scholarly journals Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families

2021 ◽  
Vol 288 (1955) ◽  
pp. 20210803
Author(s):  
Xiuping Zhang ◽  
David Blair ◽  
Justyna Wolinska ◽  
Xiaolin Ma ◽  
Wenwu Yang ◽  
...  
Keyword(s):  
Predation Risk ◽  
Community Dynamics ◽  
Transcriptional Profiling ◽  
Gene Families ◽  
Multiple Gene ◽  
Fish Kairomone ◽  
Apoptosis Pathways ◽  
Genomic Regions ◽  
Cycle Regulation ◽  
Perceived Predation Risk

Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri , a primary forage for many fish species. Transcriptional profiling of D. mitsukuri exposed to fish kairomone revealed that this cladoceran responds to predation risk through regulating activities of Wnt signalling, cuticle pattern formation, cell cycle regulation and anti-apoptosis pathways. Genes differentially expressed in response to predation risk are more likely to be members of expanded families. Our results suggest that expansions of multiple gene families associated with chemoreception and vision allow Daphnia to enhance detection of predation risk, and that expansions of those associated with detoxification and cuticle formation allow Daphnia to mount an efficient response to perceived predation risk. This study increases our understanding of the molecular basis of prey defences, being important evolutionary adaptations playing a stabilizing role in community dynamics.

scholarly journals Analysis of the chromosomal clustering of Fusarium-responsive wheat genes uncovers new players in the defence against head blight disease

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alexandre Perochon ◽  
Harriet R. Benbow ◽  
Katarzyna Ślęczka-Brady ◽  
Keshav B. Malla ◽  
Fiona M. Doohan
Keyword(s):  
Map Kinases ◽  
Gene Families ◽  
Gene Clusters ◽  
Head Blight ◽  
Orphan Gene ◽  
Metabolic Genes ◽  
Eukaryotic Gene ◽  
Blight Disease ◽  
Genomic Regions ◽  
Eukaryotic Genomes

AbstractThere is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium-responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non-metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin-like proteins. 20 of the FRGCs encode nonhomologous, non-metabolic genes (including defence-related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium-responsive genes, five of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specific traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease.

Perceived predation risk, parasitism, and the foraging behavior of a freshwater snail (Potamopyrgus antipodarum)

1998 ◽  
Vol 76 (10) ◽  
pp. 1878-1884 ◽  
Author(s):  
Edward P Levri
Keyword(s):  
Predation Risk ◽  
Foraging Behavior ◽  
Freshwater Snail ◽  
Potamopyrgus Antipodarum ◽  
Plain Water ◽  
Fish Diet ◽  
Fish Predator ◽  
Size Dependent ◽  
Individual Size ◽  
Perceived Predation Risk

Foraging behavior can be influenced by such factors as predation risk, individual size, and parasite infection. Snails (Potamopyrgus antipodarum) placed in tanks with large rocks were exposed to four types of water: (1) water with crushed snails, (2) water from a tank in which fish (Gobiomorphus cotidianus) were fed only trout chow, (3) water from a tank where the fish were also fed snails, and (4) plain water. Snails could respond by moving to the top of rocks (where algal food was present) or to the bottom of rocks (where the predation risk was lower). The snails responded to fish chemicals by moving to the bottom of rocks. The response was dependent on snail size and fish diet. Smaller snails moved to the bottom of rocks more than larger snails did. Trematode-infected snails were found on top of the rocks more than other classes of snails, but infected snails still moved to the bottom of rocks in response to the fish predator. Snails eaten by fish in the field tend to be smaller than snails in the overall available population. Thus, snails that are more vulnerable to predation respond more intensely to the odor of fish by moving to the bottom of rocks. This size-dependent response to fish appears to be independent of the occurrence of trematode infection.

Functional Traits, Flocking Propensity, and Perceived Predation Risk in an Amazonian Understory Bird Community

2016 ◽  
Vol 187 (5) ◽  
pp. 607-619 ◽  
Author(s):  
Ari E. Martínez ◽  
Juan P. Gomez ◽  
José Miguel Ponciano ◽  
Scott K. Robinson
Keyword(s):  
Predation Risk ◽  
Functional Traits ◽  
Bird Community ◽  
Perceived Predation Risk

scholarly journals The Genome-Sequenced Variant of Campylobacter jejuni NCTC 11168 and the Original Clonal Clinical Isolate Differ Markedly in Colonization, Gene Expression, and Virulence-Associated Phenotypes

2004 ◽  
Vol 186 (2) ◽  
pp. 503-517 ◽  
Author(s):  
Erin C. Gaynor ◽  
Shaun Cawthraw ◽  
Georgina Manning ◽  
Joanna K. MacKichan ◽  
Stanley Falkow ◽  
...  
Keyword(s):  
Clinical Isolate ◽  
Campylobacter Jejuni ◽  
Transcriptional Profiling ◽  
Bacterial Pathogen ◽  
Gene Families ◽  
Subtractive Hybridization ◽  
Laboratory Culture ◽  
Phenotypic Differences ◽  
Culture Cells ◽  
Colonization Potential

ABSTRACT The genome sequence of the enteric bacterial pathogen Campylobacter jejuni NCTC 11168 (11168-GS) was published in 2000, providing a valuable resource for the identification of C. jejuni-specific colonization and virulence factors. Surprisingly, the 11168-GS clone was subsequently found to colonize 1-day-old chicks following oral challenge very poorly compared to other strains. In contrast, we have found that the original clinical isolate from which 11168-GS was derived, 11168-O, is an excellent colonizer of chicks. Other marked phenotypic differences were also identified: 11168-O invaded and translocated through tissue culture cells far more efficiently and rapidly than 11168-GS, was significantly more motile, and displayed a different morphology. Serotyping, multiple high-resolution molecular genotyping procedures, and subtractive hybridization did not yield observable genetic differences between the variants, suggesting that they are clonal. However, microarray transcriptional profiling of these strains under microaerobic and severely oxygen-limited conditions revealed dramatic expression differences for several gene families. Many of the differences were in respiration and metabolism genes and operons, suggesting that adaptation to different oxygen tensions may influence colonization potential. This correlates biologically with our observation that anaerobically priming 11168-GS or aerobically passaging 11168-O caused an increase or decrease, respectively, in colonization compared to the parent strain. Expression differences were also observed for several flagellar genes and other less well-characterized genes that may participate in motility. Targeted sequencing of the sigma factors revealed specific DNA differences undetected by the other genomic methods. These observations highlight the capacity of C. jejuni to adapt to multiple environmental niches, the likelihood that this adaptation involves genetic evolution, and provides the first whole-genome molecular exploration of the effect of laboratory culture and storage on colonization and virulence properties of this pathogen.

scholarly journals Transcriptomic Analysis of Leaf Sheath Maturation in Maize

2019 ◽  
Vol 20 (10) ◽  
pp. 2472 ◽  
Author(s):  
Lei Dong ◽  
Lei Qin ◽  
Xiuru Dai ◽  
Zehong Ding ◽  
Ran Bi ◽  
...  
Keyword(s):  
Leaf Blade ◽  
Crop Yields ◽  
Transcriptional Profiling ◽  
Homeobox Gene ◽  
Lignin Biosynthesis ◽  
Gene Families ◽  
Longitudinal Axis ◽  
Leaf Sheath ◽  
Morphological Development ◽  
Maize Leaf

The morphological development of the leaf greatly influences plant architecture and crop yields. The maize leaf is composed of a leaf blade, ligule and sheath. Although extensive transcriptional profiling of the tissues along the longitudinal axis of the developing maize leaf blade has been conducted, little is known about the transcriptional dynamics in sheath tissues, which play important roles in supporting the leaf blade. Using a comprehensive transcriptome dataset, we demonstrated that the leaf sheath transcriptome dynamically changes during maturation, with the construction of basic cellular structures at the earliest stages of sheath maturation with a transition to cell wall biosynthesis and modifications. The transcriptome again changes with photosynthesis and lignin biosynthesis at the last stage of sheath tissue maturation. The different tissues of the maize leaf are highly specialized in their biological functions and we identified 15 genes expressed at significantly higher levels in the leaf sheath compared with their expression in the leaf blade, including the BOP2 homologs GRMZM2G026556 and GRMZM2G022606, DOGT1 (GRMZM2G403740) and transcription factors from the B3 domain, C2H2 zinc finger and homeobox gene families, implicating these genes in sheath maturation and organ specialization.

Sign in / Sign up

Export Citation Format

Share Document