Article
Genetics & Heredity
M. Kanakachari, R. N. Chatterjee, M. R. Reddy, M. Dange, T. K. Bhattacharya
Summary: NGS sequencing was used to investigate the mitochondrial genomes of Indian native chickens and Red Jungle fowl, revealing 23 haplotypes and six significant clades. The study confirmed the Indian Red Jungle fowl as the origin of all Indian breeds.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Gang Yao, Bine Xue, Kun Liu, Yuling Li, Jiuxiang Huang, Junwen Zhai
Summary: Pseudocerastium is a monotypic genus of the Caryophyllaceae family endemic to China. Recent studies using morphological and molecular evidence have shown its phylogenetic position within Caryophyllaceae and its close relationship with Cerastium. The genus Pseudocerastium has been synonymized with Cerastium based on the present evidence.
Article
Plant Sciences
Maria Angeles Alonso, Manuel B. Crespo, Mario Martinez-Azorin, Ladislav Mucina
Summary: The plant incorrectly named Spergularia hanoverensis Simon in central-western South Africa has been revisited. After revising herbarium material and conducting taxonomic research, it was found that this plant is distinct from other South African species and has therefore been effectively published under the name S. hanoverensis. A detailed description of its morphology, ecology, distribution, and genetic relationships has been provided.
Article
Biochemistry & Molecular Biology
Ntwai A. Moiloa, Melilia Mesbah, Stephan Nylinder, John Manning, Felix Forest, Hugo J. de Boer, Christine D. Bacon, Beng Oxelman
Summary: Silene genus is predominantly distributed in the northern Hemisphere, with the most diversity around the Mediterranean Basin and also well represented in North Africa. In southern Africa, eight native species are classified into two sections, Elisanthe and Silene s.l. Despite recent taxonomic revisions, phylogenetic relationships and biogeographic history of these species remain unclear. Analysis of DNA sequences from southern African species revealed relationships with Eurasian and Central Asian species, with evidence of late Pleistocene dispersal events into southern Africa.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Wen-Qiao Wang, Zhi-Wei Su, Zhong-Hui Ma
Summary: Over the past decade, the composition of the Alsineae tribe in the Caryophyllaceae family has undergone significant changes due to molecular phylogeny studies. However, the Brachystemma genus and its phylogenetic position have not been previously sampled. Similarly, the related species Stellaria ovatifolia has not been included in previous studies. Through phylogenetic analyses using molecular markers, it was found that Brachystemma belongs to the Alsineae tribe and is closely related to S. ovatifolia. Furthermore, characteristics such as apically lobed petals and numerous seeds may be ancestral traits in the Alsineae tribe. These findings support the inclusion of Stellaria ovatifolia within the Brachystemma genus, which now consists of two species.
Article
Biochemistry & Molecular Biology
Xin Xu, Long Yu, Fan Li, Bingjun Wang, Fengxiang Liu, Daiqin Li
Summary: This study explores the species boundaries and phylogeny of Phrynarachne spiders in China, identifying six species and providing insights into their evolution and divergence times. The results show that Phrynarachne spiders in China have a monophyletic relationship and belong to the higher 'Thomisus group'. The estimated crown age of this genus in China is in the middle Miocene.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Plant Sciences
Dong-Pil Jin, Sunhee Sim, Jong-Won Park, Ji-Eun Choi, Jiwon Yoon, Chae Eun Lim, Min-Ha Kim
Summary: This study used DNA barcoding to accurately identify Korean Caryophyllaceae and found that ITS sequences were more accurate for identification than chloroplast sequences. Among the genera, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified, while the identification of species in Cerastium, Gypsophila, Dianthus, Silene, and Spergularia showed relatively low resolutions.
Article
Agronomy
Ugorji Ogbuagu Udensi, Ikenna Lasbrey Emeagi, Victoria Ebri Daniel, Thomas Luka Tentishe, Soumya Ghosh, Conrad Chibunna Achilonu
Summary: This study investigated the genetic diversity and evolutionary relationship of pigeon pea and cowpea. The results showed a wide genetic diversity among pigeon pea and cowpea populations. This study provides a basis for further understanding the diversity of these legumes.
GENETIC RESOURCES AND CROP EVOLUTION
(2022)
Article
Genetics & Heredity
Piotr Androsiuk, Lukasz Paukszto, Jan Pawel Jastrzebski, Sylwia Eryka Milarska, Adam Okorski, Agnieszka Pszczolkowska
Summary: Mitochondrial genomes have been found to be useful in solving phylogenetic issues in plant systematics. The study of Colobanthus species revealed high sequence conservation in mitochondrial genes, with evidence of purifying and positive selection. Fewer RNA editing sites were found in these species compared to other angiosperms.
Article
Evolutionary Biology
Qin Liu, Xinhong Xie, Yayong Wu, Guocheng Shu, Keji Guo, Peng Guo, Liangwei Cui
Summary: Integrative taxonomy based on multiple data sets is crucial for species classification, especially for cryptic species. Through analysis of external morphology, mtDNA-based phylogeny, SNP-based phylogeny, and population structure, researchers identified two distinct lineages within Rhabdophis subminiatus and proposed elevating R. s. helleri to a separate species Rhabdophis helleri, with a tentative distributional boundary proposed between the two species.
JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH
(2021)
Article
Forestry
Lu Wang, Yao Li, Na He, Ye Peng, Yanming Fang, Xingwang Zhang, Feilong Zhang
Summary: By analyzing the chloroplast genomes of seven Chinese lacquer trees, it was found that they shared the same protein-coding genes and tRNA genes, but the genomes from western China were longer. A total of 466 single nucleotide polymorphisms and 141 insertion-deletion mutations were mainly found between the eastern and western lineages. The genomic resources obtained from this study are important for studying the evolutionary patterns and resource protection of Chinese lacquer trees.
Article
Plant Sciences
Eugeny Boltenkov, Elena Artyukova, Anna Trias-Blasi
Summary: This study revised the taxonomy of Iris subser. Chrysographes through molecular and morphological studies, confirming its monophyletic nature and identifying four distinct lineages within the group. Additionally, it provided a revised taxonomic treatment and an identification key for the species in this group.
Article
Ecology
Ronghui Fan, Keyi Tang, Liang Dou, Changkun Fu, Abu ul Hassan Faiz, Xuming Wang, Yufan Wang, Shunde Chen, Shaoying Liu
Summary: In this study, the phylogenetic relationship of the elegant water shrew, Nectogale elegans, was inferred using sequencing of mitochondrial and nuclear genes. The results revealed two species within the genus Nectogale: N. elegans and N. sikhimensis. The split between these two species may be related to the uplift of the Qinghai-Tibet Plateau, which is supported by both molecular and morphological evidence.
ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Bine Xue, Zhuqiu Song, Jie Cai, Zhonghui Ma, Jiuxiang Huang, Yuling Li, Gang Yao
Summary: Alsineae is a taxonomically difficult tribe in Caryophyllaceae with over 500 species distributed in the northern temperate zone. Phylogenetic analyses and divergence time estimation based on genetic and morphological evidence suggest the recognition of new genera within Alsineae, including Stellaria bistylata, Pseudostellaria jamesiana, Stellaria americana, Reniostellaria, Torreyostellaria, Hesperostellaria, and Schizotechium delavayi. Molecular dating analysis provides insights into the historical assembly of herbaceous flora in northern temperate regions.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Vladimir L. Semerikov, Svetlana A. Semerikova, Yuliya Y. Khrunyk, Yuliya A. Putintseva
Summary: The study used genomic libraries enrichment and sequence capture method to obtain mtDNA data of the genus Abies and reconstructed the phylogenetic tree of the species. The results showed that Abies species can be divided into two sister branches, representing Eurasian and American species, with high support for most clades. Intraspecific variability was also found, which can be used for phylogeographic and population studies.
Article
Infectious Diseases
Ekaterina Chernyaeva, Mikhail Rotkevich, Ksenia Krasheninnikova, Alla Lapidus, Dmitrii E. Polev, Natalia Solovieva, Viacheslav Zhuravlev, Piotr Yablonsky, Stephen J. O'Brien
Summary: This study analyzed whole-genome sequences of Mycobacterium tuberculosis strains from pulmonary and extrapulmonary tuberculosis cases, finding genetic sub-strains associated with differences in disease localization and drug resistance patterns. HIV was significantly associated with the development of extrapulmonary tuberculosis in certain genetic subgroups.
Article
Genetics & Heredity
Yury A. Barbitoff, Andrew G. Matveenko, Anton B. Matiiv, Evgeniia M. Maksiutenko, Svetlana E. Moskalenko, Polina B. Drozdova, Dmitrii E. Polev, Alexandra Y. Beliavskaia, Lavrentii G. Danilov, Alexander Predeus, Galina A. Zhouravleva
Summary: This study utilized Oxford Nanopore and Illumina technologies to assemble complete genomes of Peterhof Genetic Collection (PGC) strains and identified numerous structural differences compared to the reference strain S288C. Notable features included mid-length insertions and deletions, reciprocal unbalanced translocations, and the formation of hybrid alleles of FLO genes. The high contiguity of assemblies allowed for tracing the evolutionary history of these laboratory yeast strains.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Elena Stepchenkova, Anna S. Zhuk, Jian Cui, Elena R. Tarakhovskaya, Stephanie R. Barbari, Polina Shcherbakova, Dmitrii E. Polev, Roman Fedorov, Eugenia Poliakov, Igor B. Rogozin, Artem G. Lada, Youri Pavlov
Summary: Research has shown that mutants lacking the catalytic N-terminal part of DNA polymerase ε gradually accumulate fast-growing clones through the positive selection of variants with improved growth. Single nucleotide changes in the cell cycle-dependent kinase gene CDC28 can enhance the growth of these mutants, alleviate their sensitivity to replication inhibitors, and reduce mutation rates. This study suggests that alterations in mammalian homologs of cyclin-dependent kinases may play a role in cellular responses to defects in the leading strand polymerase.
Article
Plant Sciences
E. M. Arnautova, N. N. Nosov, A. Shmakov, L. Shi, X-Ch Zhang, A. Rodionov
Summary: This article investigates the phylogenetic position of the rare endemic banana, Musa huangbaioa, and its uncertain affinity within the Musaceae family. Through molecular phylogenetic analysis, it was found that M. huangbaioa belongs to the M. basjoo-M. itinerans clade of Chinese bananas, possibly indicating a modern hybrid species.
Article
Agronomy
A. A. Gnutikov, N. N. Nosov, I. G. Loskutov, E. M. Machs, E. Blinova, N. S. Probatova, T. Langdon, A. Rodionov
Summary: The study clarified the origin of diploid C-genome oat Avena bruhnsiana from Azerbaijan, its relationship with A. ventricosa and A. clauda, as well as revealed the rDNA sources of A. bruhnsiana and its relationship with other species.
Article
Genetics & Heredity
Andrey S. Glotov, Irina E. Zelenkova, Elena S. Vashukova, Anna R. Shuvalova, Alexandra D. Zolotareva, Dmitrii E. Polev, Yury A. Barbitoff, Oleg S. Glotov, Andrey M. Sarana, Sergey G. Shcherbak, Mariya A. Rozina, Victoria L. Gogotova, Alexander Predeus
Summary: This study investigates the physiological changes and potential biomarkers of high altitude adaptation in endurance athletes. The researchers used transcriptional profiling of whole blood to measure gene expression changes associated with exercise. They identified specific genes regulated at high altitudes and found that platelet and erythrocyte counts uniquely respond to altitude exercise, while changes in neutrophils represent a more generic marker of intense exercise.
Article
Genetics & Heredity
Sergey G. Shcherbak, Anton Changalidi, Yury A. Barbitoff, Anna Yu Anisenkova, Sergei Mosenko, Zakhar P. Asaulenko, Victoria V. Tsay, Dmitrii E. Polev, Roman S. Kalinin, Yuri A. Eismont, Andrey S. Glotov, Evgeny Y. Garbuzov, Alexander N. Chernov, Olga A. Klitsenko, Mikhail O. Ushakov, Anton E. Shikov, Stanislav P. Urazov, Vladislav S. Baranov, Oleg S. Glotov
Summary: The COVID-19 pandemic has sparked interest in the interaction between pathogen and host genomes, with studies identifying candidate genes and genetic variants associated with quantitative traits in COVID-19 patients. These findings may contribute to the identification of genetic risk factors for severe COVID-19.
Review
Genetics & Heredity
Mariia E. Turkunova, Yury A. Barbitoff, Elena A. Serebryakova, Dmitrii E. Polev, Olga S. Berseneva, Elena B. Bashnina, Vladislav S. Baranov, Oleg S. Glotov, Andrey S. Glotov
Summary: This study reports the first case of FHS in the Russian Federation and identifies a pathogenic mutation in the SRCAP gene associated with FHS using WES. The study also evaluates the efficacy of GH treatment for FHS. The findings expand our understanding of FHS and provide new insights into its pathogenesis and treatment.
FRONTIERS IN GENETICS
(2022)
Article
Marine & Freshwater Biology
Yulia M. Polyak, Nadezhda A. Berezina, Dmitrii E. Polev, Andrey N. Sharov
Summary: In this study, the abundance and diversity of bacteria in the digestive tract of bivalve mollusks were examined after exposure to petroleum hydrocarbon pollution. It was found that polluted sites had a different microbial composition compared to unpolluted sites, with specific hydrocarbon-oxidizing bacteria being more abundant in the polluted sites. These findings suggest that hydrocarbon-oxidizing bacteria can serve as a sensitive bioindicator for monitoring and assessing marine ecosystems.
ESTUARINE COASTAL AND SHELF SCIENCE
(2022)
Article
Plant Sciences
Alexander A. Gnutikov, Nikolai N. Nosov, Tatiana M. Koroleva, Elizaveta O. Punina, Nina S. Probatova, Victoria S. Shneyer, Alexander V. Rodionov
Summary: In our article, we analyzed new data on the origin of the hybrid genus xTrisetokoeleria. The results showed that xT. jurtzevii is a hybrid between Koeleria asiatica and Trisetum spicatum, xT. taimyrica originated from Koeleria asiatica and Trisetum subalpestre, and xT. gorodkowii is a hybrid between Koeleria asiatica and Trisetum ruprechtianum. Next-generation sequencing methods were used to clarify the relationships between these genera. The study also provided insights into the pollen fertility of xTrisetokoeleria and its possible progenitors.
