Estimated Genome Size Research Articles

The first high-quality chromosome-level genome assembly of Phyllanthaceae (Phyllanthus cochinchinensis) provides insights into flavonoid biosynthesis.

We report the genome assembly of P. cochinchinensis, as the first high-quality chromosome-level genome of Phyllanthaceae which is rich in medicinal plants. Phyllanthus cochinchinensis, a member of the Phyllanthaceae, is one of the famous medicinal plants in South China. Here, we report a de novo chromosome-level genome assembly for P. cochinchinensis using a combination of Nanopore and Illumina sequencing technologies. In total, the assembled genome consists of 284.88Mb genomic sequences with a contig N50 of 10.32Mb, representing ~ 95.49% of the estimated genome size. By applying Hi-C data, 13 pseudochromosomes of P. cochinchinensis were constructed, covering ~ 99.87% of the assembled sequences. The genome is annotated with 59.12% repetitive sequences and 20,836 protein-coding genes. Whole-genome duplication of P. cochinchinensis is likely shared with Ricinus communis as well as Vitis vinifera. Homologous genes within the flavonoid pathway for P. cochinchinensis were identified and copy numbers and expression level of related genes revealed potential critical genes involved in flavonoid biosynthesis. This study provides the first whole-genome sequence for the Phyllanthaceae, confirms the evolutionary status of Phyllanthus from the genomic level, and provides foundations for accelerating functional genomic research of species from Phyllanthus.

De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'.

The first genome sequence of an interspecific grape hybrid (Vitis labruscana × Vitis vinifera), 'Shine Muscat', an elite table grape cultivar bred in Japan, is presented. The resultant genome assemblies included two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a 'pseudo-haploid' genome. The unphased sequences, assembled to the chromosome level with Hi-C reads, spanned 488.97 Mb in length, 99.1% of the estimated genome size, with 4,595 scaffold sequences and a 23.9-Mb N50 length. The phased sequences had 15,650 scaffolds spanning 1.0 Gb and a 4.2-Mb N50 length. 32,827 high-confidence genes were predicted on the unphased genomes. Clustering analysis of the 'Shine Muscat' gene sequences with three other Vitis species and Arabidopsis indicated that 11,279 orthologous gene clusters were common to Vitis spp. and Arabidopsis, 4,385 were Vitis specific, and 234 were 'Shine Muscat' specific. Whole-genome resequencing was also performed for the parental lines of 'Shine Muscat', Akitsu-21 and 'Hakunan', and parental-specific copy number variations were identified. The obtained genome resources provide new insights that could assist in cultivation and breeding strategies to produce high-quality table grapes.

Genome Survey Sequencing and Genetic Background Characterization of the Wolf Spider Pardosa pseudoannulata (Araneae: Lycosidae)

The wolf spider Pardosa pseudoannulata is a typical wandering spider and is frequently viewed as a biological indicator. However, published information on the P. pseudoannulata genome is limited. To explore the genomic structure of P. pseudoannulata, we performed a genome survey using high-throughput sequencing technologies at approximately 16.41X coverage depth. We obtained 67.48 Gb of sequence data, with an estimated genome size of 4.11 Gb and guanine plus cytosine (GC) content of 35.34%. The repeat ratio of the P. pseudoannulata genomic sequence was 79.16% and the heterozygote rate was 0.4%. By analysing the characteristics of the genome, 150,288 simple sequence repeats (SSRs) were identified. Among these SSRs, the mononucleotide repeat type was the most abundant (62.56% of total SSRs), followed by the dinucleotide (23.84%), trinucleotide (7.39%), tetranucleotide (3.94%), pentanucleotide (2.24%), and hexanucleotide (0.03%) repeat types. This is the first genome-wide characterization of P. pseudoannulata, which highlighted the genomic characteristics of low hybridization, high repetition, large size, and complex structure. The data obtained from our genome survey will not only aid the design of future P. pseudoannulata whole-genome sequencing projects but will also be valuable for further studies on genetic diversity and evolutionary analysis.

De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.)

Cashew is the second most important tree nut crop in the global market. Cashew is a diploid and heterozygous species closely related to the mango and pistachio. Its improvement by conventional breeding is slow due to the long juvenile phase. Despite the economic importance, very little genomics/transcriptomics information is available for cashew. In this study, the Oxford nanopore reads and Illumina reads were used for de novo assembly of the cashew genome. The hybrid assembly yielded a 356.6 Mb genome corresponding to 85% of the estimated genome size (419 Mb). The BUSCO analysis showed 91.8% of genome completeness. Transcriptome mapping showed 92.75% transcripts aligned with the assembled genome. Gene predictions resulted in the identification of 31,263 genes coding for a total of 35,000 gene isoforms. About 46% (165 Mb) of the cashew genome comprised of repetitive sequences. Phylogenetic analyses of the cashew with nine species showed that it was closely related to Mangifera indica. Analysis of cashew genome revealed 3104 putative R-genes. The first draft assembly of the genome, transcriptome and R gene information generated in this study would be the foundation for understanding the molecular basis of economic traits and genomics-assisted breeding in cashew.

Comparative Study on Genome Size and Phytochemical Profile of Three Potential Species of Acacia: Threatened and Endemic to Saudi Arabia

Acacias are widely distributed in tropical and subtropical regions of the world and have both economic as well as medicinal value. The estimation of genome size is very important as it changes due to the change in noncoding DNA sequence as well as genome duplication among organisms for their evolutionary aspects. Three potential species of the genus Acacia including Acacia etbaica, Acacia johnwoodii and Acacia origena, which are threatened and nearly endemic to Saudi Arabia, were collected. The present study was carried out to determine the genome size (2C DNA contents), total phenolic content (TPC), total flavonoid (TFC) and some bioactive compounds in these species for their comparison. The genome size ranged from 1.91 pg (A. etbaica) to 2.45 pg/2C (A. origena) among the Acacia species, which correspond to genome sizes 1843.15–2364.25 Mbp, respectively. The variation was observed in genome size within Acacia species as nuclei were extracted using different extraction buffers except for GB and MB01 buffers. The FTIR analysis revealed the presence of various functional groups in compounds that might be responsible for different types of phytochemicals in these Acacia species. Total flavonoid content (TFC) ranged from 0.647 (A. origena) to 1.084 mg QE/g DW (A. etbaica), whereas the total phenolic f content (TPC) ranged between 15.322 (A. origena) to 28.849 (A. johnwoodii) mg/g DW of GAE. HPLC analysis revealed the presence of quercetin 3-β-D-glucoside and luteolin 7-rutinoside in the leaves of all three Acacia species in considerable amounts, and these might have good health-promoting effects. This is our first study on genome size (2C DNA content) using flow cytometry and phytochemical profiling on these Acacias. Thus, estimated genome size and phytochemical study of these species could help to understand the biosynthesis of secondary metabolites under various genes and the evolutionary relationships among them.

Draft Whole-Genome Sequence of Penicillium simplicissimum A4, a Putative Endophyte from Echium plantagineum.

We report the draft whole-genome sequence of the putative endophytic fungus Penicillium simplicissimum A4, isolated from the roots of Echium plantagineum plants. The genome was sequenced using PacBio technology with an estimated genome size of 39 Mb.

Limibaculum sediminis sp. nov., isolated from mangrove sediment.

A Gram-stain-negative, cream-coloured, aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT325T, was isolated from mangrove sediment collected in Shenzhen, PR China. The taxonomic position of strain FT325T was established by phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT325T grew optimally at 37-40 °C and pH 6.0 in the presence of 0 % (w/v) NaCl. Results of 16S rRNA gene sequence analysis showed that strain FT325T was most similarly related to Limibaculum halophilum CAU 1123T (96.2 %), Phaeovulum vinaykumarii DSM 18714T (93.9%) and Amaricoccus solimangrovi HB 172011T (93.7 %). The major fatty acids (>10 %) were C18 : 1 ω7c (60.0 %) and 11-methyl C18 : 1 ω7c (16.7 %). The sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, one unidentified glycolipid, three unidentified aminolipids and three unidentified phospholipids. Its estimated genome size was 4 318 768 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT325T represents a novel species of the genus Limibaculum, for which the name Limibaculum sediminis sp. nov. is proposed (=MCCC 1K07397T=KCTC 92313T).

Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti.

Simple SummaryCrocodile icefish inhabit the deep sea around the Southern Ocean and belong to the family Channichthyidae. The species lacks hemoglobin and has evolved an antifreeze protein, unlike other teleosts. In this study, the whole-genome survey and microsatellite motifs were analyzed, which provide relevant information on genetic diversity, population genetics, and the genomic study of crocodile icefish.The crocodile icefish, Chionobathyscus dewitti, belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species, shows unique physiological and genetic features, unlike other teleosts. It lacks hemoglobin and has evolved antifreeze proteins. Here, we report the genome sequencing data of crocodile icefish produced using the Illumina Novaseq 6000 platform. The estimated genome size was 0.88 Gb with a K-value of 19, and the unique sequence, heterozygosity, error, and duplication rates were 57.4%, 0.421%, 0.317%, and 0.738%, respectively. A genome assembly of 880.69 Mb, with an N50 scaffold length of 2401 bp, was conducted. We identified 2,252,265 microsatellite motifs from the genome assembly data, and dinucleotide repeats (1,920,127; 85.25%) had the highest rate. We selected 84 primer pairs from the genome survey assembly and randomly selected 30 primer pairs for validation. As a result, 15 primer pairs were validated as microsatellite markers.

First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq.

Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F1 mapping populations, whose female parents were a genotype of a so called ‘ponpon’ and of a ‘double flower’ varieties, while the common male parental (‘Cipro’) was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F1 population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.

Curtobacterium allii sp. nov., the actinobacterial pathogen causing onion bulb rot.

A Gram-stain-positive, aerobic, and non-spore-forming bacterial strain, 20TX0166T, was isolated from a diseased onion bulb in Texas, USA. Upon testing its pathogenicity on onion bulb, it produced pathogenic response which makes it first species of pathogen belonging to the phylum actinobacteria detected in onion. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the strain belonged to the genus Curtobacterium and was most similar to Curtobacterium flaccumfaciens LMG 3645T (100%), C. pusillum DSM 20527T (99.5%), and C. oceanosedimentum ATCC 31317T (99.5%). The estimated genome size of the novel species was 4.0Mbp with a G + C content of 70.8%. The orthologous ANI (orthoANIu), ANI based on blast (ANIb), and dDDH values between the novel strain and the closest relative, C. flaccumfaciens LMG 3645T, were 95.7%, 95.4%, and 63.3%, respectively. These values were below the recommended species cut-off threshold of 96% (ANI) and 70% (dDDH), suggesting the strain may be a novel species. Physiologic and phenotypic characters of this novel strain were also unique when compared with the closely related species. The major cellular fatty acids of this strain were anteiso-C15:0 and anteiso-C17:0. Using a polyphasic approach based on phenotypic and genotypic analyses, strain 20TX0166T represents a novel species of the genus Curtobacterium, and the name Curtobacterium allii sp. nov. is proposed. The type strain is 20TX0166T (= LMG 32517T = CIP112023T = NCIMB 15427T).

Cohnella herbarum sp. nov., isolated from wild grass fermentation broth.

A novel strictly aerobic, Gram-stain-positive, rod-shaped, motile, endospore-forming, white-coloured bacterium, designated strain MFER-1T, was isolated from a fermented liquor of wild grasses sampled in the Republic of Korea. The respiratory quinone of strain MFER-1T was menaquinone-7 and its major cellular fatty acids were anteiso-C15 : 0 (55.3 %), iso-C16 : 0 (17.5 %) and C16 : 0 (12.1 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids and an unidentified phospholipid. The 16S rRNA gene sequence of strain MFER-1T showed similarity of 98.1 % to 'Cohnella cholangitidis' 1 605-214T and below 98.0 % sequence similarity to the other Cohnella species. The phylogenomic tree indicated that strain MFER-1T formed a reliable cluster with several Cohnella species. The estimated genome size of strain MFER-1T was 8.52 Mb. Genomic DNA G+C content was 50.7mol%. The orthologous average nucleotide identity, digital DNA-DNA hybridization and amino acid identity values of strain MFER-1T with the most closely related species 'Cohnella cholangitidis' 1 605-214T were 78.7, 23.0 and 79.6 %, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic results, strain MFER-1T should represent a novel species of the genus Cohnella, for which the name Cohnella herbarum sp. nov. is proposed, with strain MFER-1T (=KACC 21 257T=NBRC 114 628T) as the type strain.

Genome-Wide Identification of the PYL Gene Family in Chenopodium quinoa: From Genes to Protein 3D Structure Analysis

The halophytic crop Chenopodium quinoa has a remarkable resistance to harsh growth conditions in suboptimal environments and marginal soils. Additionally, quinoa is a pseudocereal and produces seeds with outstanding nutritional value. Quinoa is an allotetraploid (2n = 4× = 36) with an estimated genome size of approximately 1.5 Gbp. In plants, the family of pyrabactin resistance 1 (PYR1)/PYR1-like (PYL)/regulatory components of ABA receptors (RCAR) play a vital role in the initial step of ABA signaling, leading to abiotic stress resistance. Here 20 CqPYL genes were identified using the genome-search method. Based on the phylogenetic analysis, these CqPYL genes were divided into three classes or subfamilies. These genes have different structures and intron numbers, even within the same subfamily. Analysis of conserved motifs showed the presence of the PYR_PYL_RCAR motif domain in each PYL protein sequence. Furthermore, the tissue-specific expression of CqPYLs was analyzed through public available RNA-seq data. CqPYL4a/b and CqPYL8c/d showed higher expression levels in seedlings. Finally, 3D structures of the CqPYL proteins were predicted by homology modeling and analyzed through topology inspection to speculate on putative new ABA receptor features. This study provides a theoretical basis for further functional study of PYL genes for stress-resistance breeding of quinoa and other crops.

Isolation, Partial Characterization and Application of Bacteriophages in Eradicating Biofilm Formation by Bacillus cereus on Stainless Steel Surfaces in Food Processing Facilities

The Bacillus cereus (B. cereus) group is a widespread foodborne pathogen with a persistent ability to form biofilm, and with inherent resistance to traditional treatment in the food industry. Bacteriophages are a promising biocontrol agent that could be applied to prevent or eliminate biofilms formation. We have described, in this study, the isolation from sewage samples and preliminary characterization of bacteriophages that are active against the B. cereus group. The effectiveness of phage treatment for reducing B. cereus attachment and biofilms on stainless steel surfaces has been also assessed using three incubation periods at different titrations of each phage. Out of 62 phages isolated, seven showed broad-spectrum lytic action against 174 B. cereus isolates. All selected phages appeared to be of the Siphoviridae family. SDS-PAGE proved that two phages have a similar profile, while the remainder are distinct. All isolated phages have the same restriction pattern, with an estimated genome size of around 37 kb. The isolated bacteriophages have been shown to be effective in preventing biofilm formation. Reductions of up to 1.5 log10 UFC/cm2 have been achieved, compared to the untreated biofilms. Curative treatment reduced the bacterial density by 0.5 log10 UFC/cm2. These results support the prospect of using these phages as a potential alternative strategy for controlling biofilms in food systems.

Genome Sequence Resource of Albifimbria verrucaria Causing the Leaf Spot Disease of the Spinach Plant Spinacia oleracea.

Genome Sequence Resource of Albifimbria verrucaria Causing the Leaf Spot Disease of the Spinach Plant Spinacia oleracea.

Genome and Transcriptome Sequence Resources and Effector Repertoire of Pythium myriotylum Drechsler.

Genome and Transcriptome Sequence Resources and Effector Repertoire of Pythium myriotylum Drechsler.

A Feulgen glimpse into genome evolution during range expansion: a case study of the subterranean amphipod Niphargus schellenbergi

In 1923, Robert Feulgen designed a quantitative approach to measure the relative DNA content of a species (its so-called “C-value”, which is defined as half of the DNA content of a somatic cell and is expressed in pg). The Feulgen approach has several advantages: it can be used on ethanol-preserved samples, it is relatively inexpensive, and it does not require sophisticated equipment (Hardie et al. 2002, Jeffery and Gregory 2014, Kasten 2003). Gathering DNA content information is a key preliminary step for whole-genome sequencing of non-model species and also yield important information for ecological and evolutionary studies as well as for conservation (Jeffery et al. 2013), since genome size has been shown to be strongly correlated to extinction risk in animals and plants (Vinogradov 2004, Vinogradov 2003). Among invertebrates, Niphargidae is among the largest families of freshwater subterranean amphipods in the world, and more than 450 niphargid species have been described (Horton et al. 2021). Thus, it is considered an ideal model for evolutionary and ecological studies. Using a new, improved Feulgen protocol, we generated novel genome size estimates for 26 samples of Niphargus schellenbergi collected from central and western European niphargids. The obtained C-values ranged from 2.75 to 5.25 pg. Such a two-fold intraspecific variation is unusual but not unheard of: it occurs also in the monogonont rotifer Brachionus asplanchnoidis (Stelzer et al. 2021). Further research will be required to find out the mechanisms responsible for this variation, which may result from copy-number variation, polyploidy and/or various amounts of transposable elements.

Genome Size Variation of Chagas Disease Vectors of the Rhodniini Tribe.

The genome size of five Rhodnius species (R. milesi, R. nasutus, R. neivai, R. prolixus, and R. robustus) and two Psammolestes species (P. coroedes and P. tertius) were estimated using flow cytometry and/or k-mer distributions in genome sequences. Phylogenetic generalized linear mixed models highlighted significant genome size variations among species and between sexes, with R. prolixus showing the largest genome. In this study we provide the first data on female genome size in Triatominae. For five species, female genome size did not differ from males, except for R. robustus, where females had smaller genomes. Genome size estimations based on the k-mer distribution method were less than those estimated from flow cytometry, but both methods exhibited the same pattern of sexual differences. Further genomic studies are needed to infer whether genome size variation could be an adaptive trait in Rhodnius.

The telomere-to-telomere gap-free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding.

The telomere-to-telomere gap-free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding.

The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta).

Simple SummaryMackerel species are commercially important marine species in Southeast Asia, especially short mackerel and Indian mackerel. However, genomic information about them is still limited. Genome survey of these two mackerel species was reported in this study. Next-generation sequencing and comprehensive bioinformatics were performed to obtain the genetic information. The estimated genome size of both species is around 680 Mbp. The heterozygosity of these species was very similar, while the repeat content for Indian mackerel was slightly higher than for short mackerel. Functional annotation also was reported in this study. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.Rastrelliger brachysoma (short mackerel) and Rastrelliger kanagurta (Indian mackerel) are commercially important marine species in Southeast Asia. In recent years, numbers of these two species have been decreasing in the wild, and genomic information about them is still limited. We conducted a genome survey of these two mackerel species to acquire essential genomic information using next-generation sequencing data. To obtain this genetic information, comprehensive bioinformatics analyses were performed, including de novo assembly, gene prediction, functional annotation, and phylogenetic analysis. The estimated genome sizes were around 680.14 Mbp (R. brachysoma) and 688.82 Mbp (R. kanagurta). The heterozygosity of these species was very similar (≈0.81), while the repeat content for R. kanagurta (9.30%) was slightly higher than for R. brachysoma (8.30%). Functional annotation indicated that most of the genes predicted in these two species shared very close average amino acid identities (94.06%). The phylogenetic analysis revealed close phylogenetic relationships between these two species and other scombrids. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.

Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza.

Genome size variation and evolutionary forces behind have been long pursued in flowering plants. The genus Oryza, consisting of approximately 25 wild species and two cultivated rice, harbors eleven extant genome types, six of which are diploid (AA, BB, CC, EE, FF, and GG) and five of which are tetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL). To obtain the most comprehensive knowledge of genome size variation in the genus Oryza, we performed flow cytometry experiments and estimated genome sizes of 166 accessions belonging to 16 non-AA genome Oryza species. k-mer analyses were followed to verify the experimental results of the two accessions for each species. Our results showed that genome sizes largely varied fourfold in the genus Oryza, ranging from 279 Mb in Oryza brachyantha (FF) to 1,203 Mb in Oryza ridleyi (HHJJ). There was a 2-fold variation (ranging from 570 to 1,203 Mb) in genome size among the tetraploid species, while the diploid species had 3-fold variation, ranging from 279 Mb in Oryza brachyantha (FF) to 905 Mb in Oryza australiensis (EE). The genome sizes of the tetraploid species were not always two times larger than those of the diploid species, and some diploid species even had larger genome sizes than those of tetraploids. Nevertheless, we found that genome sizes of newly formed allotetraploids (BBCC-) were almost equal to totaling genome sizes of their parental progenitors. Our results showed that the species belonging to the same genome types had similar genome sizes, while genome sizes exhibited a gradually decreased trend during the evolutionary process in the clade with AA, BB, CC, and EE genome types. Comparative genomic analyses further showed that the species with different rice genome types may had experienced dissimilar amplification histories of retrotransposons, resulting in remarkably different genome sizes. On the other hand, the closely related rice species may have experienced similar amplification history. We observed that the contents of transposable elements, long terminal repeats (LTR) retrotransposons, and particularly LTR/Gypsy retrotransposons varied largely but were significantly correlated with genome sizes. Therefore, this study demonstrated that LTR retrotransposons act as an active driver of genome size variation in the genus Oryza.