Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants DOI Creative Commons
Donat Wulf, Andrea Bräutigam

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 21, 2023

Abstract Gene regulatory networks based on transcription factors control development and environmental responses in plants. Networks calculated by the machine learning algorithm random forest decision tree-based regression for grasses barley, maize, wheat, Brachypodium, sorghum, rice compared with Arabidopsis an alga show substantial conservation. The degree of conservation depends phylogenetic closeness. processes, which are conserved between all species include basic cellular functions while processes also more specific gene ontology terms. In three a carbon concentration mechanism, photorespiration is partially disassociated from photosynthetic regulation. contrast, C4 species, regulation genes associates comparative analyses reveal factors, photosynthesis seed plants but not alga. An analysis pipeline general transfer information small weed commercially relevant presented.

Язык: Английский

Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis DOI Creative Commons

Kai Thoris,

Miguel Marrero,

Martijn Fiers

и другие.

Nucleic Acids Research, Год журнала: 2024, Номер unknown

Опубликована: Окт. 30, 2024

Abstract Many plant transcription factors (TFs) are multifunctional and regulate growth development in more than one tissue. These TFs can generally associate with different protein partners depending on the tissue type, thereby regulating tissue-specific target gene sets. However, how interaction specificity is ensured still largely unclear. Here, we examine protein–protein using subfunctionalized co-orthologs of FRUITFULL (FUL) subfamily MADS-domain TFs. In Arabidopsis, FUL multifunctional, playing important roles flowering fruiting, whereas these functions have partially been divided tomato FUL1 FUL2. By linking sequence function, discovered a key amino acid motif that determines TFs, which Arabidopsis AGAMOUS SEPALLATA proteins, linked to regulation subset targets. This insight offers great opportunities dissect biological MADS

Язык: Английский

Процитировано

0
Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis. DOI Creative Commons
Damian J. Hernandez, Gwendolyn B. Pohlmann, Michelle E. Afkhami

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 15, 2024

Abstract As environments worldwide change at unprecedented rates during the Anthropocene, understanding context-dependency – how species regulate interactions to match changing is crucial. However, generalizable molecular mechanisms underpinning remain elusive. Combining comparative genomics across 42 angiosperms with transcriptomics, genome-wide association mapping, and gene duplication origin analyses, we show for first time that family expansions undergird context-dependent regulation of interactions. Gene families expanded in mycorrhizal fungi-associating plants display up 200% more expression double genetic variation associated benefits plant fitness. Moreover, discover these arise primarily from tandem duplications >2-times genome-wide, indicating continuously supply allowing fine-tuning throughout evolution. One-Sentence Summary arising underpin fitness effects

Язык: Английский

Процитировано

0
A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication DOI Creative Commons
John T. Davis,

Qionghou Li,

Christopher J. Grassa

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 22, 2024

Abstract The Streptanthoid complex, a clade of primarily Streptanthus and Caulanthus genera in the Thelypodieae tribe (Brassicaceae) is an emerging model system for ecological evolutionary studies. This Complex spans full range California Floristic Province including desert, foothill, mountain environments. ability these related species to radiate into dramatically different environments makes them desirable study subject exploring how plant expand their ranges adapt new over time. Ecological studies this complex have revealed fascinating variation serpentine soil adaptation, defense compounds, germination, flowering, life history strategies. Until now lack available genomic resources has hindered relate phenotypic observations underlying genetic molecular mechanisms. To help remedy situation we present here chromosome-level genome assembly diversifolius , member Complex, developed using Illumina, Hi-C, HiFi sequencing technologies. Construction also provides further evidence support previously reported recent whole duplication unique tribe. may provided individuals arsenal rapidly throughout occupy commonly inhospitable soils.

Язык: Английский

Процитировано

0
Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus DOI Creative Commons

Weiqi Sun,

Mengdi Li, Jianbo Wang

и другие.

BMC Plant Biology, Год журнала: 2024, Номер 24(1)

Опубликована: Июнь 8, 2024

Abstract Plant polyploidization increases the complexity of epigenomes and transcriptional regulation, resulting in genome evolution enhanced adaptability. However, few studies have been conducted on relationship between gene expression epigenetic modification different plant tissues after allopolyploidization. In this study, we studied DNA methylation patterns four (stems, leaves, flowers siliques) Brassica napus its diploid progenitors. On basis, alternative splicing cis - trans regulation B. progenitors were also analyzed. It can be seen that number occurs is higher than progenitors, IR type most during allopolyploidy. addition, fate changes duplicated genes allopolyploidization . We found conserved, but neofunctionalization specialization large. The genetic was classified according to five replication types (WGD, PD, DSD, TD, TRD). This study analyzed generational transmission analysis patterns. Our provides a reference for differentiation

Язык: Английский

Процитировано

0
Regulatory Subfunctionalization drives OXPHOS evolution in teleosts DOI Open Access
Ανδρέας Τσιπουρλιάνος,

JCR Cardoso,

Rafael Angelakopoulos

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 30, 2024

Abstract Oxidative phosphorylation (OXPHOS) supplies over 90% of the cellular ATP requirements through orchestrated function five multiprotein complexes located in inner mitochondrial membrane. The study explores how evolutionary constraints imposed by indispensable OXPHOS guide outcome Whole Genome Duplication (WGD) events. Two teleosts, gilthead seabream ( Sparus aurata ) and European seabass Dicentrarchus labrax ), which have undergone three rounds WGDs were used as models gene expression was assessed during highly plastic energy-demanding period early development. Fish ontogeny is a unique fish life marked with dramatic changes morphology, physiology, metabolism behavior. tightly regulated landscape cell divisions, migrations differentiation driving these demands high energy supplies. discovery 24 22 families genome, respectively, subsequent phylogenetic analysis showed most cases divergence from common ancestor at base teleost lineage, process attributed to teleost-specific WGD. Overall results indicate that WGD events resulted retention paralogue genes species- or lineage-specific losses. levels compared following RNA sequencing within between distinct developmental stages seabass. Different patterns paralogs revealed; some dosage balance, others expressed only particular stage(s) lot them differentially stages. Differences both number location SNPs revealed paralogs, after merging data whole genome data. A considerable mutations mapped UTRs mostly synonymous substitutions identified CDS. ratio non-synonymous when comparing CDS variants neutral positions while are subject purifying selection, safeguarding protein structural integrity and/or function. Overall, regulatory subfunctionalization appeared mechanism behind genomes favor ontogenetic plasticity.

Язык: Английский

Процитировано

0
Advancing plant biology through deep learning-powered natural language processing DOI
Shuang Peng, Loïc Rajjou

Plant Cell Reports, Год журнала: 2024, Номер 43(8)

Опубликована: Авг. 1, 2024

Язык: Английский

Процитировано

0
Genomic correlates of vascular plant reproductive complexity and the uniqueness of angiosperms DOI
Andrew B. Leslie, Luke Mander

New Phytologist, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 29, 2024

Summary Whole genome duplication (WGD) likely plays an important role in plant macroevolution, and has been implicated diversification rate shifts, structural innovations, increased disparity. But the general effects of WGD are challenging to evaluate, part due difficulty directly comparing morphological patterns across disparate clades. We explored relationships between evolution reproductive complexity vascular plants using a metric based on number types. used multiple regression models evaluate relative importance inferred events, size, suite additional variables relating growth habit biology explaining type complexity. was consistent predictor only among angiosperms. Across generally, biology, clade identity, presence bisexual strobili (those that produce microsporangiate megasporangiate organs) were better predictors Angiosperms unique combining frequent polyploidy with high‐reproductive Whether is mechanistically linked floral unclear, but we suggest widespread ultimately facilitated by herbaceous habits early

Язык: Английский

Процитировано

0
Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants DOI Creative Commons
Donat Wulf, Andrea Bräutigam

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 21, 2023

Abstract Gene regulatory networks based on transcription factors control development and environmental responses in plants. Networks calculated by the machine learning algorithm random forest decision tree-based regression for grasses barley, maize, wheat, Brachypodium, sorghum, rice compared with Arabidopsis an alga show substantial conservation. The degree of conservation depends phylogenetic closeness. processes, which are conserved between all species include basic cellular functions while processes also more specific gene ontology terms. In three a carbon concentration mechanism, photorespiration is partially disassociated from photosynthetic regulation. contrast, C4 species, regulation genes associates comparative analyses reveal factors, photosynthesis seed plants but not alga. An analysis pipeline general transfer information small weed commercially relevant presented.

Язык: Английский

Процитировано

0