Genome evolution and diversity of wild and cultivated potatoes

Nature, Journal Year: 2022, Volume and Issue: 606(7914), P. 535 - 541

Published: June 8, 2022

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have potential to revolutionize future potato production1-4. So far, relatively few studies examined genome evolution diversity wild cultivated landrace potatoes, which limits application their breeding. Here we assemble 44 high-quality genomes from 24 20 accessions that representative Solanum section Petota, tuber-bearing clade, as well 2 neighbouring section, Etuberosum. Extensive discordance phylogenomic relationships suggests complexity evolution. We find substantially expanded its repertoire disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative effect tuber-based propagation strategies genome. discover a transcription factor determines tuber identity interacts mobile tuberization inductive signal SP6A. also identify 561,433 high-confidence structural variants construct map large inversions, provides insights for improving inbred lines precluding linkage drag, exemplified by 5.8-Mb inversion associated carotenoid content tubers. This study will accelerate enrich our understanding biology global staple crop.

Language: Английский

---

The Chinese pine genome and methylome unveil key features of conifer evolution

Cell, Journal Year: 2021, Volume and Issue: 185(1), P. 204 - 217.e14

Published: Dec. 28, 2021

Conifers dominate the world's forest ecosystems and are most widely planted tree species. Their giant complex genomes present great challenges for assembling a complete reference genome evolutionary genomic studies. We 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) revealed that its size is mostly attributable to huge intergenic regions long introns with high transposable element (TE) content. Large genes exhibited higher expressions levels. Despite lack recent whole-genome duplication, 91.2% were duplicated through dispersed expanded gene families mainly related stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network distinct compared angiosperms. Slow removal TEs high-level methylation have contributed expansion. This study provides insights into conifer evolution resources advancing research on adaptation development.

Language: Английский

---

NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: April 26, 2024

Long-read sequencing data, particularly those derived from the Oxford Nanopore platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient correction and assembly tool for noisy long reads, which achieves a level of accuracy in genome assembly. We apply NextDenovo assemble 35 diverse human genomes around world using long-read data. These allow us identify landscape segmental duplication gene copy number variation modern populations. The use should pave way population-scale

Language: Английский

---

An efficient error correction and accurate assembly tool for noisy long reads

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

Published: March 12, 2023

Abstract Long read sequencing data, particularly those derived from the Oxford Nanopore (ONT) platform, tend to exhibit a high error rate. Here, we present NextDenovo, highly efficient correction and assembly tool for noisy long reads, which achieves level of accuracy in genome assembly. NextDenovo can rapidly correct reads; these corrected reads contain fewer errors than other comparable tools are characterized by chimeric alignments. We applied quality reference genomes 35 diverse humans across world using ONT data. Based on de novo assemblies, were able identify landscape segmental duplications gene copy number variation modern human population. The use program should pave way population-scale long-read assembly, thereby facilitating construction pan-genomes,

Language: Английский

---

The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights

Cell, Journal Year: 2023, Volume and Issue: 186(6), P. 1279 - 1294.e19

Published: March 1, 2023

Antarctic krill (Euphausia superba) is Earth’s most abundant wild animal, and its enormous biomass vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level genome, whose large genome size appears have resulted from inter-genic transposable element expansions. Our assembly reveals molecular architecture of circadian clock uncovers expanded gene families associated with molting energy metabolism, providing insights into adaptations cold highly seasonal environment. Population-level re-sequencing four geographical sites around continent no clear population structure but highlights natural selection environmental variables. An apparent drastic reduction in 10 mya subsequent rebound 100 thousand years ago coincides climate change events. findings uncover genomic basis provide valuable resources for future research.

Language: Английский

---

Diversity and evolution of the vertebrate chemoreceptor gene repertoire

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

Published: Feb. 15, 2024

Abstract Chemoreception – the ability to smell and taste is an essential sensory modality of most animals. The number type chemical stimuli that animals can perceive depends primarily on diversity chemoreceptors they possess express. In vertebrates, six families G protein-coupled receptors form core their chemosensory system, olfactory/pheromone receptor gene OR , TAAR V1R V2R T1R T2R . Here, we study vertebrate chemoreceptor repertoire its evolutionary history. Through examination 1,527 genomes, uncover substantial differences in composition across vertebrates. We show are co-evolving, highly dynamic, characterized by lineage-specific expansions (for example, tetrapods; teleosts; mammals; amphibians) losses. Overall, amphibians, followed mammals, clades with largest repertoires. While marine tetrapods feature a convergent reduction numbers, genes correlates habitat mammals birds migratory behavior birds, diet aquatic environment fish.

Language: Английский

---

A 160 Gbp fork fern genome shatters size record for eukaryotes

iScience, Journal Year: 2024, Volume and Issue: 27(6), P. 109889 - 109889

Published: May 31, 2024

Vascular plants are exceptional among eukaryotes due to their outstanding genome size diversity which ranges ∼2,400-fold, including the largest so far recorded in angiosperm

Language: Английский

---

Evolutionary study and structural basis of proton sensing by Mus GPR4 and Xenopus GPR4

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

---

Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

Water Biology and Security, Journal Year: 2021, Volume and Issue: 1(1), P. 100002 - 100002

Published: Nov. 22, 2021

Fish biology has been developed for more than 100 years, but some important breakthroughs have made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent mostly focused genetics, molecular biology, genomics, genome biotechnologies, which provided a solid foundation enhancing aquaculture to ensure food security improving aquatic environments sustain ecosystem health. Here, we review research advances five major areas: (1) biological innovations genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid Asian cyprinid fishes; (2) evolutionary fates consequences natural polyploid (3) domestication selection; (4) development innovation breeding biotechnologies; (5) applicable approaches potential genetic biotechnologies. Moreover, precision biotechniques are examined discussed detail gene editing introgression or removal beneficial detrimental alleles, use sex-specific markers production mono-sex populations, controllable primordial germ cell on-off strategy producing sterile offspring, surrogate broodstock-based strategies accelerate breeding, incorporation sexual regain-based approach create synthetic polyploids. Based these scientific technological advances, propose blueprint improvement new breed creation species analyze seed industry strengthening security.

Language: Английский

---

Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

Cell, Journal Year: 2021, Volume and Issue: 184(5), P. 1377 - 1391.e14

Published: Feb. 5, 2021

Language: Английский

---