scholarly journals Evolutionary basis of high-frequency hearing in the cochleae of echolocators revealed by comparative genomics

2019 ◽  
Author(s):  
Hui Wang ◽  
Hanbo Zhao ◽  
Keping Sun ◽  
Xiaobin Huang ◽  
Longru Jin ◽  
...  
Keyword(s):  
Positive Selection ◽  
High Frequency ◽  
Genetic Basis ◽  
Comparative Genomic ◽  
Rna Seq ◽  
Physiological Processes ◽  
Genomic Analyses ◽  
Physiological Pathways ◽  
Almost All ◽  
Auditory Processes

Abstract High-frequency hearing is important for the survival of both echolocating bats and whales, but our understanding of its genetic basis is scattered and segmented. In this study, we combined RNA-Seq and comparative genomic analyses to obtain insights into the comprehensive gene expression profile of the cochlea and the adaptive evolution of hearing-related genes. A total of 144 genes were found to have been under positive selection in various species of echolocating bats and toothed whales, 34 of which were identified to be related to hearing behavior or auditory processes. Subsequently, multiple physiological processes associated with those genes were found to have adaptively evolved in echolocating bats and toothed whales, including cochlear bony development, antioxidant activity, ion balance, and homeostatic processes, along with signal transduction. In addition, abundant convergent/parallel genes and sites were detected between different pairs of echolocator species; however, no specific hearing-related physiological pathways were enriched by them and almost all of the convergent/parallel signals were selectively neutral, as previously reported. Notably, two adaptive parallel evolved sites in TECPR2 were shown to have been under positive selection, indicating their functional importance for the evolution of echolocation and high-frequency hearing in laryngeal echolocating bats. This study deepens our understanding of the genetic bases underlying high-frequency hearing in the cochlea of echolocating bats and toothed whales.

Comparative Analysis of The Daily Brain Transcriptomes of Asian Particolored Bat

2021 ◽  
Author(s):  
Guoting Zhang ◽  
Yujia Chu ◽  
Tinglei Jiang ◽  
Jingjing Li ◽  
Lei Feng ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Biological Rhythms ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Sleep State ◽  
Physiological Processes ◽  
Living Things ◽  
Basic Characteristics ◽  
Almost All ◽  
The Brain

Abstract Circadian rhythms are found in almost all organisms, and they comprise one of the most basic characteristics of living things. Bats have attracted interest from researchers because of their unique biological rhythms. However, little is known about the molecular underpinnings of circadian signaling in bats. In this study, we used RNA-Seq to uncover the rhythms of expressed genes and biological processes in the brains of Asian particolored bats. Four collected time points corresponding to four biological states, rest, sleep, wakefulness, and active, were selected over the 24-hour day, and six comparisons of differentially expressed genes were obtained. Downstream functional enrichment analyses suggested that different physiological processes were active at various biological states, including drug metabolism, signaling pathways, and the circadian clock. Furthermore, trend analysis suggested that groups of genes are significantly clustered and are expressed at the lowest levels during the sleep state while being highly expressed during the active stat. In addition, we also identified the Per2 locus as an important circadian clock gene in the brain of Asian particolored bat. Our study provides a new overview of the molecular basis underlying the circadian clock in the brain of bats.

scholarly journals An updated assembly strategy helps parsing the cryptic mitochondrial genome evolution in plants

2021 ◽  
Author(s):  
Yanlei Feng ◽  
Xiaoguo Xiang ◽  
Zhixi Fu ◽  
Xiaohua Jin
Keyword(s):  
Large Scale ◽  
Gc Content ◽  
Comparative Genomic ◽  
Genomic Analyses ◽  
Evolutionary Trajectories ◽  
Mitochondrial Genome Evolution ◽  
Foreign Dna ◽  
Almost All ◽  
Horizontal Transfers ◽  
Main Chromosome

AbstractAlthough plant mitogenomes are small in size, their variations are no less than any other complex genomes. They are under rapid structure and size changes. These characters make the assembly a great challenge. This caused two intertwined problems, a slow growth of known mitogenomes and a poor knowledge of their evolution. In many species, mitogenome becomes the last genome that undeciphered. To have a better understanding of these two questions, we developed a strategy using short sequencing reads and combining current tools and manual steps to get high quality mitogenomes. This strategy allowed us to assembled 23 complete mitogenomes from 5 families in Fagales. Our large-scale comparative genomic analyses indicated the composition of mitogenomes is very mosaic that “horizontal transfers” can be from almost all taxa in seed plants. The largest mitogenome contains more homologous DNA with other Fagales, rather than unique sequences. Besides of real HGTs, sometimes mitovirus, nuclear insertions and other third-part DNA could also produce HGT-like sequences, accounting partially for the unusual evolutionary trajectories, including the cryptic size expansion in Carpinus. Mitochondrial plasmid was also found. Its lower GC content indicates that it may be only an interphase of a foreign DNA before accepting by the main chromosome. Our methods and results provide new insights into the assembly and mechanisms of mitogenome evolution.

scholarly journals Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)

2021 ◽  
Vol 12 ◽  
Author(s):  
Sun-Jung Kwon ◽  
Sohrab Bodaghi ◽  
Tyler Dang ◽  
Kiran R. Gadhave ◽  
Thien Ho ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Yellow Vein ◽  
Comparative Genomic ◽  
Rna Seq ◽  
Ribosomal Frameshifting ◽  
The Family ◽  
Genomic Analyses ◽  
Vein Disease ◽  
Reading Frames

Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae. Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids.

scholarly journals Comparative Genomics Highlight the Importance of Lineage-Specific Gene Families in Evolutionary Divergence of the Coral Genus, Montipora

2021 ◽  
Author(s):  
Yuki Yoshioka ◽  
Go Suzuki ◽  
Yuna Zayasu ◽  
Hiroshi Yamashita ◽  
Chuya Shinzato
Keyword(s):  
Positive Selection ◽  
Early Life ◽  
Gene Families ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Biological Traits ◽  
Life Stages ◽  
Early Life Stages ◽  
Genomic Analyses ◽  
Lineage Specific Gene

Abstract Background: Scleractinian corals of the genus Montipora (Anthozoa, Cnidaria) possess some unusual biological traits, such as vertical transmission of algal symbionts; however, the genetic bases for those traits remain unknown. We performed extensive comparative genomic analyses among members of the family Acroporidae (Montipora, Acropora and Astreopora) to explore genomic novelties to explain unique biological traits of Montipora using improved genome assemblies and gene predictions for M. cactus, M. efflorescens and Astreopora myriophthalma. Results: We obtained genomic data for the three species, of comparable high quality to other published coral genomes. Comparative genomic analyses revealed that the number of gene families restricted to Montipora are significantly higher than those of Acropora and Astreopora, but their functions are largely unknown. The number of gene families specifically expanded in Montipora was much lower than the number specifically expanded in Acropora. In addition, we found that evolutionary rates of the Montipora-specific gene families were significantly higher than other gene families shared with Acropora and/or Astreopora. Of 40 gene families under positive selection (Ka/Ks ratio > 1) in Montipora, 30 were specifically detected in Montipora-specific gene families. Comparative transcriptome analysis of early life stages of Montipora, which possesses maternally inherited symbionts, and Acropora, which lacks them, revealed that most gene families continuously expressed in Montipora, but not expressed in Acropora do not have orthologs in Acropora. Among the 30 Montipora-specific gene families under positive selection, 27 are expressed in early life stages. Conclusions: Lineage-specific gene families were important to establish the genus Montipora, particularly genes expressed throughout early life stages, which under positive selection, gave rise to biological traits unique to Montipora. Our findings highlight evolutionarily acquired genomic bases that may support symbiosis in these stony corals and provide novel insights into mechanisms of coral-algal symbiosis, the physiological foundation of coral reefs.

scholarly journals Development of central auditory processes in Polish children and adolescents at the age from 7 to 16 years

2021 ◽  
Author(s):  
Monika Lewandowska ◽  
Rafał Milner ◽  
Małgorzata Ganc ◽  
Elżbieta Włodarczyk ◽  
Joanna Dołżycka ◽  
...  
Keyword(s):  
Children And Adolescents ◽  
School Students ◽  
Frequency Pattern ◽  
Speech In Noise ◽  
Age Related ◽  
Right Ear Advantage ◽  
The Right ◽  
Almost All ◽  
Test Retest Reliability ◽  
Auditory Processes

AbstractThere are discrepancies in the literature regarding the course of central auditory processes (CAP) maturation in typically developing children and adolescents. The purpose of the study was to provide an overview of age – related improvement in CAP in Polish primary and secondary school students aged 7–16 years. 180 children/adolescents, subdivided into 9 age categories, and 20 adults (aged 18–24 years) performed the Dichotic Digit Test (DDT), Duration Pattern Test (DPT), Frequency Pattern Test (FPT), Gap Detection Test (GDT) and adaptive Speech-in-Noise (aSpN). The 12-year-olds was retested after w week. We found the age effects only for the DDT, DPT and FPT. In the right ear DDT the 7-year-olds performed more poorly than all groups ≥12. In the left ear DDT both 7- and 8-year-olds achieved less correct responses compared with the 13-, 14-, 15-year-olds and with the adults. The right ear advantage was greater in the 7-year-olds than in the 15-year-olds and adult group. At the age of 7 there was lower DPT and FPT scores than in all participants ≥13 whereas the 8-year-olds obtained less correct responses in the FPT than all age categories ≥12. Almost all groups (except for the 7-year-olds) performed better in the DPT than FPT. The test-retest reliability for all tests was satisfactory. The study demonstrated that different CAP have their own patterns of improvement with age and some of them are specific for the Polish population. The psychoacoustic battery may be useful in screening for CAP disorders in Poland.

scholarly journals High-Altitude Adaptation: Mechanistic Insights from Integrated Genomics and Physiology

2021 ◽  
Author(s):  
Jay F Storz
Keyword(s):  
High Altitude ◽  
Hypoxia Inducible Factor ◽  
Feedback Regulation ◽  
Genomic Analyses ◽  
Manipulative Experiments ◽  
Altitude Adaptation ◽  
Mechanisms Of Adaptation ◽  
Physiological Pathways ◽  
Underlying Mechanisms ◽  
Integrated Genomics

AbstractPopulation genomic analyses of high-altitude humans and other vertebrates have identified numerous candidate genes for hypoxia adaptation, and the physiological pathways implicated by such analyses suggest testable hypotheses about underlying mechanisms. Studies of highland natives that integrate genomic data with experimental measures of physiological performance capacities and subordinate traits are revealing associations between genotypes (e.g., hypoxia-inducible factor gene variants) and hypoxia-responsive phenotypes. The subsequent search for causal mechanisms is complicated by the fact that observed genotypic associations with hypoxia-induced phenotypes may reflect second-order consequences of selection-mediated changes in other (unmeasured) traits that are coupled with the focal trait via feedback regulation. Manipulative experiments to decipher circuits of feedback control and patterns of phenotypic integration can help identify causal relationships that underlie observed genotype–phenotype associations. Such experiments are critical for correct inferences about phenotypic targets of selection and mechanisms of adaptation.

scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽  
2021 ◽  
pp. 145715
Author(s):  
Ying Zhang ◽  
Zhengfeng Wang ◽  
Yanan Guo ◽  
Sheng Chen ◽  
Xianyi Xu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Comparative Genomic ◽  
Chloroplast Genomes ◽  
Genomic Analyses

Evidence from comparative genomic analyses indicating that Lactobacillus-mediated irritable bowel syndrome alleviation is mediated by the conjugated linoleic acid synthesis

2021 ◽  
Author(s):  
Yang Liu ◽  
Wei Xiao ◽  
Leilei Yu ◽  
Fengwei Tian ◽  
Gang Wang ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Linoleic Acid ◽  
Gut Microbiota ◽  
Acid Synthesis ◽  
Comparative Genomic ◽  
Low Grade ◽  
Genomic Analyses ◽  
Irritable Bowel ◽  
Low Grade Inflammation ◽  
Gut Microbiota Dysbiosis

Irritable bowel syndrome (IBS) is a chronic intestinal disorder accompanied by low-grade inflammation, visceral hypersensitivity, and gut microbiota dysbiosis. Several studies have indicated that Lactobacillus supplementation can help to alleviate...

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