scholarly journals Chromosome-level genome assemblies of Channa argusandChanna maculata and comparative analysis of their temperature adaptability

GigaScience ◽  
2021 ◽  
Vol 10 (10) ◽  
Author(s):  
Mi Ou ◽  
Rong Huang ◽  
Cheng Yang ◽  
Bin Gui ◽  
Qing Luo ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Low Temperature ◽  
Gene Families ◽  
Temperature Adaptation ◽  
Fish Family ◽  
Transcription Factor Genes ◽  
Immune Related Genes ◽  
Genome Assemblies ◽  
Temperature Adaptability ◽  
Chromosome Level

Abstract Background Channa argus and Channa maculata are the main cultured species of the snakehead fish family, Channidae. The relationship between them is close enough that they can mate; however, their temperature adaptability is quite different. Results In this study, we sequenced and assembled the whole genomes of C. argus and C. maculata and obtained chromosome-level genome assemblies of 630.39 and 618.82 Mb, respectively. Contig N50 was 13.20 and 21.73 Mb, and scaffold N50 was 27.66 and 28.37 Mb, with 28,054 and 24,115 coding genes annotated for C. argus and C. maculata, respectively. Our analyses showed that C. argus and C. maculata have 24 and 21 chromosomes, respectively. Three pairs of chromosomes in C. argus correspond to 3 chromosomes in C. maculata, suggesting that 3 chromosomal fusion events occurred in C. maculata. Comparative analysis of their gene families showed that some immune-related genes were unique or expandable to C. maculata, such as genes related to herpes simplex infection. Analysis of the transcriptome differences related to temperature adaptation revealed that the brain and liver of C. argus rapidly produced more differentially expressed genes than C. maculata. Genes in the FoxO signalling pathway were significantly enriched in C. argus during the cooling process (P < 0.05), and the expression of 3 transcription factor genes in this pathway was significantly different between C. argus and C. maculata (P < 0.01). Conclusions C. maculata may have higher resistance to certain diseases, whereas C. argus has a faster and stronger response to low-temperature stress and thus has better adaptability to a low-temperature environment. This study provides a high-quality genome research platform for follow-up studies of Channidae and provides important clues regarding differences in the low-temperature adaptations of fish.

scholarly journals A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators

2021 ◽  
Author(s):  
Emma Bailey ◽  
Linda Field ◽  
Christopher Rawlings ◽  
Rob King ◽  
Fady Mohareb ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Insecticide Resistance ◽  
Genome Assembly ◽  
Crop Yields ◽  
Hybrid Approach ◽  
Gene Families ◽  
Genomic Information ◽  
Predator Species ◽  
Crop Pests ◽  
Chromosome Level

Abstract Background: Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs). Methods and findings: In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily levels between S. rueppellii and some crop pests. Conclusion and significance: This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.

scholarly journals Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher Alan Smith
Keyword(s):  
Evolutionary History ◽  
Lentinula Edodes ◽  
Reference Genome ◽  
Genomic Change ◽  
Diverse Species ◽  
The World ◽  
Cultivated Mushroom ◽  
Genome Assemblies ◽  
High Degree ◽  
Chromosome Level

AbstractThe basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

scholarly journals COMPARATIVE ANALYSIS OF LOW TEMPERATURE RESISTANCE FOR NANOCARBON AND OTHER BITUMENS

2020 ◽  
Vol 5 (443) ◽  
pp. 89-96
Author(s):  
Zhurinov M.Zh., ◽  
◽  
Teltayev B.B., ◽  
Kalybay A.A., ◽  
Rossi C.O., ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Low Temperature ◽  
Polyphosphoric Acid ◽  
Crumb Rubber ◽  
Petrochemical Plant ◽  
Short Term ◽  
Temperature Resistance ◽  
Coal Rock ◽  
Low Temperature Resistance

A comparative analysis of the low temperature resistance for a nanocarbon bitumen and other 30 neat and modified bitumens has been performed in the work. The stiffness at the temperatures of -24°С, -30°С and -36°С under technical system Superpave has been accepted as an indicator of low temperature resistance of the bitumens. The stiffness of the bitumens has been determined on a bending beam rheometer (standard ASTM D 6648-08). Before testing the bitumens have been subjected to the double artificial aging: short-term aging – under standard AASHTO Т 240-13 and long-term aging – under standard ASTM D 6521-08. The nanocarbon bitumen has been prepared in the laboratory of the Kazakhstan Highway Research Institute (KazdorNII) with the use of a road bitumen of the grade BND 70/100 produced by the Pavlodar petrochemical plant (PNHZ) and a nanocarbon powder (2% by weight) manufactured from a coal rock of the deposit “Saryadyr” “Corporation “ON-Olzha” LLP, Akmola region, Kazakhstan). The nanocarbon powder (150-200 nm) has been manufactured by three-stage size reduction of the coal rock: I – a mechanical dispergator (up to 2-3 mm), II – an aerodynamic mill (up to 20 mcm), III – a reactor with a rotating electromagnetic field. The neat bitumens of the grades BND 50/70, BND 70/100, BND 100/130 have been produced by the plants of Kazakhstan and Russia; they satisfy the requirements of the standard ST RK 1373-2013. The modified bitumens have been prepared in the laboratory of KazdorNII with the use of the neat bitumens, 7 types of the polymers, crumb rubber and polyphosphoric acid and they satisfy the requirements of the standard ST RK 2534-2014. It has been determined that the nanocarbon bitumen is one of the most resistant at the low temperatures: -24°С, -30°С and -36°С.

scholarly journals Giant African snail genomes provide insights into molluscan whole-genome duplication and aquatic-terrestrial transition

2020 ◽  
Author(s):  
Conghui Liu ◽  
Yuwei Ren ◽  
Zaiyuan Li ◽  
Qi Hu ◽  
Lijuan Yin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Terrestrial Ecosystems ◽  
Gene Families ◽  
Gene Clusters ◽  
Immune Defense ◽  
Whole Genome ◽  
Genomic Plasticity ◽  
Ecological Adaptability ◽  
Chromosome Level

AbstractWhole-genome duplication (WGD) has been observed across a wide variety of eukaryotic groups, contributing to evolutionary diversity and environmental adaptability. Mollusks are the second largest group of animals, and are among the organisms that have successfully adapted to the nonmarine realm through aquatic-terrestrial (A-T) transition, and no comprehensive research on WGD has been reported in this group. To explore WGD and the A-T transition in Mollusca, we assembled a chromosome-level reference genome for the giant African snail Achatina immaculata, a global invasive species, and compared the genomes of two giant African snails (A. immaculata and Achatina fulica) to the other available mollusk genomes. The chromosome-level macrosynteny, colinearity blocks, Ks peak and Hox gene clusters collectively suggested the occurrence of a WGD event shared by A. immaculata and A. fulica. The estimated timing of this WGD event (∼70 MYA) was close to the speciation age of the Sigmurethra-Orthurethra (within Stylommatophora) lineage and the Cretaceous-Tertiary (K-T) mass extinction, indicating that the WGD reported herein may have been a common event shared by all Sigmurethra-Orthurethra species and could have conferred ecological adaptability and genomic plasticity allowing the survival of the K-T extinction. Based on macrosynteny, we deduced an ancestral karyotype containing 8 conserved clusters for the Gastropoda-Bivalvia lineage. To reveal the mechanism of WGD in shaping adaptability to terrestrial ecosystems, we investigated gene families related to the respiration, aestivation and immune defense of giant African snails. Several mucus-related gene families expanded early in the Stylommatophora lineage, functioning in water retention, immune defense and wound healing. The hemocyanins, PCK and FBP families were doubled and retained after WGD, enhancing the capacity for gas exchange and glucose homeostasis in aestivation. After the WGD, zinc metalloproteinase genes were highly tandemly duplicated to protect tissue against ROS damage. This evidence collectively suggests that although the WGD may not have been the direct driver of the A-T transition, it provided an important legacy for the terrestrial adaptation of the giant African snail.

scholarly journals Selection for wide temperature adaptation in Chrysanthemum morifolium (Ramat.) Hemsl.

1978 ◽  
Vol 26 (1) ◽  
pp. 110-118
Author(s):  
J. de Jong
Keyword(s):  
Low Temperature ◽  
Chrysanthemum Morifolium ◽  
Temperature Adaptation ◽  
Optimum Temperature ◽  
Selected Abstract ◽  
Days To Flowering ◽  
Selection For ◽  
High Or Low Temperature ◽  
Chrysanthemum Morifolium Ramat ◽  
Short Days

Rooted cuttings of commercial cvs were grown to flowering at five temperatures and the the number of short days to flowering was recorded. The optimum temperature for rapid flowering varied between cvs. The number of days to flowering at the optimum temperature was not related to the delay in flowering caused by either high or low temperature. In many cvs the delay in flowering at low temperature was accompanied by a similar delay at high temperature. It was concluded that for the character 'time to flowering' genotypes should preferably be selected at low temperatures. If low temperature cannot be realized, only rapidly flowering genotypes should be selected. (Abstract retrieved from CAB Abstracts by CABI’s permission)

scholarly journals Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

2021 ◽  
Vol 9 ◽  
Author(s):  
Madeleine E. Aase-Remedios ◽  
David E. K. Ferrier
Keyword(s):  
Chromosomal Rearrangements ◽  
Expression Patterns ◽  
Gene Families ◽  
Evolutionary Transitions ◽  
Whole Genome Duplications ◽  
Chordate Evolution ◽  
Genome Duplications ◽  
The Many ◽  
Genome Assemblies ◽  
The Impact

Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.

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