variation.
Article
Genetics & Heredity
Violetta R. Beklemisheva, Natalya A. Lemskaya, Dmitry Yu. Prokopov, Polina L. Perelman, Svetlana A. Romanenko, Anastasia A. Proskuryakova, Natalya A. Serdyukova, Yaroslav A. Utkin, Wenhui Nie, Malcolm A. Ferguson-Smith, Fentang Yang, Alexander S. Graphodatsky
Summary: We studied the variation of constitutive heterochromatin in the genome by analyzing a group of species with conserved euchromatin. Our findings showed the distribution of different tandemly repeated sequences and the conservation of euchromatin among these species. The variation and prevalence of these repetitive sequences are responsible for the species-specific variation of heterochromatic blocks.
Article
Genetics & Heredity
Aliya Yakupova, Andrey Tomarovsky, Azamat Totikov, Violetta Beklemisheva, Maria L. Logacheva, Polina Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik A. Tamazian, Natalia Serdyukova, Mike Rayko, Tatiana Bulyonkova, Nikolay Cherkasov, Vladimir Pylev, Vladimir Peterfeld, Aleksey Penin, Elena Balanovska, Alla J. Lapidus, Stephen OBrien, Alexander Graphodatsky, Klaus-Peter Koepfli, Sergei Kliver
Summary: This study investigates the genetic diversity and demographic history of the Baikal seal. The researchers found that the Baikal seal experienced a more severe population decline compared to other similar species, which could be attributed to the environmental changes during glacial-interglacial cycles. Additionally, they observed high conservation of chromosomal features in the Baikal seal's genome, similar to other marine pinniped species.
Article
Genetics & Heredity
Mariya A. Kusliy, Anna A. Yurlova, Alexandra I. Neumestova, Nadezhda V. Vorobieva, Natalya V. Gutorova, Anna S. Molodtseva, Vladimir A. Trifonov, Kseniya O. Popova, Natalia V. Polosmak, Vyacheslav I. Molodin, Sergei K. Vasiliev, Vladimir P. Semibratov, Tumur-O. Iderkhangai, Alexey A. Kovalev, Diimaajav Erdenebaatar, Alexander S. Graphodatsky, Alexey A. Tishkin
Summary: This study aimed to expand our knowledge on the genetic diversity of Altai horses in Siberia. By studying modern horses from two Altai regions and ancient horse bone samples, the study confirmed the hypothesis that Altai horses are represented by two populations (Eastern and Southern) and that Mongolian horses have a closer genetic relationship with Eastern Altai horses. The results also showed that most ancient horse haplotypes are present in modern Altai horses, and the differences between the mitochondrial gene pools of ancient Altai and Mongolia horses are more significant than those of modern horses in the respective regions due to increased migration processes.
Article
Genetics & Heredity
Larisa S. Biltueva, Nadezhda V. Vorobieva, Natalya A. Lemskya, Polina L. Perelman, Vladimir A. Trifonov, Victor V. Panov, Alexey V. Abramov, Shin-ichiro Kawada, Natalya A. Serdukova, Alexandr S. Graphodatsky
Summary: Researchers have described the karyotype of the small-toothed mole from Vietnam for the first time and identified cytogenetic signatures for this species and other related moles. They have also proposed a possible ancestral karyotype and found that pericentric inversions and heterochromatin amplifications are the most occurring types of chromosomal rearrangements in moles.
Article
Biochemistry & Molecular Biology
Marlys L. Houck, Klaus-Peter Koepfli, Taylor Hains, Ruqayya Khan, Suellen J. Charter, Julie A. Fronczek, Ann C. Misuraca, Sergei Kliver, Polina L. Perelman, Violetta Beklemisheva, Alexander Graphodatsky, Shu-Jin Luo, Stephen J. O'Brien, Norman T. -L. Lim, Jason S. C. Chin, Vanessa Guerra, Gaik Tamazian, Arina Omer, David Weisz, Kenneth Kaemmerer, Ginger Sturgeon, Joseph Gaspard, Alicia Hahn, Mark McDonough, Isabel Garcia-Trevino, Jordan Gentry, Rob L. Coke, Jan E. Janecka, Ryan J. Harrigan, Jen Tinsman, Thomas B. Smith, Erez Lieberman Aiden, Olga Dudchenko
Summary: We present the first complete genome assemblies for three species of pangolins, showing remarkable karyotypic plasticity within the order Pholidota. The white-bellied pangolin exhibited the largest chromosome number reported in a mammal of the Laurasiatheria clade. We discovered a Y-autosome fusion in white-bellied pangolins, and a novel strategy involving analyzing the pseudoautosomal region (PAR) confirmed the fusion event and identified the autosome involved. Our findings highlight the need for further research on these unique and endangered mammals.
CHROMOSOME RESEARCH
(2023)
Article
Zoology
M. P. Tiunov, A. A. Proskuryakova, A. K. Baturina, P. L. Perelman, A. S. Graphodatsky
Summary: A bat captured in the south of the Primorye Province, Russian Far East, has been identified as a new species to Russia based on comparative morphometrics and molecular genetic analysis, further research is needed to accurately determine the subspecies.
ZOOLOGICHESKY ZHURNAL
(2022)
