A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Science China Life Sciences, Journal Year: 2023, Volume and Issue: 66(10), P. 2214 - 2256

Published: March 6, 2023

Language: Английский

---

A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 5, 2023

Abstract As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to complex routes of origin and migration, suggesting possible omission some population-specific sequences in current genome. Conversely, pangenome is collection all DNA contains shared by individuals (core genome) also able display sequence information unique each individual (variable genome). The progress research humans, plants proved missing components identification large structural variants (SVs) can be explored through pangenomic studies. Many specific shown related biological adaptability, phenotype important economic traits. maturity technologies methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic reference-free assembly will further promote development pangenome. In future, combined with long-read data multi-omics help resolve SVs their relationship main traits interest domesticated animals, providing better insights into animal domestication, evolution breeding. this review, we mainly discuss how analysis reveals variations (sheep, cattle, pigs, chickens) impacts on phenotypes contribute understanding diversity. Additionally, go potential issues future perspectives livestock poultry.

Language: Английский

---

Technology-enabled great leap in deciphering plant genomes

Nature Plants, Journal Year: 2024, Volume and Issue: 10(4), P. 551 - 566

Published: March 20, 2024

Language: Английский

---

Plant pangenomes for crop improvement, biodiversity and evolution

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(8), P. 563 - 577

Published: Feb. 20, 2024

Language: Английский

---

Evolutionary dynamics of mitochondrial genomes and intracellular transfers among diploid and allopolyploid cotton species

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: Jan. 10, 2025

Plant mitochondrial genomes (mitogenomes) exhibit extensive structural variation yet extremely low nucleotide mutation rates, phenomena that remain only partially understood. The genus Gossypium, a globally important source of cotton, offers wealth long-read sequencing resources to explore mitogenome and plastome dynamics accompanying the evolutionary divergence its approximately 50 diploid allopolyploid species. Here, we assembled 19 mitogenomes from Gossypium species, representing all genome groups (diploids A through G, K, allopolyploids AD) based on uniformly applied strategy. graph-based assembly method revealed more alternative conformations than previously recognized, some which confirmed structure reported in earlier studies cotton. Using data, quantified mediated by recombination events between repeats, phylogenetically informative variants were noted. Nucleotide substitution rate comparisons coding non-coding regions rates across entire mitogenome. Genome-wide mapping nuclear organellar DNA transfers (NUOTs) nonrandom distribution genome. In fate NUOT varied, with mitochondrion-to-nucleus transfer (NUMT) predominantly retained as short fragments genome, plastid sequences integrated into nucleus. Phylogenetic relationships inferred using different data sets highlighted distinct histories among these cellular compartments, providing ancillary evidence relevant history Gossypium. comprehensive analysis demonstrates complex reveals three throughout cotton genus. findings enhance our general understanding evolution, comparative inter-compartment genomic integration.

Language: Английский

---

Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Summary Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within among species, as well the roles host genes non‐coding RNAs in transposition process, remain elusive. With advancements large‐scale pan‐genome sequencing development open data sharing, comparative genomics studies have become feasible. Here, we performed complete de novo TE annotations identified active TEs 310 plant assemblies across 119 species seven crop populations. Using 811 high‐quality genomes, detected 13 844 553 TE‐induced structural variants (TE‐SVs), providing unprecedented resolution delineating activities. Our integrative analysis revealed a mutual evolutionary relationship between genomes. On one hand, ncRNAs involved evidenced by colocalization coactivation with TEs, may play role chromatin regulation. other drive genetic innovation promoting duplication inserting into regulatory regions. Moreover, influenced linked to growth, nutrient absorption, storage metabolism environmental adaptation, aiding domestication adaptation. This atlas not only reveals functional features activity but also highlights paving way for future exploration TE‐mediated evolution improvement strategies.

Language: Английский

---

Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(11), P. 1987 - 1997

Published: Oct. 16, 2023

Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic gene expression between coresident subgenomes polyploids remains to be understood. Here we document the fiber development allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 modules that control staged uncover components governing their partitioned relative subgenomic duplicated (homoeologs). Only about 30% quality-related homoeologs show phenotypically favorable allele aggregation cultivars, highlighting potential for subgenome additivity improvement. envision a genome-enabled breeding strategy, with particular attention 48 alleles related phenotypes have been subjected purifying selection during domestication. Our work delineates highlights coordination underpinning polyploid plants.

Language: Английский

---

From genome size to trait evolution during angiosperm radiation

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(10), P. 728 - 735

Published: Aug. 14, 2023

Language: Английский

---

A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification

Plant Communications, Journal Year: 2024, Volume and Issue: 5(2), P. 100791 - 100791

Published: Jan. 1, 2024

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns organ development. Here we report a graph-based pan-genome B. constructed high-quality genome assemblies different morphotypes. harbors over 200 structural variant (SV) hotspot regions enriched auxin and flowering-related genes. Population genomic analyses reveal that early focused on leaf or stem Gene flows resulting from agricultural practices variety improvement are detected among Selective sweep identify an auxin-responsive SAUR gene CLE family as crucial players the leaf-stem differentiation during stage domestication, BoKAN1 instrumental shaping leafy heads cabbage Brussels sprouts. Our functional further discover variations BoFLC2 play key roles divergence vernalization flowering characteristics morphotypes, first intron BoFLC3 involved fine-tuning process cauliflower. This study provides comprehensive understanding sheds light differential development this globally important crop species.

Language: Английский

---

Time-Course Transcriptomics Analysis Reveals Molecular Mechanisms of Salt-Tolerant and Salt-Sensitive Cotton Cultivars in Response to Salt Stress

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(1), P. 329 - 329

Published: Jan. 2, 2025

Salt stress is an environmental factor that limits plant seed germination, growth, and survival. We performed a comparative RNA sequencing transcriptome analysis during germination of the seeds from two cultivars with contrasting salt tolerance responses. A transcriptomic comparison between salt-tolerant cotton cv Jin-mian 25 salt-sensitive Su-mian 3 revealed both similar differential expression patterns genotypes stress. The genes related to aquaporins, kinases, reactive oxygen species (ROS) scavenging, trehalose biosynthesis, phytohormone biosynthesis signaling include ethylene (ET), gibberellin (GA), abscisic acid (ABA), jasmonic (JA), brassinosteroid (BR) were systematically investigated cultivars. Despite involvement these in cotton’s response positive or negative ways, their levels mostly genotypes. Interestingly, PXC2 gene (Ghir_D08G025150) was identified, which encodes leucine-rich repeat receptor-like protein kinase (LRR-RLK). This showed induced pattern after treatment but not 3. Our multifaceted approach illustrated cotton.

Language: Английский

---