scholarly journals Repetitive Elements in the Siberian Larch (Larix Sibirica Ledeb.) Nuclear Genome

2021 ◽  
Author(s):  
Kseniya A. Miroshnikova ◽  
Vasilina S. Akulova ◽  
Vladislav V. Biriukov ◽  
Eugeniya I. Bondar ◽  
Dmitry A. Kuzmin ◽  
...  
Keyword(s):  
Resistance Genes ◽  
De Novo ◽  
Plant Immunity ◽  
Nuclear Genome ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Repetitive Elements ◽  
Structural Element ◽  
Total Size ◽  
First Time

Abstract Background: Repetitive elements (REs) or repeats are sequences that occur multiple times in the genome. They represent a significant part of the gigantic conifer genomes (70-80%) relative to mammals and other plants and complicate whole genome sequencing and annotation. However, REs play important roles in evolution and adaptation processes in both plants and animals. Moreover, amino acid repeats play an important role in plant immunity being a structural element of the products of some disease resistance genes. Analysis of REs in conifer genomes is an important fundamental task.Results: REs were identified de novo and partly classified in the Siberian larch (Larix sibirica Ledeb.) nuclear genome for the first time. In total, 20.9 million REs were detected with the total size of 4.8 Gbp, which comprises about 39% of the 12.3 Gbp larch genome. Resistance genes with leucine-rich repeats (LRRs) were also identified and analyzed in the transcriptome data of autumn buds obtained using RNA-seq.Conclusions: For the first time, REs were identified and classified in the Siberian larch genome and transcriptome. In addition, LRRs and resistance genes were identified and analyzed in the Siberian larch transcriptomes from autumn buds. The larch genome contains twice as less RE compared to other conifers in the same Pinaceae family (39 vs 70-80%), and it might explain why it also has almost twice as smaller genome size (12 vs 18-31 Gbp).

scholarly journals Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuliya A. Putintseva ◽  
Eugeniya I. Bondar ◽  
Evgeniy P. Simonov ◽  
Vadim V. Sharov ◽  
Natalya V. Oreshkova ◽  
...  
Keyword(s):  
Dna Sequences ◽  
De Novo ◽  
Keystone Species ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Flowering Plant ◽  
Rrna Genes ◽  
Total Size ◽  
Protein Coding ◽  
Sequencing Project

Abstract Background Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

Monomeric phenolic compounds in the Siberian larch needles

2016 ◽  
Author(s):  
Н.В. Транчук ◽  
В.И. Рощин
Keyword(s):  
Fatty Acids ◽  
Phenolic Acids ◽  
Group Composition ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Aromatic Acids ◽  
Cinnamic Acids ◽  
Cis And Trans ◽  
First Time ◽  
Live Organism

Представлены результаты исследования состава группы фенолокислот хвои Larix sibirica, извлеченной диэтиловым эфиром из изопропанольного экстракта. Приведены данные по хроматографическому разделению исследуемой группы веществ на такие классы соединений, как бензойные, коричные и кумаровые ки- слоты, фенолоальдегиды, фенолокетоны, флавонолы. Показано, что в наиболь- шем количестве содержатся флавонолы, их выход составил 6,78% от группы фенолокислот, выход ароматических кислот немного меньше – 6,21%, аромати- ческие кетоны и альдегиды содержатся в примерно равных количествах – 0,4 и 0,34% соответственно. Гидроксибензойная и ванилиновая кислоты являются до- минирующими в своем классе, их содержание достигает 3,67 и 1,49% соответст- венно от массы фенолокислот. Среди фенолоальдегидов идентифицированы п- гидроксибензальдегид и ванилин. Идентифицированы и выделены три флавоно- ла: кемпферол, изорамнетин, мирицитин. Кемпферол содержится в наибольшем количестве – 3,92%, содержание изорамнетина и мирицитина составляет 2,08 и 0,78% соответственно. Впервые сообщается об обнаружении в хвое Larix sibirica п-гидроксибензойной, дигидрокоричной, цис- и транс-коричных кислот, 4-(4- гидроксифенил)-2-бутанона (реозмин), 4-(4-гидрокси-3-метоксифенил)-2- бутанона (зингерон). Установлено, что наряду с ароматическими соединениями, группа фенолокислот содержит смоляные и высшие жирные кислоты, доля ко- торых не превышает 1 и 6% соответственно. Отмечено высокое содержание ян- тарной и яблочной кислот, являющихся незаменимыми для живого организма, так как принимают участие в цикле Кребса. The results of investigation of phenolic acids group composition in Larix sibirica needles are presented in this research. The group was derived from isopropyl extract by diethyl ether. Phenolic acids group was divided into fraction using the method of column chromatography. It is shown that the researched group of substances consists of flavonols for 6.78%, aromatic acids for 6.21%, phenolic ketones and phenolic aldehydes for 0.40 and 0.34% respectively. 4-Hydroxybenzoic and vanilic acids dominate in its class, their content reaches 3.67 and 1.49% of phenolic acids group mass. 4-Hydroxybenzaldehyde and vanillin are detected. Three flavonols are obtained and identified: kaempferol, isorhamnetin, myricitin. Kaempferol is the main flavonol, its content is 3.9%. Contents of isorhamnetin and myricitin are 2.08 and 0.78% respectively. It is the first time it is reported about detection in needles of Larix sibirica 4-hydroxybenzoic, dihydrocinnamic, cis- and trans-cinnamic acids, 4-(4 hydroxyphenyl)- 2 butanone (rheosmin), 4-(4-hydroxy-3-methoxyphenyl)-2 butanone (zingerone). It is determined that phenolic acids group contains resin and highest fatty acids, which share doesn't exceed 1 and 6% respectively. It is significant that high content of succinic and malic acids present, because such acids are irreplaceable for a live organism since they take part in Krebs's cycle.

scholarly journals Novel Antibiotic-Free Plasmid Selection System Based on Complementation of Host Auxotrophy in the NAD De Novo Synthesis Pathway

2010 ◽  
Vol 76 (7) ◽  
pp. 2295-2303 ◽  
Author(s):  
Wei-Ren Dong ◽  
Li-Xin Xiang ◽  
Jian-Zhong Shao
Keyword(s):  
Resistance Genes ◽  
De Novo ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Host Cells ◽  
Selection System ◽  
E Coli ◽  
Horizontal Spread ◽  
First Time ◽  
Rapid Emergence

ABSTRACT The use of antibiotic resistance genes in plasmids causes potential biosafety and clinical hazards, such as the possibility of horizontal spread of resistance genes or the rapid emergence of multidrug-resistant pathogens. This paper introduces a novel auxotrophy complementation system that allowed plasmids and host cells to be effectively selected and maintained without the use of antibiotics. An Escherichia coli strain carrying a defect in NAD de novo biosynthesis was constructed by knocking out the chromosomal quinolinic acid phosphoribosyltransferase (QAPRTase) gene. The resistance gene in the plasmids was replaced by the QAPRTase gene of E. coli or the mouse. As a result, only expression of the QAPRTase gene from plasmids can complement and rescue E. coli host cells in minimal medium. This is the first time that a vertebrate gene has been used to construct a nonantibiotic selection system, and it can be widely applied in DNA vaccine and gene therapy. As the QAPRTase gene is ubiquitous in species ranging from bacteria to mammals, the potential environmental biosafety problems caused by horizontal gene transfer can be eliminated.

scholarly journals Development of microsatellite genetic markers in Siberian larch (Larix sibirica Ledeb.) based on the de novo whole genome sequencing

2017 ◽  
Vol 53 (11) ◽  
pp. 1194-1199 ◽  
Author(s):  
N. V. Oreshkova ◽  
Yu. A. Putintseva ◽  
V. V. Sharov ◽  
D. A. Kuzmin ◽  
K. V. Krutovsky
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
De Novo ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Whole Genome

Estimate of annual carbon balance of a young Siberian larch (Larix sibirica) plantation in Iceland

Tellus B ◽  
2007 ◽  
Vol 59 (5) ◽  
Author(s):  
Brynhildur Bjarnadottir ◽  
Bjarni D. Sigurdsson ◽  
Anders Lindroth
Keyword(s):  
Carbon Balance ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Annual Carbon ◽  
Annual Carbon Balance

Study of the properties larch and larch wood construction materials

2016 ◽  
Author(s):  
М.А. Чубинский ◽  
К.В. Чаузов
Keyword(s):  
Weight Loss ◽  
Urea Formaldehyde ◽  
Construction Materials ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Average Weight ◽  
Biological Stability ◽  
Laminated Beam ◽  
Coniophora Puteana ◽  
Larch Wood

Несмотря на огромные запасы, древесина лиственницы до сего времени в незначительных объемах используется в строительной индустрии, других отраслях экономики, что связано как с технологическими сложностями ее переработки, так и недостаточной изученностью ее свойств. Одним из уникальных свойств древесины лиственницы сибирской (Larix sibirica) является ее повышенная естественная биостойкость, наряду с максимально высокой среди отечественных хвойных пород прочностью. Стойкость древесины лиственницы (Larix sibirica) к воздействию дереворазрушающих грибов Coniofora puteana значительно превышает стойкость сосны. В среднем потеря массы ядровой древесины лиственницы сибирской под воздействием дереворазрушающего гриба Coniophora puteana составляет 14,84%, снижаясь с увеличением возраста дерева, а контрольные образцы из ядровой древесины сосны в возрасте 90 лет имели потерю массы 57,8%. Возраст дерева является одним из наиболее значимых факторов, влияющих на степень биостойкости древесины. По мере его увеличения значительно повышается устойчивость деструктивному воздействию дереворазрушающих грибов Coniophora puteana. Положение образцов также влияет на степень биостойкости древесины, однако эта зависимость слабо выражена по сравнению с влиянием возраста и плотности древесины. Исследования кинетики разложения древесины лиственницы сибирской и роли экстрактивных веществ в развитии дереворазрушающих грибов позволяют утверждать наличие связи биостойкости и содержания в древесине экстрактивных веществ. Для изготовления клееного бруса из древесины лиственницы предложена клеевая композиция, включающая карбамидомеламиноформальдегидный клей и карбамидоформальдегидную смолу, модифицированную шунгитами. Ее применение позволяет получать клеевые соединения, не уступающие по прочности при скалывании массивной древесине, как по сухому образцу, так и после его вымачивания. Таким образом, клееный брус из древесины лиственницы сибирской характеризуется высокими показателями биостойкости, прочности и водостойкости. Despite vast reserves, larch wood so far in small volumes used in the construction industry and other sectors of the economy, which is connected as the technological difficulties of its treatment, as well as insufficient knowledge of its properties. One of the unique properties of the wood of Siberian larch (Larix sibirica) is its increased natural biological stability (decay resistant), along with the highest among the domestic softwood strength. Resistance Larch (Larix sibirica) to the effects of wood-destroying fungi Coniofora puteana is much higher than pine. The average weight loss of Siberian larch heartwood exposed wood-destroying fungi Coniophora puteana is 14.84%, decreasing with increasing age of the tree, and control samples of heartwood pine at age 90 had a weight loss of 57.8%. Age of a tree is one of the most significant factors affecting the degree of biological stability of wood. With the increase it significantly increases the stability of the destructive effects of wood-destroying fungi and Coniophora puteana. The position of the sample in tree also affects the degree of biological stability of wood, but this dependence is poorly developed in comparison with the influence of age and wood density. Studies of the kinetics of decomposition of Siberian larch wood and the role of extractives in the development of wood-destroying fungi suggest a link, and the decay resistant of the content in the wood extractives. For the manufacture of larch glued laminated beam proposed adhesive composition comprising urea and melamine-formaldehyde glue and urea-formaldehyde resins, modified shungites. Its use allows to obtain the bonds are not inferior in strength at shearing solid wood as dry sample, and after soaking. Thus, glued laminated beam from Siberian larch wood is characterized by high decay resistant, strength and water resistance.

Sign in / Sign up

Export Citation Format

Share Document