Discarded sequencing reads uncover natural variation in pest resistance inThlaspi arvense DOI Creative Commons
Dario Galanti, Jun Hee Jung, Caroline Müller

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 20, 2023

Abstract Understanding the genomic basis of natural variation in plant pest resistance is an important goal science, but it usually requires large and labour-intensive phenotyping experiments. Here, we explored possibility that non-target reads from DNA sequencing can serve as proxies for addressing such questions. We used data a whole-genome -epigenome study 207 lines field pennycress ( Thlaspi arvense ) were grown common environment spontaneously colonized by aphids, mildew other microbes. found numbers assigned to species differed between populations, had significant SNP-based heritability, associated with climate origin baseline glucosinolates content. Specifically, cold thermally fluctuating habitats, presumably less favorable showed higher aphid load, i.e. decreased resistance. Genome-wide association analyses identified genetic variants at known defense genes also novel regions load. Moreover, several differentially methylated pathogen loads, particular differential methylation transposons hypomethylation promoter gene involved stomatal closure, likely induced pathogens. Our provides first insights into mechanisms , rising crop model species, demonstrates whole genome reads, discarded, be leveraged estimate intensities biotic interactions. With rapidly increasing datasets worldwide, this approach should have broad application fundamental applied research.

Language: Английский

Derivation of Allometric Equations and Carbon Content Estimation in Mangrove Forests of Malaysia DOI Creative Commons
Waseem Razzaq Khan, Michele Giani, Stanislao Bevilacqua

et al.

Environmental and Sustainability Indicators, Journal Year: 2025, Volume and Issue: unknown, P. 100618 - 100618

Published: Jan. 1, 2025

Language: Английский

Citations

2
Population genetic structure and historical demography of Saccostrea echinata in the Northern South China sea and Beibu Gulf DOI Creative Commons
Yafang Li, Lianggen Wang, Yingmin Wang

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 10, 2025

Marine invertebrates, such as oysters, were once thought to form large, panmictic populations with little genetic differentiation due their high reproductive capacity and dual life stages. However, recent studies have shown significant structuring moderate gene flow across populations, influenced by factors like ocean currents, historical climate events, environmental changes. The black-lip oyster (Saccostrea echinata), its extensive dispersal potential, is ideal for population genetics studies. In current study, mitochondrial DNA (COI gene) was utilized investigate the structure, diversity, demographic history of S. echinata in northern South China Sea (NSCS) Beibu Gulf. Results revealed diversity 82 haplotypes from 190 specimens, a star-shaped haplotype network, differentiation, most variation occurring within populations. Genetic analysis identified three distinct groups sampled regions. Historical indicated expansion approximately 44–155 Kya after Last Glacial Maximum. structure shaped climatic events causing isolation secondary contact, well contemporary currents influencing flow. study highlights complex interplay dynamics echinata, implications conservation aquaculture Asia-Pacific region.

Language: Английский

Citations

0
Genetic basis of local adaptation in the cold-tolerant mangrove Kandelia obovata DOI Creative Commons

Chuangchao Zou,

Yushuai Wang,

Renchao Zhou

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: April 24, 2024

Understanding the genetic basis of local adaption is crucial in context global climate change. Mangroves, as salt-tolerant trees and shrubs intertidal zone tropical subtropical coastlines, are particularly vulnerable to Kandelia obovata, most cold-tolerant mangrove species, has undergone ecological speciation from its cold-intolerant counterpart, candel, with geographic separation by South China Sea. In this study, we conducted whole-genome re-sequencing K. obovata populations along China's southeast coast, elucidate responsible for adaptation climate. Our analysis revealed a strong population structure among three populations, complex demographic histories involving expansion, bottleneck, gene flow. Genome-wide scans unveiled pronounced patterns selective sweeps highly differentiated regions pairwise stronger signatures observed northern compared southern population. Additionally, significant genotype-environment associations temperature-related variables were identified, while no detected precipitation. A set 39 high-confidence candidate genes underlying which distinct under selection comparison between relative candel. These results significantly contribute our understanding underpinnings provide valuable insights into evolutionary processes shaping diversity response

Language: Английский

Citations

2
Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense DOI Creative Commons
Dario Galanti, Jun Hee Jung, Caroline Müller

et al.

eLife, Journal Year: 2024, Volume and Issue: 13

Published: April 3, 2024

Understanding the genomic basis of natural variation in plant pest resistance is an important goal science, but it usually requires large and labor-intensive phenotyping experiments. Here, we explored possibility that non-target reads from DNA sequencing can serve as proxies for addressing such questions. We used data a whole-genome -epigenome study 207 lines field pennycress ( Thlaspi arvense ) were grown common environment spontaneously colonized by aphids, mildew, other microbes. found numbers assigned to species differed between populations, had significant SNP-based heritability, associated with climate origin baseline glucosinolate contents. Specifically, cold thermally fluctuating habitats, presumably less favorable showed higher aphid load, i.e., decreased resistance. Genome-wide association analyses identified genetic variants at known defense genes also novel regions mildew load. Moreover, several differentially methylated pathogen loads, particular differential methylation transposons hypomethylation promoter gene involved stomatal closure, likely induced pathogens. Our provides first insights into mechanisms , rising crop model species, demonstrates reads, discarded, be leveraged estimate intensities biotic interactions. With rapidly increasing datasets worldwide, this approach should have broad application fundamental applied research.

Language: Английский

Citations

1
Signs of Neutral Genetic Differentiation and Phenotypic Adaptive Divergence Across an Environmental Gradient in Sri Lanka's Grey Mangrove Avicennia Marina (Forssk.) Vierh DOI

Mehak Sangani,

Guillermo Friis,

Anique Ahmad

et al.

Published: Jan. 1, 2024

Evolutionary change results from the interactions among neutral and selective factors understanding their relative roles in driving population divergence is critical speciation research. Biological systems occurring across environmental gradients provide an ideal opportunity to test contribution of natural selection, drift, gene flow shaping variability. In this study, we compared levels genetic phenotypic differentiation leaf morphological traits Grey mangrove Avicennia marina (Forssk.) Vierh. populations Sri Lanka. Population structure analyses statistics based on 39,413 selectively biallelic SNPs revealed pronounced inhabiting distinct climatic zones defined by rainfall patterns, with mangroves dry zone Mollikulum exhibiting highest divergence. Phenotypic analysis uncovered a significant reduction area population, suggesting potential adaptive response cope aridity its habitat. Observed may be explained limited flow, mediated coastal currents. However, observed patterns variation suggests that local adaptation have also played role Lankan mangroves. This study underscores importance considering both aspects when investigating divergence, offering valuable insights into intricate processes species evolution diverse environments.

Language: Английский

Citations

0
MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi‐Omics Data DOI
Chaoqun Xu, Lingyu Song, Jing Li

et al.

Plant Cell & Environment, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 11, 2024

Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological economic value. Recently, genomes mangroves have been decoded, massive omics data were generated deposited in public databases. Reanalysis multi-omics can provide new biological insights excluded original studies. However, requirements for computational resource lack bioinformatics skill experimental researchers limit effective use data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing provided 13 reference 40 transcriptomes 53 mangroves. Finally, built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to comprehensive gene expression datasets facilitate their exploration equipped with several online analysis tools, including principal components analysis, differential tissue-specific GO KEGG enrichment analysis. not only provides query functions about genes annotation, but also supports some useful visualization results, such as volcano plot, heatmap, dotplot, PCA bubble population structure, so on. In conclusion, is a valuable research community efficiently datasets.

Language: Английский

Citations

0
Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense DOI Creative Commons
Dario Galanti, Jun Hee Jung, Caroline Müller

et al.

eLife, Journal Year: 2024, Volume and Issue: 13

Published: Dec. 19, 2024

Understanding the genomic basis of natural variation in plant pest resistance is an important goal science, but it usually requires large and labor-intensive phenotyping experiments. Here, we explored possibility that non-target reads from DNA sequencing can serve as proxies for addressing such questions. We used data a whole-genome -epigenome study 207 lines field pennycress ( Thlaspi arvense ) were grown common environment spontaneously colonized by aphids, mildew, other microbes. found numbers assigned to species differed between populations, had significant SNP-based heritability, associated with climate origin baseline glucosinolate contents. Specifically, cold thermally fluctuating habitats, presumably less favorable showed higher aphid load, i.e., decreased resistance. Genome-wide association analyses identified genetic variants at known defense genes also novel regions mildew load. Moreover, several differentially methylated pathogen loads, particular differential methylation transposons hypomethylation promoter gene involved stomatal closure, likely induced pathogens. Our provides first insights into mechanisms , rising crop model species, demonstrates reads, discarded, be leveraged estimate intensities biotic interactions. With rapidly increasing datasets worldwide, this approach should have broad application fundamental applied research.

Language: Английский

Citations

0
Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense DOI Open Access
Dario Galanti, Jun Hee Jung, Caroline Müller

et al.

Published: Oct. 29, 2024

Understanding the genomic basis of natural variation in plant pest resistance is an important goal science, but it usually requires large and labour-intensive phenotyping experiments. Here, we explored possibility that non-target reads from DNA sequencing can serve as proxies for addressing such questions. We used data a whole-genome -epigenome study 207 lines field pennycress ( Thlaspi arvense ) were grown common environment spontaneously colonized by aphids, mildew other microbes. found numbers assigned to species differed between populations, had significant SNP-based heritability, associated with climate origin baseline glucosinolates content. Specifically, cold thermally fluctuating habitats, presumably less favorable showed higher aphid load, i.e. decreased resistance. Genome-wide association analyses identified genetic variants at known defense genes also novel regions load. Moreover, several differentially methylated pathogen loads, particular differential methylation transposons hypomethylation promoter gene involved stomatal closure, likely induced pathogens. Our provides first insights into mechanisms , rising crop model species, demonstrates whole genome reads, discarded, be leveraged estimate intensities biotic interactions. With rapidly increasing datasets worldwide, this approach should have broad application fundamental applied research.

Language: Английский

Citations

0
Discarded sequencing reads uncover natural variation in pest resistance inThlaspi arvense DOI Creative Commons
Dario Galanti, Jun Hee Jung, Caroline Müller

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 20, 2023

Abstract Understanding the genomic basis of natural variation in plant pest resistance is an important goal science, but it usually requires large and labour-intensive phenotyping experiments. Here, we explored possibility that non-target reads from DNA sequencing can serve as proxies for addressing such questions. We used data a whole-genome -epigenome study 207 lines field pennycress ( Thlaspi arvense ) were grown common environment spontaneously colonized by aphids, mildew other microbes. found numbers assigned to species differed between populations, had significant SNP-based heritability, associated with climate origin baseline glucosinolates content. Specifically, cold thermally fluctuating habitats, presumably less favorable showed higher aphid load, i.e. decreased resistance. Genome-wide association analyses identified genetic variants at known defense genes also novel regions load. Moreover, several differentially methylated pathogen loads, particular differential methylation transposons hypomethylation promoter gene involved stomatal closure, likely induced pathogens. Our provides first insights into mechanisms , rising crop model species, demonstrates whole genome reads, discarded, be leveraged estimate intensities biotic interactions. With rapidly increasing datasets worldwide, this approach should have broad application fundamental applied research.

Language: Английский

Citations

0