33 research outputs found
Pinniped Karyotype Evolution Substantiated by Comparative Chromosome Painting of 10 Pinniped Species (Pinnipedia, Carnivora)
Numerous Carnivora karyotype evolution investigations have been performed by classical and molecular cytogenetics and were supplemented by reconstructions of the Ancestral Carnivora Karyotype (ACK). However, the group of Pinnipedia was not studied in detail. Here we reconstruct pinniped karyotype evolution and refine ACK using published and our new painting data for 10 pinniped species. The combination of human (HSA) and domestic dog (CFA) whole-chromosome painting probes was used for the construction of the comparative chromosome maps for species from all three pinniped families: Odobenidaeβ Odobenus rosmarus Linnaeus, 1758, Phocidae β Phoca vitulina Linnaeus, 1758, Pusa sibirica Gmelin, 1788, Erignathus barbatus Erxleben, 1777, Phoca largha Pallas, 1811, Phoca hispida Schreber, 1775 and Otariidae β Eumetopias jubatus Schreber, 1775, Callorhinus ursinus Linnaeus, 1758, Phocarctos hookeri Gray, 1844, Arctocephalus forsteri Lesson, 1828. HSA and CFA autosome painting probes have delineated 32 and 68 conservative autosome segments in the studied genomes. The comparative painting in Pinnipedia supports monophyletic origin of pinnipeds, shows that pinniped karyotype evolution was characterized by slow rate of genome rearrangements (less then one rearrangement per 10 million years), provides strong support for refined structure of ACK with 2n = 38 and specifies plausible order of dog chromosome synthenic segments on ancestral Carnivora chromosomes. The heterochromatin, telomere and ribosomal DNA distribution was studied in all 10 species
X Chromosome Evolution in Cetartiodactyla
The mammalian X chromosome is characterized by high level of conservation. On the contrary the Cetartiodactyl X chromosome displays variation in morphology and G-banding pattern. It is hypothesized that X chromosome has undergone multiple rearrangements during Cetartiodactyla speciation. To investigate the evolution of this sex chromosome we have selected 26 BAC clones from cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution maps were obtained by fluorescence in situ hybridisation in a representative range of cetartiodactyl species from different families: pig (Suidae), gray whale (Eschrichtiidae), pilot whale (Delphinidae), hippopotamus (Hippopotamidae), Java mouse deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), giraffe (Giraffidae). To trace the X chromosome evolution during fast radiation in speciose families, we mapped more than one species in Cervidae (moose, Siberian roe deer, fallow deer and Pere Davidβs deer) and Bovidae (musk ox, goat, sheep, sable antelope, nilgau, gaur, saola, and cattle). We have identified three major conserved synteny blocks and based on this data reconstructed the structure of putative ancestral cetartiodactyl X chromosome. We demonstrate that intrachromosomal rearrangements such as inversions and centromere reposition are main drivers of cetartiodactylβs chromosome X evolution
Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting
Backgroun
X Chromosome Evolution in Cetartiodactyla
The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern between species. It is hypothesized that this sex chromosome has undergone multiple rearrangements that changed the centromere position and the order of syntenic segments over the last 80 million years of Cetartiodactyla speciation. To investigate its evolution we have selected 26 evolutionarily conserved bacterial artificial chromosome (BAC) clones from the cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution BAC maps of the X chromosome on a representative range of cetartiodactyl species from different branches: pig (Suidae), alpaca (Camelidae), gray whale (Cetacea), hippopotamus (Hippopotamidae), Java mouse-deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), and giraffe (Giraffidae) were obtained by fluorescent in situ hybridization. To trace the X chromosome evolution during fast radiation in specious families, we performed mapping in several cervids (moose, Siberian roe deer, fallow deer, and Pere Davidβs deer) and bovid (muskox, goat, sheep, sable antelope, and cattle) species. We have identified three major conserved synteny blocks and rearrangements in different cetartiodactyl lineages and found that the recently described phenomenon of the evolutionary new centromere emergence has taken place in the X chromosome evolution of Cetartiodactyla at least five times. We propose the structure of the putative ancestral cetartiodactyl X chromosome by reconstructing the order of syntenic segments and centromere position for key groups
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution
ΠΠ½ΡΠ΅Π³ΡΠ°ΡΠΈΠ²Π½ΡΠΉ ΠΏΠΎΠ΄Ρ ΠΎΠ΄ ΠΊΠ°ΠΊ Π²Π΅ΠΊΡΠΎΡ ΠΏΠ΅ΡΡΠΎΠ½Π°Π»ΠΈΠ·Π°ΡΠΈΠΈ ΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°ΡΠ΅Π»ΡΠ½ΡΡ ΠΏΡΠ°ΠΊΡΠΈΠΊ Π² ΠΌΠ΅Π΄ΠΈΡΠΈΠ½ΡΠΊΠΎΠΌ Π²ΡΠ·Π΅
Introduction. The article discusses the formation of a model of a high quality educational process in a medical university in order to prepare a highly qualified specialist and a versatile educated person. Purpose setting. The objective of the study was to analyze the process of formation of clinical thinking, intellectual and communicative competencies in the process of preparing future specialists for professional activities in a medical university, based on the use of an integrative approach, assessment of the type of thinking and learning; constitutional features of the student and teacher; semantic differential method. Methodology and methods of the study. The methodology of the material presented in the article is based on the introduction of a systematic (holistic) approach to study the individual constitutional (mental and physical) characteristics of teachers and medical students in connection with training and further professional activities. Results. The article analyzes current trends and problematic issues of the educational process in pedagogy and andragogy, due to technological progress, the development of digital technologies, distance types and forms of education, the formation of the so-called Β«digital generationΒ» of students, requiring the development and implementation of innovative methodological approaches and methods in the educational process training of specialists in medical universities. The necessity of forming not only intellectual and communicative competencies in the process of mastering a profession, but also conceptual and logical schemes of clinical thinking using the method of semantic differential is demonstrated. The role of the constitutional features of the teacher and student in the training of future specialists is shown. The relationship between the professional and personal qualities of a high school teacher and students is illustrated.Conclusion. The use of an integrative approach greatly contributes to improving the quality of the educational process in the professional training of a future medical specialist.ΠΠ²Π΅Π΄Π΅Π½ΠΈΠ΅. ΠΠ±ΡΡΠΆΠ΄Π°Π΅ΡΡΡ ΡΠΎΡΠΌΠΈΡΠΎΠ²Π°Π½ΠΈΠ΅ ΠΌΠΎΠ΄Π΅Π»ΠΈ ΠΊΠ°ΡΠ΅ΡΡΠ²Π΅Π½Π½ΠΎΠ³ΠΎ ΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°ΡΠ΅Π»ΡΠ½ΠΎΠ³ΠΎ ΠΏΡΠΎΡΠ΅ΡΡΠ° Π² ΠΌΠ΅Π΄ΠΈΡΠΈΠ½ΡΠΊΠΎΠΌ Π²ΡΠ·Π΅ Ρ ΡΠ΅Π»ΡΡ ΠΏΠΎΠ΄Π³ΠΎΡΠΎΠ²ΠΊΠΈ Π²ΡΡΠΎΠΊΠΎΠΊΠ²Π°Π»ΠΈΡΠΈΡΠΈΡΠΎΠ²Π°Π½Π½ΠΎΠ³ΠΎ ΡΠΏΠ΅ΡΠΈΠ°Π»ΠΈΡΡΠ° ΠΈ ΡΠ°Π·Π½ΠΎΡΡΠΎΡΠΎΠ½Π½Π΅ ΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°Π½Π½ΠΎΠΉ Π»ΠΈΡΠ½ΠΎΡΡΠΈ. ΠΠΎΡΡΠ°Π½ΠΎΠ²ΠΊΠ° Π·Π°Π΄Π°ΡΠΈ. ΠΠ°Π΄Π°ΡΠ° ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ β ΠΏΡΠΎΠ°Π½Π°Π»ΠΈΠ·ΠΈΡΠΎΠ²Π°ΡΡ ΠΏΡΠΎΡΠ΅ΡΡ ΡΠΎΡΠΌΠΈΡΠΎΠ²Π°Π½ΠΈΡ ΠΊΠ»ΠΈΠ½ΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ ΠΌΡΡΠ»Π΅Π½ΠΈΡ, ΠΈΠ½ΡΠ΅Π»Π»Π΅ΠΊΡΡΠ°Π»ΡΠ½ΡΡ
ΠΈ ΠΊΠΎΠΌΠΌΡΠ½ΠΈΠΊΠ°ΡΠΈΠ²Π½ΡΡ
ΠΊΠΎΠΌΠΏΠ΅ΡΠ΅Π½ΡΠΈΠΉ Π² ΠΏΡΠΎΡΠ΅ΡΡΠ΅ ΠΏΠΎΠ΄Π³ΠΎΡΠΎΠ²ΠΊΠΈ Π±ΡΠ΄ΡΡΠΈΡ
ΡΠΏΠ΅ΡΠΈΠ°Π»ΠΈΡΡΠΎΠ² ΠΊ ΠΏΡΠΎΡΠ΅ΡΡΠΈΠΎΠ½Π°Π»ΡΠ½ΠΎΠΉ Π΄Π΅ΡΡΠ΅Π»ΡΠ½ΠΎΡΡΠΈ Π² ΠΌΠ΅Π΄ΠΈΡΠΈΠ½ΡΠΊΠΎΠΌ Π²ΡΠ·Π΅ Π½Π° ΠΎΡΠ½ΠΎΠ²Π΅ ΠΏΡΠΈΠΌΠ΅Π½Π΅Π½ΠΈΡ ΠΈΠ½ΡΠ΅Π³ΡΠ°ΡΠΈΠ²Π½ΠΎΠ³ΠΎ ΠΏΠΎΠ΄Ρ
ΠΎΠ΄Π°, ΠΎΡΠ΅Π½ΠΊΠΈ ΡΠΈΠΏΠ° ΠΌΡΡΠ»Π΅Π½ΠΈΡ ΠΈ ΠΎΠ±ΡΡΠ΅Π½ΠΈΡ, ΠΊΠΎΠ½ΡΡΠΈΡΡΡΠΈΠΎΠ½Π°Π»ΡΠ½ΡΡ
ΠΎΡΠΎΠ±Π΅Π½Π½ΠΎΡΡΠ΅ΠΉ ΠΎΠ±ΡΡΠ°ΡΡΠ΅Π³ΠΎΡΡ ΠΈ ΠΏΡΠ΅ΠΏΠΎΠ΄Π°Π²Π°ΡΠ΅Π»Ρ, ΠΌΠ΅ΡΠΎΠ΄Π° ΡΠ΅ΠΌΠ°Π½ΡΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ Π΄ΠΈΡΡΠ΅ΡΠ΅Π½ΡΠΈΠ°Π»Π°. ΠΠ΅ΡΠΎΠ΄ΠΈΠΊΠ° ΠΈ ΠΌΠ΅ΡΠΎΠ΄ΠΎΠ»ΠΎΠ³ΠΈΡ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ. ΠΠ΅ΡΠΎΠ΄ΠΎΠ»ΠΎΠ³ΠΈΡ ΠΌΠ°ΡΠ΅ΡΠΈΠ°Π»Π°, ΠΏΡΠ΅Π΄ΡΡΠ°Π²Π»Π΅Π½Π½ΠΎΠ³ΠΎ Π² ΡΡΠ°ΡΡΠ΅, Π±Π°Π·ΠΈΡΡΠ΅ΡΡΡ Π½Π° Π²Π½Π΅Π΄ΡΠ΅Π½ΠΈΠΈ ΡΠΈΡΡΠ΅ΠΌΠ½ΠΎΠ³ΠΎ (ΡΠ΅Π»ΠΎΡΡΠ½ΠΎΠ³ΠΎ) ΠΏΠΎΠ΄Ρ
ΠΎΠ΄Π° Π΄Π»Ρ ΠΈΠ·ΡΡΠ΅Π½ΠΈΡ ΠΈΠ½Π΄ΠΈΠ²ΠΈΠ΄ΡΠ°Π»ΡΠ½ΡΡ
ΠΊΠΎΠ½ΡΡΠΈΡΡΡΠΈΠΎΠ½Π°Π»ΡΠ½ΡΡ
(ΠΏΡΠΈΡ
ΠΈΡΠ΅ΡΠΊΠΈΡ
ΠΈ ΡΠΈΠ·ΠΈΡΠ΅ΡΠΊΠΈΡ
) ΠΎΡΠΎΠ±Π΅Π½Π½ΠΎΡΡΠ΅ΠΉ ΠΏΠ΅Π΄Π°Π³ΠΎΠ³ΠΎΠ² ΠΈ ΡΡΡΠ΄Π΅Π½ΡΠΎΠ²-ΠΌΠ΅Π΄ΠΈΠΊΠΎΠ² Π² ΡΠ²ΡΠ·ΠΈ Ρ ΠΎΠ±ΡΡΠ΅Π½ΠΈΠ΅ΠΌ ΠΈ Π΄Π°Π»ΡΠ½Π΅ΠΉΡΠ΅ΠΉ ΠΏΡΠΎΡΠ΅ΡΡΠΈΠΎΠ½Π°Π»ΡΠ½ΠΎΠΉ Π΄Π΅ΡΡΠ΅Π»ΡΠ½ΠΎΡΡΡΡ. Π Π΅Π·ΡΠ»ΡΡΠ°ΡΡ. Π ΡΡΠ°ΡΡΠ΅ ΠΏΡΠΎΠ°Π½Π°Π»ΠΈΠ·ΠΈΡΠΎΠ²Π°Π½Ρ ΡΠΎΠ²ΡΠ΅ΠΌΠ΅Π½Π½ΡΠ΅ ΡΠ΅Π½Π΄Π΅Π½ΡΠΈΠΈ ΠΈ ΠΏΡΠΎΠ±Π»Π΅ΠΌΠ½ΡΠ΅ Π²ΠΎΠΏΡΠΎΡΡ ΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°ΡΠ΅Π»ΡΠ½ΠΎΠ³ΠΎ ΠΏΡΠΎΡΠ΅ΡΡΠ° Π² ΠΏΠ΅Π΄Π°Π³ΠΎΠ³ΠΈΠΊΠ΅ ΠΈ Π°Π½Π΄ΡΠ°Π³ΠΎΠ³ΠΈΠΊΠ΅, ΠΎΠ±ΡΡΠ»ΠΎΠ²Π»Π΅Π½Π½ΡΠ΅ ΡΠ΅Ρ
Π½ΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΠΌ ΠΏΡΠΎΠ³ΡΠ΅ΡΡΠΎΠΌ, ΡΠ°Π·Π²ΠΈΡΠΈΠ΅ΠΌ ΡΠΈΡΡΠΎΠ²ΡΡ
ΡΠ΅Ρ
Π½ΠΎΠ»ΠΎΠ³ΠΈΠΉ, Π΄ΠΈΡΡΠ°Π½ΡΠΈΠΎΠ½Π½ΡΡ
Π²ΠΈΠ΄ΠΎΠ² ΠΈ ΡΠΎΡΠΌ ΠΎΠ±ΡΡΠ΅Π½ΠΈΡ, ΡΠΎΡΠΌΠΈΡΠΎΠ²Π°Π½ΠΈΠ΅ΠΌ ΡΠ°ΠΊ Π½Π°Π·ΡΠ²Π°Π΅ΠΌΠΎΠ³ΠΎ Β«ΡΠΈΡΡΠΎΠ²ΠΎΠ³ΠΎ ΠΏΠΎΠΊΠΎΠ»Π΅Π½ΠΈΡΒ» ΡΡΡΠ΄Π΅Π½ΡΠΎΠ², ΡΡΠ΅Π±ΡΡΡΠΈΠ΅ ΡΠ°Π·ΡΠ°Π±ΠΎΡΠΊΠΈ ΠΈ Π²Π½Π΅Π΄ΡΠ΅Π½ΠΈΡ ΠΈΠ½Π½ΠΎΠ²Π°ΡΠΈΠΎΠ½Π½ΡΡ
ΠΌΠ΅ΡΠΎΠ΄ΠΎΠ»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΡ
ΠΏΠΎΠ΄Ρ
ΠΎΠ΄ΠΎΠ² ΠΈ ΠΌΠ΅ΡΠΎΠ΄ΠΎΠ² Π² ΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°ΡΠ΅Π»ΡΠ½ΡΠΉ ΠΏΡΠΎΡΠ΅ΡΡ ΠΏΠΎΠ΄Π³ΠΎΡΠΎΠ²ΠΊΠΈ ΡΠΏΠ΅ΡΠΈΠ°Π»ΠΈΡΡΠΎΠ² Π² ΠΌΠ΅Π΄ΠΈΡΠΈΠ½ΡΠΊΠΈΡ
Π²ΡΠ·Π°Ρ
. ΠΡΠΎΠ΄Π΅ΠΌΠΎΠ½ΡΡΡΠΈΡΠΎΠ²Π°Π½Π° Π½Π΅ΠΎΠ±Ρ
ΠΎΠ΄ΠΈΠΌΠΎΡΡΡ ΡΠΎΡΠΌΠΈΡΠΎΠ²Π°Π½ΠΈΡ Π½Π΅ ΡΠΎΠ»ΡΠΊΠΎ ΠΈΠ½ΡΠ΅Π»Π»Π΅ΠΊΡΡΠ°Π»ΡΠ½ΡΡ
ΠΈ ΠΊΠΎΠΌΠΌΡΠ½ΠΈΠΊΠ°ΡΠΈΠ²Π½ΡΡ
ΠΊΠΎΠΌΠΏΠ΅ΡΠ΅Π½ΡΠΈΠΉ Π² ΠΏΡΠΎΡΠ΅ΡΡΠ΅ ΠΎΠ²Π»Π°Π΄Π΅Π½ΠΈΡ ΠΏΡΠΎΡΠ΅ΡΡΠΈΠ΅ΠΉ, Π½ΠΎ ΠΈ ΠΏΠΎΠ½ΡΡΠΈΠΉΠ½ΠΎ-Π»ΠΎΠ³ΠΈΡΠ΅ΡΠΊΠΈΡ
ΡΡ
Π΅ΠΌ ΠΊΠ»ΠΈΠ½ΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ ΠΌΡΡΠ»Π΅Π½ΠΈΡ Ρ ΠΈΡΠΏΠΎΠ»ΡΠ·ΠΎΠ²Π°Π½ΠΈΠ΅ΠΌ ΠΌΠ΅ΡΠΎΠ΄Π° ΡΠ΅ΠΌΠ°Π½ΡΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ Π΄ΠΈΡΡΠ΅ΡΠ΅Π½ΡΠΈΠ°Π»Π°. ΠΠΎΠΊΠ°Π·Π°Π½Π° ΡΠΎΠ»Ρ ΠΊΠΎΠ½ΡΡΠΈΡΡΡΠΈΠΎΠ½Π°Π»ΡΠ½ΡΡ
ΠΎΡΠΎΠ±Π΅Π½Π½ΠΎΡΡΠ΅ΠΉ ΠΏΡΠ΅ΠΏΠΎΠ΄Π°Π²Π°ΡΠ΅Π»Ρ ΠΈ ΡΡΡΠ΄Π΅Π½ΡΠ° Π² ΠΏΠΎΠ΄Π³ΠΎΡΠΎΠ²ΠΊΠ΅ Π±ΡΠ΄ΡΡΠΈΡ
ΡΠΏΠ΅ΡΠΈΠ°Π»ΠΈΡΡΠΎΠ². ΠΡΠΎΠΈΠ»Π»ΡΡΡΡΠΈΡΠΎΠ²Π°Π½Π° Π·Π°Π²ΠΈΡΠΈΠΌΠΎΡΡΡ ΠΌΠ΅ΠΆΠ΄Ρ ΠΏΡΠΎΡΠ΅ΡΡΠΈΠΎΠ½Π°Π»ΡΠ½ΡΠΌΠΈ ΠΈ Π»ΠΈΡΠ½ΡΠΌΠΈ ΠΊΠ°ΡΠ΅ΡΡΠ²Π°ΠΌΠΈ ΠΏΡΠ΅ΠΏΠΎΠ΄Π°Π²Π°ΡΠ΅Π»Ρ Π²ΡΡΡΠ΅ΠΉ ΡΠΊΠΎΠ»Ρ ΠΈ ΠΎΠ±ΡΡΠ°ΡΡΠΈΡ
ΡΡ. ΠΡΠ²ΠΎΠ΄Ρ. ΠΡΠΈΠΌΠ΅Π½Π΅Π½ΠΈΠ΅ ΠΈΠ½ΡΠ΅Π³ΡΠ°ΡΠΈΠ²Π½ΠΎΠ³ΠΎ ΠΏΠΎΠ΄Ρ
ΠΎΠ΄Π° Π² Π·Π½Π°ΡΠΈΡΠ΅Π»ΡΠ½ΠΎΠΉ ΡΡΠ΅ΠΏΠ΅Π½ΠΈ ΡΠΏΠΎΡΠΎΠ±ΡΡΠ²ΡΠ΅Ρ ΠΏΠΎΠ²ΡΡΠ΅Π½ΠΈΡ ΠΊΠ°ΡΠ΅ΡΡΠ²Π° ΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°ΡΠ΅Π»ΡΠ½ΠΎΠ³ΠΎ ΠΏΡΠΎΡΠ΅ΡΡΠ° ΠΏΡΠΈ ΠΏΡΠΎΡΠ΅ΡΡΠΈΠΎΠ½Π°Π»ΡΠ½ΠΎΠΉ ΠΏΠΎΠ΄Π³ΠΎΡΠΎΠ²ΠΊΠ΅ Π±ΡΠ΄ΡΡΠ΅Π³ΠΎ ΡΠΏΠ΅ΡΠΈΠ°Π»ΠΈΡΡΠ° ΠΌΠ΅Π΄ΠΈΡΠΈΠ½ΡΠΊΠΎΠ³ΠΎ ΠΏΡΠΎΡΠΈΠ»Ρ
An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)
Background
The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes.
Findings
Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions.
Conclusions
We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years
Comparative Chromosome Mapping of Musk Ox and the X Chromosome among Some Bovidae Species
Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably variable, with several morphological types in the family. Here we built a detailed chromosome map of musk ox (Ovibos moschatus), a relic species originating from Pleistocene megafauna, with dromedary and human probes using chromosome painting. We trace chromosomal rearrangements during Bovidae evolution by comparing species already studied by chromosome painting. The musk ox karyotype differs from the ancestral pecoran karyotype by six fusions, one fission, and three inversions. We discuss changes in pecoran ancestral karyotype in the light of new painting data. Variations in the X chromosome structure of four bovid species nilgai bull (Boselaphus tragocamelus), saola (Pseudoryx nghetinhensis), gaur (Bos gaurus), and Kirkβs Dikdik (Madoqua kirkii) were further analyzed using 26 cattle BAC-clones. We found the duplication on the X in saola. We show main rearrangements leading to the formation of four types of bovid X: Bovinae type with derived cattle subtype formed by centromere reposition and Antilopinae type with Caprini subtype formed by inversion in XSB1
The Case of X and Y Localization of Nucleolus Organizer Regions (NORs) in Tragulus javanicus (Cetartiodactyla, Mammalia)
There are differences in number and localization of nucleolus organizer regions (NORs) in genomes. In mammalian genomes, NORs are located on autosomes, which are often situated on short arms of acrocentric chromosomes and more rarely in telomeric, pericentromeric, or interstitial regions. In this work, we report the unique case of active NORs located on gonΠΎsomes of a eutherian mammal, the Javan mouse-deer (Tragulus javanicus). We have investigated the position of NORs by FISH experiments with ribosomal DNA (rDNA) sequences (18S, 5.8S, and 28S) and show the presence of a single NOR site on the X and Y chromosomes. The NOR is localized interstitially on the p-arm of the X chromosome in close proximity with prominent C-positive heterochromatin blocks and in the pericentromeric area of mostly heterochromatic Y. The NOR sites are active on both the X and Y chromosomes in the studied individual and surrounded by GC enriched heterochromatin. We hypothesize that the surrounding heterochromatin might have played a role in the transfer of NORs from autosomes to sex chromosomes during the karyotype evolution of the Javan mouse-deer