Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: 51(1), P. 1 - 2
Published: Jan. 1, 2024
Language: Английский
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(5)
Published: March 24, 2024
Abstract Tools for visualizing genomes are essential investigating genomic features and their interactions. Currently, tools designed originally animal mitogenomes plant plastomes used to visualize the mitogens of plants but cannot accurately display specific mitogenomes, such as nonlinear exon arrangement genes, prevalence functional noncoding complex chromosomal architecture. To address these problems, a software package, mitochondrial genome map (PMGmap), was developed using Python programming language. PMGmap can draw genes at levels; cis‐ trans‐splicing gene maps, repetitive sequences; scale genic regions by scaling on mitogenome (SAGM) algorithm. It also multiple chromosomes simultaneously. Compared with other state‐of‐the‐art tools, showed better performance in 405 showing potential an invaluable tool research. The web container versions source code be accessed through following link: http://www.1kmpg.cn/pmgmap .
Language: Английский
Citations
25
Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown
Published: July 1, 2024
Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles chromosomal segments that are identical descent, to understand kinship, migration patterns, population dynamics. Within forensic science, investigative genetic (FIGG) has gained prominence leveraging next-generation sequencing technologies population-specific genomic resources, opening new avenues. In this review, we synthesize current knowledge, underscore recent advancements, discuss growing role of FIGG in genomics. been pivotal revitalizing dormant inquiries offering leads numerous cold cases. Its effectiveness relies on extensive SNP profiles contributed individuals from diverse specialized databases. Advances computational genomics growth databases have spurred a profound shift application across forensics, anthropology, DNA studies. As field progresses, is evolving nascent practice more sophisticated discipline, shaping future investigations.
Language: Английский
Citations
12
Plant Communications, Journal Year: 2024, Volume and Issue: unknown, P. 100856 - 100856
Published: March 1, 2024
Actinidia arguta, the most widely distributed and second cultivated species within genus, has distinguished difference from current kiwifruit in biological characters like small smooth fruit, rapid-softening excellent cold tolerance. Knowledge of adaptive evolution tetraploid genetic basis its important agronomic traits is still unclear. A chromosome-scale genome assembly an autotetraploid male A. arguta been generated. The was 2.77 Gb length with a contig N50 9.97Mb anchored into 116 pseudo-chromosomes. Resequencing clustering 101 geographically representative accessions showed they could be divided two geographical groups, Southern Northern Groups, which first diverged 12.9 Mya ago. underwent prominent expansions one demographic bottleneck mid-Pleistocene climate transition (MPT) to late-Pleistocene. Population genomics study using paleoclimate data allow us discern adaptation different historical environments. Three genes (AaCEL1, AaPME1 AaDOF1) have identified by multi-omics verified their accelerating softening flesh through transient assay. set localized sex chromosome (Chr3), or autosomal chromosomes are biasedly expressed during stamen carpel development, characteristically regulate sexual dimorphism. This at level detail uncover related paves way facilitate functional improvement arguta.
Language: Английский
Citations
9
Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: 51(5), P. 517 - 530
Published: Oct. 11, 2023
Tibeto-Burman (TB) people have endeavored to adapt the hypoxic, cold, and high-UV high-altitude environments in Tibetan Plateau complex disease exposures lowland rainforests since late Paleolithic period. However, full landscape of genetic history biological adaptation geographically diverse TB-speaking people, as well their interaction mechanism remain unknown. We generate a whole-genome meta-database 500 individuals from 39 populations East Asia Southeast present comprehensive diversity, admixture history, differentiated adaptative features different people. identify differentiation related geography language among consistent with process incoming or indigenous ancestral source populations. A robust connection between Tibetan-Yi corridor ancient Yellow River supports Northern China origin hypothesis. finally report substructure-related signatures highland Tibetans Loloish speakers. Adaptative associated physical pigmentation (EDAR SLC24A5) metabolism (ALDH9A1) are identified which differed architecture Tibetan. TB-related genomic resources provide new insights into basis better reference for anthropologically-informed sampling design biomedical cohort research.
Language: Английский
Citations
20
Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown
Published: April 1, 2024
Language: Английский
Citations
4
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 25(1)
Published: May 27, 2024
Abstract The improvement and decreasing costs of third‐generation sequencing technologies has widened the scope biological questions researchers can address with de novo genome assemblies. With increasing number reference genomes, validating their integrity minimal overhead is vital for establishing confident results in applications. Here, we present Klumpy, a tool detecting visualizing both misassembled regions assembly genetic elements (e.g. genes) interest set sequences. By leveraging initial raw reads combination respective assembly, illustrate Klumpy's utility by investigating antifreeze glycoprotein ( afgp ) loci across two icefishes, searching reported absent gene northern snakehead fish, scanning genomes mudskipper bumblebee regions. In former cases, were able to provide support noncanonical placement an locus icefishes locate missing gene. Furthermore, our scans identify unmappable putative repetitive element shared among several species bees.
Language: Английский
Citations
4
GigaScience, Journal Year: 2025, Volume and Issue: 14
Published: Jan. 1, 2025
Abstract Background The genus Ormosia belongs to the Fabaceae family; almost all species are endemic China, which is considered one of centers this genus. Thus, genomic studies on needed better understand evolution and ensure conservation utilization these species. We performed a chromosome-scale assembly O. purpureiflora updated assemblies emarginata semicastrata for comparative genomics. Findings genome sizes 3 ranged from 1.42 1.58 Gb, with being largest. Repetitive sequences accounted 74.0–76.3% genomes, predicted gene counts 50,517 55,061. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis indicated 97.0–98.4% completeness, whereas long terminal repeat (LTR) index values 13.66 17.56, meeting “reference genome” quality standard. Gene assessed using BUSCO OMArk, 95.1% 96.3% 97.1% 98.1%, respectively. Characterizing architectures further revealed that inversions were main structural rearrangements in Ormosia. In numbers, density distributions repetitive elements types Helitron inverted (TIR) Gypsy unknown LTR retrotransposons (LTR-RTs) concentrated different regions chromosomes, Copia LTR-RTs generally evenly distributed along chromosomes Compared sister Lupinus albus, had lower numbers percentages resistance (R) genes transcription factor genes. Genes related alkaloid, terpene, flavonoid biosynthesis found be duplicated through tandem or proximal duplications. Notably, some associated growth defense absent purpureiflora. By resequencing 153 genotypes (∼30 Gb data per sample) 6 (sub)populations, we identified 40,146 single nucleotide polymorphisms. Corresponding its very small populations, exhibited low genetic diversity. Conclusions provide valuable resources studying evolution, conservation, potential utility both
Language: Английский
Citations
0
BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)
Published: Aug. 8, 2023
Abstract Background Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) natural diploid–autotetraploid species. We generated an allele-aware autotetraploid genome, chimeric chromosome-level diploid resequencing data 106 individuals at average depth of 60 × per individual, along with 12 90 individual. Results Autotetraploid C. had 64 chromosomes clustered into 16 homologous groups, majority demonstrated similar chromosome length, gene numbers, expression. The regions synteny, variation nonalignment to genome accounted 81.3%, 8.8% 9.9% respectively. Our analyses identified 20,626 genes (69.18%) four alleles 9191 (30.82%) one, two, or three alleles, suggesting post-polyploid allelic loss. Genes loss were found more often proximity within variations exhibited marked overlap transposable elements. Additionally, such showed reduced tendency interact other genes. also 102 than copies their expression levels significantly higher counterparts. These enriched enzymes involved stress response plant defense, potentially contributing evolutionary success autotetraploids. population suggested single origin autotetraploids recent divergence (~ 0.57 Mya) from diploids, minimal interploidy admixture. Conclusions results indicate potential reorganization, which may contribute .
Language: Английский
Citations
7
Advanced Science, Journal Year: 2024, Volume and Issue: unknown
Published: Sept. 4, 2024
Abstract Fokienia hodginsii ( F . ), belonging to the genus of Cupressaceae. has significant application value due its wood properties and great research in evolutionary studies as a gymnosperm. However, genome remains unknown large size gymnosperms genome. Pacific Bioscience sequencing, Hi‐C mapping, whole‐genome Bisulfite Sequencing (BS‐Seq), long‐read isoform sequencing (Iso‐Seq), direct RNA (DRS), quantitative proteomics, metabonomics analysis are employed facilitate assembly, gene annotation, investigation into epigenetic mechanisms. In this study, 10G is assembled 11 chromosomes. Furthermore, 50 521 protein‐coding genes annotated determined that 65% comprises repetitive sequences. It discovered transposable element (TE)‐including introns associated with higher expression. The DNA methylome reveals xylem methylation level compared callus. Moreover, DRS alterations full‐length ratio, which potentially poly(A) length (PAL) alternative polyadenylation (APA). Finally, morphology measurement revealed difference 14 cultivars. summary, genomes epigenetics datasets provide molecular basis for callus formation gymnosperm family.
Language: Английский
Citations
2
Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown
Published: Nov. 1, 2024
Language: Английский
Citations
2