Genome Size Research Articles

Assembly and Annotation of the Tetraploid Salsola tragus (Russian thistle) Genome.

This report presents two phased chromosome-scale genome assemblies of allotetraploid Salsola tragus (2n=4x=36) and fills the current genomics resource gap for this species. Flow cytometry estimated 1C genome size was 1.319 Gbp. PacBio HiFi reads were assembled and scaffolded with Hi-C chromatin contact mapping and Bionano optical mapping data. For annotation, a PacBio Iso-Seq library was generated from root, stem, leaf, and floral tissues followed by annotation using a modified Maker pipeline. The assembled haploid S. tragus genomes contained 18 chromosomes each, with 9 chromosomes assigned to subgenome A and 9 chromosomes to subgenome B. Each haplome assembly represented 95% of the total flow cytometry estimated genome size. Haplome 1 and haplome 2 contained 43,354 and 42,221 annotated genes, respectively. The availability of high-quality reference genomes for this economically important weed will facilitate future omics analysis of S. tragus and a better understanding of chenopod plants.

ZW sex chromosome differentiation in paleognathous birds is associated with mitochondrial effective population size but not mitochondrial genome size or mutation rate.

Eukaryotic genome size varies considerably, even among closely related species. The causes of this variation are unclear, but weak selection against supposedly costly "extra" genomic sequences has been central to the debate for over 50 years. The mutational hazard hypothesis, which focuses on the increased mutation rate to null alleles in superfluous sequences, is particularly influential, though challenging to test. This study examines the sex chromosomes and mitochondrial genomes of 15 flightless or semi-flighted paleognathous bird species. In this clade, the non-recombining portion of the W chromosome has independently expanded stepwise in multiple lineages. Given the shared maternal inheritance of the W chromosome and mitochondria, theory predicts that mitochondrial effective population size (Ne) should decrease due to increased Hill-Robertson Interference in lineages with expanded non-recombining W regions. Our findings support the extent of the non-recombining W region with three indicators of reduced selective efficiency: (1) the ratio of non-synonymous to synonymous nucleotide changes in the mitochondrion, (2) the probability of radical amino acid changes, and (3) the number of ancient, W-linked genes lost through evolution. Next, we tested whether reduced Ne affects mitochondrial genome size, as predicted by weak selection against genome expansion. We find no support for a relationship between mitochondrial genome size and expanded non-recombining W regions, nor with increased mitochondrial mutation rates (predicted to modulate selective costs). These results highlight the utility of non-recombining regions and mitochondrial genomes for studying genome evolution and challenge the general idea of a negative relation between the efficacy of selection and genome size.

Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication.

Ornamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. (Hydrangeaceae), and are valued in gardens, households and landscapes across the globe. The phenotypic diversity of hortensia cultivars, hybrids and wild relatives is mirrored by their genomic variation, with differences in genome size, base chromosome numbers and ploidy level. We aim to understand the genomic and chromosomal basis of hortensia genome variation. Therefore, we analysed six hortensias with different origins and chromosomal setups for repeatome divergence, the genome fraction with the highest sequence turnover. This holds information from the hortensias' evolutionary paths and can guide breeding initiatives. We compiled a hortensia genotype panel representing members of the sections Macrophyllae, Hydrangea, Asperae and Heteromallae and reconstructed a plastome-based phylogenetic hypothesis as the evolutionary basis for all our analyses. We comprehensively characterized the repeatomes by whole-genome sequencing and comparative repeat clustering. Major tandem repeats were localized by multicolour FISH. The Hydrangea species show differing repeat profiles reflecting their separation into the two major Hydrangea clades: diploid Hydrangea species from Japan show a conserved repeat profile, distinguishing them from Japanese polyploids as well as Chinese and American hortensias. These results are in line with plastome-based phylogenies. The presence of specific repeats indicates that H. paniculata was not polyploidized directly from the common ancestor of Japanese Hydrangea species, but evolved from a distinct progenitor. Major satellite DNAs were detected over all H. macrophylla chromosomes. Repeat composition among the Hydrangea species varies in congruence with their origins and phylogeny. Identified species-specific satDNAs may be used as cytogenetic markers to identify Hydrangea species and cultivars, and to infer parental species of old Hydrangea varieties. This repeatome and cytogenetics information helps to expand the genetic toolbox for tracing hortensia evolution and guiding future hortensia breeding.

Genome size variation and whole-genome duplications in the monocot order Poales

Nuclear genome sizes of 54 representative species from 44 genera of the monocot order Poales were investigated by flow cytometry. Small holoploid genomes with < 2 pg/2C are characteristic of the Poales; only some families have larger 2C values, although this is not consistently the case. The sizes of monoploid genomes as well as mean DNA content per chromosome (MC) show a similar pattern. A comparison of the genome size data with current molecular phylogenetic data suggests that small monoploid genomes (1Cx < 0.4 pg) and small chromosomes (MC ≤ 0.05 pg), as found in some families, are likely the ancestral features of the order Poales. Conspicuous increases in genome size occurred particularly in the Poaceae (grasses) and to a lesser extent in the xyrid clade and the Restionaceae. According to previous phylogenomic studies, the Poaceae are characterized by a whole-genome duplication (WGD) called ρ, which is absent in all other Poales families. However, it is clear from the 1Cx values that the ρ event is not, or no longer, associated with a significant increase in the minimum 1Cx genome sizes of grasses compared to other Poales families. Future studies need to clarify whether the smallest 1Cx values in the Poaceae are due to a secondary reduction of the nuclear genome after the ρ event and whether the relatively large minimal 1Cx values of the xyrid clade were caused by a further WGD within Poales.

New insights into interspecies relationships, chromosomal evolution, and hybrid identification in the Lycoris Herb.

BackgroundFrequent interspecific hybridization, unclear genetic backgrounds, and ambiguous evolutionary relationships within the genus Lycoris pose significant challenges to the identification and classification of hybrids, thereby impacting the application and development of Lycoris. This study utilizes karyotype structure, genome size, and fluorescent in situ hybridization (FISH) technology to explore the chromosomal evolution and hybrid identification of Lycoris employing three approaches at the cytogenetic level.ResultsThe findings indicate that species with a smaller basic chromosome number exhibit less asymmetry than those with a larger basic chromosome number, suggesting that species with different basic chromosome numbers may have followed different evolutionary pathways. Lycoris aurea has a more symmetrical karyotype, which may be the plesiomorphic state, reflecting an evolutionary transition from symmetry to asymmetry in Lycoris chromosomes. Systematic clustering of 18 Lycoris species is consistent with chromosomal karyotype classification, primarily dividing into two groups: species with M + T + A type an M + T type as one group, and A type as another group. The average nuclear genome size (C-value) of the Lycoris genus is 22.99 Gb, with the smallest genome being that of L. wulingensis (17.10 Gb) and the largest being L. squamigera (33.06 Gb). Chromosome length is positively correlated with the C-value, and the haploid genome size (Cx-value) decreases with an increase in basic chromosome number (x). The FISH technique can quickly identify and authenticate artificial hybrids, thus inferring the parentage of natural hybrids.ConclusionThe study reveals the genetic background and interspecific relationships of 18 Lycoris species, identifies the authenticity of artificial Lycoris hybrids, and infers the possible parentage of natural hybrids, offering technical insights for the identification, classification, and genomic projects of Lycoris.

Evolutionary diversification and succession of soil huge phages in glacier foreland

BackgroundHuge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes.ResultsHere, we conduct a size-fractioned (< 0.22 μm) metagenomic analysis across a 130-year chronosequence of a glacier foreland in the Tibetan Plateau and discovered 412 novel viral operational taxonomic units (vOTUs) of huge phages. The phylogenomic and gene-shared network analysis gained insights into their unique evolutionary history compared with smaller phages. Their communities in glacier foreland revealed a distinct pattern between the early (≤ 41 years) and late stages (> 41 years) based on the macrodiveristy (interspecies diversity) analysis. A significant increase in the diversity of huge phages communities following glacier retreat were observed according to current database. The phages distributed across sites within late stage demonstrated a remarkable higher microdiversity (intraspecies diversity) compared to other geographic range such as the intra early stage, suggesting that glacial retreat is key drivers of the huge phage speciation. Alongside the shift in huge phage communities, we also noted an evolutionary and functional transition between the early and late stages. The identification of abundant CRISPR-Cas12 and type IV restriction-modification (RM) systems in huge phages indicates their complex mechanisms for adaptive immunity.ConclusionsOverall, this study unravels the importance of climate change in shaping the composition, evolution, and function of soil huge phage communities, and such further understanding of soil huge phages is vital for broader inclusion in soil ecosystem models.36NkSuBhymqeFDHZtwigi8Video

A chromosome-level genome assembly of Meteorus pulchricornis Wesmael (Hymenoptera: Braconidae)

Meteorus pulchricornis Wesmael (Hymenoptera: Braconidae) is an important parasitoid of lepidopteran insects. So far, only three scaffold-level genomes have been published for the genus Meteorus. In this study, we present a high-quality, chromosome-level genome assembly of M. pulchricornis, characterized by high accuracy and contiguity. This assembly was achieved using Oxford Nanopore Technologies long-read, MGI-SEQ short-read, and Hi-C sequencing methods. The final assembly was 158.5 Mb in genome size, with 153.8 Mb (97.03%) assigned to ten pseudochromosomes. The scaffold N50 length reached 17.51 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 99.3%. The genome contains 28.29 Mb of repetitive elements, accounting for 18.39% of the total genome size. We identified 12,342 protein-coding genes, of which 12,308 genes were annotated functionally. Our investigation into gene family evolution in M. pulchricornis showed that 563 gene families expanded, 1,739 contracted, and 58 underwent rapid evolution. The high-quality genome assembly we report here is advantageous for further research on parasitoid wasps and provides a foundational data resource for natural enemy studies.

Chromosome-level genome assembly of Cyperus iria, an aggressive weed of rice

Cyperus iria is an aggressive weed of rice throughout the world. Until now, the reference genome of C. iria has not been published. Here, we completed the chromosome-level genome assembly of C. iria based on Illumina, PacBio and Hi-C reads. The assembled genome size of C. iria was 479.08 Mb with a contig N50 of 7.02 Mb. 68 pseudochromosomes were produced using Hi-C scaffolding, accounting for 99.65% of the assembled genome. The number of predicted protein-coding genes is 47,395, of which 93.26% were annotated, and 37.69% repetitive sequences were identified. Our study provided a valuable genomic resource for the molecular biology research and the management of C. iria.

A near-complete genome assembly of Cinchona calisaya

Rubiaceae plants are globally widespread and possess significant economic and medicinal value. Such as the globally important crop of coffee, and Cinchona calisaya Wedd., which is rich in alkaloids, is an important medicinal resource for treating malaria. In recent years, several genome resources of Rubiaceae have been reported. However, the comprehensive phylogenetic relationships of Rubiaceae are still unknown. In this study, we present a nearly complete diploid genome assembly of C. calisaya, characterized by a genome size of 869.93 Mb, and contig N50 length of 44.34 Mb. Notably, 99.75% of the sequences have been successfully anchored to 17 chromosomes, with only 12 gaps remaining. BUSCO assessment indicates that 97.40% of complete core genes are present in the assembly. We identified a total of 42,741 protein-coding genes, among which 38,022 (89.00%) have received functional annotation. The high continuity and integrity of the C. calisaya genome provide a robust foundation for functional genomics research, varietal improvement, and the conservation of genomic resources in medicinal plants.

De novo genome assembly and annotations of Bombus lapidarius and Bombus niveatus provide insights into the environmental adaptability

Bumblebees are ubiquitous, cold-adapted, primitively eusocial bees and important pollinators for crops and vegetation. However, many species are declining worldwide due to multiple factors, including human-induced habitat loss, agricultural chemicals, global warming, and climate change. In particular, future climate scenarios predict a shift in the spatial distribution of bumblebees under global warming, with some species declining and others potentially expanding. Here, we report a de novo genome assembly and annotation for Bombus lapidarius and Bombus niveatus to decipher species-specific potential genomic capacity against such environmental stressors. With harboring more than 23,000 protein-coding genes, the assembled genomes of B. lapidarius and B. niveatus are 244.44 Mb (scaffold N50 of 9.45 Mb) and 259.84 Mb (scaffold N50 of 10.94 Mb), respectively, which exhibit similar trends in terms of genome size and composition with other bumblebees. Gene family analysis reveals differences in species-specific expanded gene families. B. lapidarius exhibits expanded genes related to pre/postsynaptic organization, while B. niveatus shows a distinct expansion in gene families regulating cellular growth, aging, and responses to abiotic and biotic stressors, such as those containing SCAN domains, WD-repeats, and Ras-related proteins. Our genome-wide screens revealed positive selection on environmental stress-responsive genes such as dip2, yme1l, and spg7 in B. lapidarius, whereas positive selection signatures were found in genes such as myd88, mybbp1A, and rhau, which are involved in environmental stress resistance for B. niveatus. These high-quality genome assemblies and comparative genome analysis unveil potential drivers that underlie genome evolution in bumblebees, offering valuable insights into environmental adaptation and conservation efforts.

Genomic and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders.

Pardosa spiders, belonging to the wolf spider family Lycosidae, play a vital role in maintaining the health of forest and agricultural ecosystems due to their function in pest control. This study presents chromosome-level genome assemblies for two allied Pardosa species, P. laura and P. agraria. Both species' genomes show a notable expansion of helitron transposable elements, which contributes to their large genome sizes. Methylome analysis indicates that P. laura has higher overall DNA methylation levels compared to P. agraria. DNA methylation may not only aids in transposable element-driven genome expansion but also positively affects the three-dimensional organisation of P. laura after transposon amplification, thereby potentially enhancing genome stability. Genes associated with hyper-differentially methylated regions in P. laura (compared to P. agraria) are enriched in functions related to mRNA processing and energy production. Furthermore, combined transcriptome and methylome profiling has uncovered a complex regulatory interplay between DNA methylation and gene expression, emphasising the important role of gene body methylation in the regulation of gene expression. Comparative genomic analysis shows a significant expansion of cuticle protein and detoxification-related gene families in P. laura, which may improve its adaptability to various habitats. This study provides essential genomic and methylomic insights, offering a deeper understanding of the relationship between transposable elements and genome stability, and illuminating the adaptive evolution and species differentiation among allied spiders.

Chromosome-level genome assembly of the pine wood nematode carrier Arhopalus unicolor

Arhopalus unicolor is a carrier of the pine wood nematode (PWN), which causes pine wilt disease, killing pine trees and causing considerable economic and environmental losses. While the A. unicolor mitochondrial genome has been published, a high-quality genome assembly and annotation of A. unicolor is not yet available. To address this, we assembled a chromosome-level reference genome assembly of A. unicolor with a combination of Illumina, PacBio, and Hi-C sequencing technologies. The final genome size was determined to be 1268.11 Mb, with a GC% of 32.44%, and the scaffold N50 value was 19.30 Mb. A total of 98.77% of the assembled sequences mapped to 10 pseudochromosomes, and BUSCO analysis revealed high completeness, with 97.15% gene coverage. Furthermore, the genome contains 71.74% repeat elements and encompasses 16,450 predicted protein-coding genes. This genome sequence of A. unicolor will be a valuable resource for understanding the genetics and evolutionary history of this species and for developing effective management strategies for this PWN carrier.

Chromosome-level and haplotype-resolved genome assembly of Bougainvillea glabra

Bougainvillea glabra Choisy, a common perennial shrub or climbing vine in tropical and subtropical areas, has significant ornamental and ecological value due to its showy floriferous blooms and adaptability to multiple environmental stresses. In this study, based on PacBio and Hi-C sequencing data, we presented the haplotype-resolved, and chromosome-level assembled genomes for B. glabra (2n = 34). We obtained two haplotypes with genome size of 2,855,692,602 bp and 2,889,511,499 bp, N50 of 165 Mbp and 167 Mbp, and both anchored to 17 chromosomes with anchor ratio of 97.07% and 97.55%, respectively. Through the BUSCO evaluation process, the two assembled haplotypes both exhibited the high score of 96%. By combining the high-confidence different evidence of genome structure annotation pipeline we annotated each haplotype containing ~33,000 predicted genes, of which 86% were functionally annotated by different databases. These high-quality haplotypes assembly and annotation results will serve as a great genomic resource to explore the ornamental traits and environmental adaptability and accelerate improvement in future.

Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs

This research aimed to characterize the mitochondrial genome of the Ghoongroo (GH) pig, a notable breed in India, along with its crossbred varieties, to elucidate their matrilineal components, evolutionary history, and implications for conservation. Seven pigs (5 GH, 2 crossbred, namely Rani and Asha) were sequenced for complete mitochondrial genome, while 24 pigs (11 GH, 6 Rani, and 7 Asha) were sequenced for the complete D-loop of the mitochondrial genome. The genome size of these pigs was determined to be 16,690 bp. Analysis of the mitochondrial sequences and phylogenetics uncovered two distinct matrilineal components within the GH population, a phenomenon also observed in its crossbred counterparts, Rani and Asha. Phylogenetic analysis demonstrated a clear clustering of GH sequences into two clades, indicating the presence of two independent maternal lineages. The phylogenetic study using complete mitogenome also indicated that GH pigs were originated locally from Indian wild boar independently from Asian and European pig population. Haplotype analysis from complete D-loop sequences revealed 10 different haplotypes, with some sequences shared among GH, Rani, and Asha, while others differed due to varying matrilineal origins. The haplotype analysis using complete mitogenome sequences revealed 16 different haplotypes with some shared sequences among GH. Furthermore, examination of tRNA genes and nucleotide composition of different genes namely rRNAs, COX1, COX2, ATP6, ND4, ND5, ND6, Cytb offered insights into genetic diversity within these pigs. The findings suggest that geographical isolation and historical events likely contributed to the emergence of distinct maternal lineages within the GH breed. This study underscores the significance of mitochondrial DNA analysis in uncovering hidden genetic diversity within seemingly uniform populations. The molecular insights gained into the genetic makeup of GH pigs could aid in designing effective breeding programs for conservation efforts and highlight its significance in understanding the broader context of pig domestication in India.

Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis

Phragmites australis is a globally distributed grass species (Poaceae) recognized for its vast biomass and exceptional environmental adaptability, making it an ideal model for studying wetland ecosystems and plant stress resilience. However, genomic resources for this species have been limited. In this study, we assembled a chromosome-level reference genome of P. australis containing one B chromosome. An explosion of LTR-RTs, centered on the Copia family, occurred during the late Pleistocene, driving the expansion of P. australis genome size and subgenomic differentiation. Comparative genomic analysis showed that P. australis underwent two whole gene duplication events, was segregated from Cleistogenes songorica at 34.6 Mya, and that 41.26% of the gene families underwent expansion. Based on multi-tissue transcriptomic data, we identified structural genes in the biosynthetic pathway of pharmacologically active Phragmitis rhizoma polysaccharides with essential roles in rhizome development. This study deepens our understanding of Arundinoideae evolution, genome dynamics, and the genetic basis of key traits, providing essential data and a genetic foundation for wetland restoration, bioenergy development, and plant stress.

Gallibacterium faecale sp. nov., Isolated from Dairy Cow Feces.

A facultative anaerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strain AGMB14963T was isolated from the feces of a dairy cow. A 16S rRNA gene sequence-based phylogenetic analysis revealed that strain AGMB14963T belongs to the genus Gallibacterium, with Gallibacterium salpingitidis F150T being the closest species (95.8% 16S rRNA gene sequence similarity). Whole-genome sequence analysis revealed that strain AGMB14963T had a 37.0% G + C genomic DNA content and a genome size of 2.58Mb. In addition, the strain contained 53 tRNA and 2 rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strains AGMB14963T and G. salpingitidis F150T were 82.3 and 24.9%, respectively. Further, strain AGMB14963T was positive for oxidase and catalase, but negative for urease. Optimal growth of strain AGMB14963T occurred at 37 ℃, pH 8, and in 0.5% NaCl-containing medium. The predominant cellular fatty acids (> 10%) in strain AGMB14963T were C14:0, C16:0, and summed feature 3. Strain AGMB14963T produced lactic acid and isobutyric acid as the major end products of glucose fermentation. Polar lipids consisted of one phospholipid and one phosphoaminolipid. According to the genomic, physiologic, and chemotaxonomic characteristics, strain AGMB14963T represents a novel species of the genus Gallibacterium, for which the name Gallibacterium faecale sp. nov. is proposed. The type strain is AGMB14963T (= KCTC 25487T = NBRC 116419T).

Different Genotypes of the Rare and Threatened Moss Physcomitrium eurystomum (Funariaceae) Exhibit Different Resilience to Zinc and Copper Stress.

The funarioid moss species Physcomitrium eurystomum, which is threatened with extinction, was the subject of this study. The riparian habitat type of this species is often under the influence of contaminated water, and, therefore, we tested the influence of selected potentially toxic elements (PTEs), namely zinc and copper, on the development, physiological features, and survival of the species on two different accessions (German and Croatian). The results obtained showed the different resilience of the two accessions to the PTEs. Flow cytometry analyses revealed that the two accessions differ significantly in terms of genome size. However, the different amplitude of resilience to the tested PTEs, the divergence in physiological responses, and survival within two accessions of the same species are confirmed, as well as the dissimilarity of their genome size, likely associated with ploidy level difference and possibly distinct hybrid origin.

Draft genome sequence of glyphosate-degrading Ochrobactrum sp. strain GPK 3 (VKM B-2554D) isolated from agricultural soil.

The genome of Ochrobactrum sp. isolated from agricultural soil polluted with the herbicide glyphosate is reported. The genome size is 5.48 Mb with an average G + C content of 56.3%. This genomic data could contribute to a better understanding of biochemistry and regulatory mechanisms of microbial degradation of glyphosate and 2-aminoethylphosphonic acid.

Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.)

Riccia sorocarpa Bisch., commonly known as common crystalwort, is a plant belonging to the Marchantiales order with a cosmopolitan distribution among a wide range of habitats: fields, gardens, waste ground, on paths, cliff tops, and thin soil over rocks or by water bodies. However, research into the genetic aspects of this species is limited. In this study, the chromosome-scale telomere-to-telomere genome of R. sorocarpa was assembled exclusively by Oxford Nanopore long-read sequencing and Pore-C technology. A high-quality chromosomal-scale assembly was obtained with a final genome size of 376.690 Mbp, contig N50 of 49.132 Mbp and 97.02% of the assembled contigs associated with the eight chromosomes. Genome assembly completeness was confirmed by BUSCO analysis accounting 91.8%. Among 27,626 total genes, 23,562 (85.29%) were functionally annotated. Moreover, collinearity of Marchantiales was analyzed as well as gene family evolution and DNA methylation profile. The availability of this genome, which is the second telomere-to-telomere liverwort assembly, opens up new avenues for in-depth analysis of R. sorocarpa genetic diversity and genomic characteristics.

A Chromosomal-level genome assembly and annotation of fat greenling (Hexagrammos otakii)

Fat greenling (Hexagrammos otakii Jordan & Starks, 1895) is a valuable marine fish species, crucial for aquaculture in Northern China due to its high-quality meat and significant economic value. However, the aquaculture industry faces challenges such as trait degradation, early sexual maturity, and disease susceptibility, necessitating advanced genomic interventions for sustainable cultivation. This study presents the first chromosomal-level genome assembly of H. otakii, achieved using PacBio long-read sequencing and Hi-C technology. The assembly yielded a genome size of 682.43 Mb with a contig N50 size of 2.39 Mb and a scaffold N50 size of 27.83 Mb. The completeness of genome assessed by BUSCO is 96.99%. A total of 22,334 protein-coding genes were predicted, with 21,619 (96.80%) functionally annotated across various protein databases. This genomic resource is a step forward in supporting the breeding, germplasm conservation, and enhancement of H. otakii, facilitating genetic studies and the development of strategies for disease resistance and growth optimization in aquaculture.