A high-quality chromosome-level genome assembly of Pelteobagrus vachelli provides insights into its environmental adaptation and population history DOI Creative Commons
Jie Li, Tao Wang, Wei Liu

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Nov. 14, 2022

Pelteobagrus vachelli is a freshwater fish with high economic value, but the lack of genome resources has severely restricted its industrial development and population conservation. Here, we constructed first chromosome-level assembly P. total length approximately 662.13 Mb contig N50 was 14.02 Mb, scaffolds covering 99.79% were anchored to 26 chromosomes. Combining comparative results transcriptome data under environmental stress (high temperature, hypoxia Edwardsiella. ictaluri infection), MAPK signaling pathway, PI3K-Akt pathway apelin play an important role in adaptation vachelli, these pathways interconnected by ErbB family involved cell proliferation, differentiation apoptosis. Population evolution analysis showed that artificial interventions have affected wild populations vachelli. This study provides useful genomic information for genetic breeding as well references further studies on biology evolution.

Language: Английский

Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat DOI
Jeffrey A. Fawcett, Ryoma Takeshima, Shinji Kikuchi

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(8), P. 1236 - 1251

Published: Aug. 10, 2023

Language: Английский

Citations

25
Polyploidy before and after domestication of crop species DOI Creative Commons
Takashi Akagi,

Katharina Jung,

Kanae Masuda

et al.

Current Opinion in Plant Biology, Journal Year: 2022, Volume and Issue: 69, P. 102255 - 102255

Published: July 21, 2022

Recent advances in the genomics of polyploid species answer some long-standing questions about role polyploidy crop species. Here, we summarize current literature to reexamine scenarios which played a both before and after domestication. The prevalence can help explain environmental robustness agroecosystems. This review also clarifies molecular basis agriculturally advantageous traits crops, including yield increments cotton via subfunctionalization, modification separated sexuality selfing persimmon neofunctionalization, transition system nonfunctionalization combined with epistatic interaction between duplicated S-loci. rapid progress genetics is discussed along how this will facilitate functional studies understudied

Language: Английский

Citations

38
Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution? DOI Creative Commons
Kentaro K. Shimizu

Current Opinion in Plant Biology, Journal Year: 2022, Volume and Issue: 69, P. 102292 - 102292

Published: Sept. 2, 2022

The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide termed "genome shock," as well ancient polyploidy. Recent bioinformatics advances empirical Arabidopsis wheat relatives are filling a research gap: functional study polyploid using RNA-seq, DNA polymorphism, epigenomics. Polyploid can become generalists natura through environmental robustness by inheriting merging parental stress responses. Their evolvability is enhanced mutational working inherited standing variation. identification key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer other species.

Language: Английский

Citations

37
Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta DOI Open Access

Garima Mishra,

Rajendra K. Meena, Rama Kant

et al.

Functional & Integrative Genomics, Journal Year: 2023, Volume and Issue: 23(1)

Published: Jan. 28, 2023

Language: Английский

Citations

17
Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses DOI Creative Commons
Nicolás Bejerman, Ralf G. Dietzgen, Humberto Debat

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(12), P. 2402 - 2402

Published: Dec. 10, 2023

Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10–16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report identification and genomic characterization 93 novel genetic evolutionary cues cytorhabdoviruses. Strikingly, five unprecedented tri-segmented were also identified. This finding represents first in Rhabdoviridae, they should be classified a within this for suggest name “Trirhavirus”. Interestingly, nucleocapsid polymerase only typical rhabdoviral proteins encoded those viruses, whereas three them, protein similar emaravirus (family Fimoviridae) silencing suppressor was found, while other predicted had no matches any sequence databases. Genetic distance insights that all these may represent species. Phylogenetic analyses, both previously plant rhabdoviruses, provide compelling support division into distinct genera. proposed reclassification not enhances our understanding dynamics group rhabdoviruses but illuminates remarkable diversity encompass. study significant expansion genomics cytorhabdoviruses will enable future research on peculiarity shows plasticity rhabdovirus genome organization discovery unique trajectory.

Language: Английский

Citations

15
Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests DOI Creative Commons
Rong Wang, Chaonan Liu, Simon T. Segar

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 23, 2024

Dipterocarpoideae species form the emergent layer of Asian rainforests. They are indicator for rainforest distribution, but they severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes seven including two autotetraploid species. We estimate divergence time between Malvaceae within be 108.2 (97.8‒118.2) 88.4 (77.7‒102.9) million years ago, identify a whole genome duplication event preceding dipterocarp lineage diversification. find several genes that showed signature selection, likely associated with By resequencing endangered species, detect an expansion effective size after last glacial period recent sharp decline coinciding history local human activities. Our findings contribute understanding diversification dipterocarps highlight anthropogenic disturbances as major factor in status.

Language: Английский

Citations

6
The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests DOI Creative Commons
Kevin Kit Siong Ng, Masaki J. Kobayashi, Jeffrey A. Fawcett

et al.

Communications Biology, Journal Year: 2021, Volume and Issue: 4(1)

Published: Oct. 7, 2021

Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) economical timber production) importance. Recent studies suggested that rare irregular drought events may be an environmental stress signal for trees. We assembled genome a widespread but near threatened dipterocarp, Shorea leprosula, analyzed transcriptome sequences ten dipterocarp species representing seven genera. Comparative genomic molecular dating analyses whole-genome duplication close to Cretaceous-Paleogene extinction event followed diversification major lineages (i.e. Dipterocarpoideae). Interestingly, retained duplicated genes were enriched upregulated no-irrigation treatment. These findings provide support relevance trees despite lack dry season.

Language: Английский

Citations

28
Genomics Resources in Shorea sps: Implications for Conservation and Tree Improvement DOI
Naseer Mohammad, Ankur Dahayat,

Anuj Maran

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
Somatic mutation rates scale with time not growth rate in long-lived tropical trees DOI Creative Commons
Akiko Satake, Ryosuke Imai, Takeshi Fujino

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: June 6, 2023

The rates of appearance new mutations play a central role in evolution. However, mutational processes natural environments and their relationship with growth are largely unknown, particular tropical ecosystems high biodiversity. Here, we examined the somatic mutation landscapes two trees, Shorea laevis (slow-growing) S. leprosula (fast-growing), Borneo, Indonesia. Using newly constructed genomes, identified greater number trees than temperate trees. In both species, observed linear increase physical distance between branches. found that rate accumulation per meter was 3.7-fold higher . This difference scaled slower compared to leprosula, resulting constant year species. We also neutral within an individual, but those transmitted next generation subject purifying selection. These findings suggest accumulate absolute time older have contribution towards generating genetic variation.

Language: Английский

Citations

9
Tree growth and survival are more sensitive to high rainfall than drought in an aseasonal forest in Malaysia DOI Creative Commons
Michael J. O’Brien, Andy Hector,

Robert C. Ong

et al.

Communications Earth & Environment, Journal Year: 2024, Volume and Issue: 5(1)

Published: April 5, 2024

Abstract Global change research has largely focused on the effects of drought forest dynamics while importance excessive rainfall that can cause waterlogged soils been assessed in riparian zones or seasonally flooded sites. However, increased may also decreased growth and survival tree species lowland aseasonal tropical forests due to risk from potentially more extensive frequent soils. We used a Bayesian modelling approach dataset 2004 2017 test concomitant excess deficit dry period length across network experimentally planted trees primary Malaysia. Growth declined 48% 92% during periods high as little 4% had with long periods. Climate is projected severe excess, our results suggest have stronger negative than drought.

Language: Английский

Citations

3