Diploid Genome Size Research Articles

A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly

Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.

Karyotype and genome size determination of Jarilla chocola, an additional sister clade of Carica papaya

Jarilla chocola is an herbaceous plant species that belongs to the Jarilla genus and the Caricaceae family. No information on chromosome number or genome size has been reported for J. chocola that confirms the occurrence of dysploidy events and explore the existence of heteromorphic sex chromosomes. Therefore, the total number of chromosomes of this species was determined by karyotyping and counting the number of chromosomes observed, and the genome size of female and male plants was estimated separately by flow cytometry. Results showed that J. chocola has eight pairs of chromosomes (2n = 2x = 16), and its chromosomes are classified as metacentric for five pairs, submetacentric for two pairs and telocentric for one pair. The nuclear DNA content (1C-value) in picograms and diploid genome size was estimated separately from female and male plants using two species as the standards, Phaseolus vulgaris (1C = 0.60 pg) and Carica papaya (1C = 0.325 pg), to look for the possible existence of heteromorphic sex chromosomes. C. papaya proved to be a better standard for the determination of J. chocola DNA content and diploid genome size. No significant difference on the DNA content was observed between female (1C = 1.02 ± 0.003 pg) and male (1C = 1.02 ± 0.008 pg) plants. The estimated genome size of J. chocola per haploid genome in base pairs was calculated from the obtained C-values. Results showed an estimated genome size per haploid genome of 1018.44 ± 3.07 Mb and 1022.08 ± 7.76 Mb for female and male plants, respectively. Due to the observed chromosome number and genome size, only the occurrence of one of two previously reported dysploidy events in Jarilla could be confirmed for J. chocola and no evidence of heteromorphic sex chromosomes was found. These results provide fundamental information of the J. chocola genome and will expedite investigation of sex chromosomes and genome evolution in this species, the Jarilla genus and the Caricaceae family

RNA-Seq-based DNA marker analysis of the genetics and molecular evolution of Triticeae species.

The release of high-quality chromosome-level genome sequences of members of the Triticeae tribe has greatly facilitated genetic and genomic analyses of important crops such as wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the large diploid genome size of Triticeae plants (ca. 5 Gbp), transcript analysis is an important method for identifying genetic and genomic differences among Triticeae species. In this review, we summarize our results of RNA-Seq analyses of diploid wheat accessions belonging to the genera Aegilops and Triticum. We also describe studies of the molecular relationships among these accessions and provide insight into the evolution of common hexaploid wheat. DNA markers based on polymorphisms within species can be used to map loci of interest. Even though the genome sequence of diploid Aegilops tauschii, the D-genome donor of common wheat, has been released, the diploid barley genome continues to provide key information about the physical structures of diploid wheat genomes. We describe how a series of RNA-Seq analyses of wheat relatives has helped uncover the structural and evolutionary features of genomic and genetic systems in wild and cultivated Triticeae species.

Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA

The macroscopic single-celled green alga Acetabularia acetabulum has been a model system in cell biology for more than a century. However, no genomic information is available from this species. Since the alga has a long life cycle, is difficult to grow in dense cultures, and has an estimated diploid genome size of almost 2 Gb, obtaining sufficient genomic material for genome sequencing is challenging. Here, we have attempted to overcome these challenges by amplifying genomic DNA using multiple displacement amplification (MDA) combined with microfluidics technology to distribute the amplification reactions across thousands of microscopic droplets. By amplifying and sequencing DNA from five single cells we were able to recover an estimated ~ 7–11% of the total genome, providing the first draft of the A. acetabulum genome. We highlight challenges associated with genome recovery and assembly of MDA data due to biases arising during genome amplification, and hope that our study can serve as a reference for future attempts on sequencing the genome from non-model eukaryotes.

Within-Population Genome Size Variation is Mediated by Multiple Genomic Elements That Segregate Independently during Meiosis.

Within-species variation in genome size has been documented in many animals and plants. Despite its importance for understanding eukaryotic genome diversity, there is only sparse knowledge about how individual-level processes mediate genome size variation in populations. Here, we study a natural population of the rotifer Brachionus asplanchnoidis whose members differ up to 1.9-fold in diploid genome size, but were still able to interbreed and produce viable offspring. We show that genome size is highly heritable and can be artificially selected up or down, but not below a certain basal diploid genome size for this species. Analyses of segregation patterns in haploid males reveal that large genomic elements (several megabases in size) provide the substrate of genome size variation. These elements, and their segregation patterns, explain the generation of new genome size variants, the short-term evolutionary potential of genome size change in populations, and some seemingly paradoxical patterns, like an increase in genome size variation among highly inbred lines. Our study suggests that a conceptual model involving only two variables, 1) a basal genome size of the population, and 2) a vector containing information on additional elements that may increase genome size in this population (size, number, and meiotic segregation behavior), can effectively address most scenarios of short-term evolutionary change of genome size in a population.

The relationship between genome size, morphological parameters and diet breadth in insect species

Abstract Genome size estimation is the first step involved in the complete genome sequencing project. Knowledge on genome size is also useful in research work related to genetics, molecular biology, and systematics. Though there are many methods of genome estimation, the Propidium Iodide (PI) based flow cytometry is simple and gives an accurate estimation. In the present investigation, the diploid genome size of four insect species viz., cotton leafhopper, Amrasca biguttula biguttula (392.47 Mb) (Cicadellidae: Hemiptera), bean pod borer, Maruca vitrata (1489.63 Mb) (Crambidae: Lepidoptera), tomato pinworm, Tuta absoluta (1128.61 Mb) (Gelechiidae: Lepidoptera) and eggplant shoot and fruit borer, Leucinodes orbonalis (944.52 Mb) (Crambidae: Lepidoptera) were estimated using chicken RBC (2.33 pg) as a reference standard. The relationship of genome size with the insect morphological traits and host plant range showed no evident correlation between them.

The Genome Size of Some Species of Hyalomma Ticks from Turkish Thrace

Hyalomma scupense, H. excavatum and H. marginatum are globally important tick species, as well as in Turkey, both in terms of human and animal health. The genome sizes of these tick species were determined in this study for the first time. From flow cytometric measurements, diploid genome sizes of female and male H. scupense were found to be 2.13 pg and 1.75 pg, respectively, while H. excavatum were 2.21 pg and 1.94 pg, and H. marginatum were 2.48 pg and 1.98 pg, respectively. Differences in diploid genome size indicate X chromosome size of females and males in these ticks because they have an XX:XO sex determination system. Thus, it was estimated that the X chromosome of H. scupense, H. excavatum, and H. marginatum may be composed of as much as 0.38 pg, 0.27 pg, and 0.50 pg of DNA, respectively. These findings indicate suitability of these three species for genome sequencing due to the relatively small size of their genomes compared with other tick species.

First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae).

Oak represents a valuable natural resource across Northern Hemisphere ecosystems, attracting a large research community studying its genetics, ecology, conservation, and management. Here we introduce a draft genome assembly of valley oak (Quercus lobata) using Illumina sequencing of adult leaf tissue of a tree found in an accessible, well-studied, natural southern California population. Our assembly includes a nuclear genome and a complete chloroplast genome, along with annotation of encoded genes. The assembly contains 94,394 scaffolds, totaling 1.17 Gb with 18,512 scaffolds of length 2 kb or longer, with a total length of 1.15 Gb, and a N50 scaffold size of 278,077 kb. The k-mer histograms indicate an diploid genome size of ∼720–730 Mb, which is smaller than the total length due to high heterozygosity, estimated at 1.25%. A comparison with a recently published European oak (Q. robur) nuclear sequence indicates 93% similarity. The Q. lobata chloroplast genome has 99% identity with another North American oak, Q. rubra. Preliminary annotation yielded an estimate of 61,773 predicted protein-coding genes, of which 71% had similarity to known protein domains. We searched 956 Benchmarking Universal Single-Copy Orthologs, and found 863 complete orthologs, of which 450 were present in > 1 copy. We also examined an earlier version (v0.5) where duplicate haplotypes were removed to discover variants. These additional sources indicate that the predicted gene count in Version 1.0 is overestimated by 37–52%. Nonetheless, this first draft valley oak genome assembly represents a high-quality, well-annotated genome that provides a tool for forest restoration and management practices.

Intraspecific variations in cardamom (Elettaria cardamomum Maton): assessment of genomic diversity by flow cytometry, cytological studies and ISSR analysis.

Background The main goal of the work was to analyse intraspecific variation in Elettaria cardamomum Maton (cardamom) using genome size, cytological studies and molecular marker data. Nuclear DNA content and molecular marker details furnish data on genome size and genetic diversity respectively among the studied accessions and both complement each other for evolutionary and taxonomic studies.ResultsThe relative 2C genome size and total number of base pairs of cardamom was determined through flow cytometric analysis using propidium iodide staining. The nuclear DNA content was estimated in various sections of the species representing individuals from wild and cultivar genotypes following Zea mays L. CE-777 (2C = 5.43 pg) as internal reference standard. Chromosome number from growing root tip was examined following standard protocols. Twenty-six ISSR primers that generated polymorphic bands were used for genetic diversity analysis of the thirty accessions of cardamom. Estimated nuclear 2C DNA content ranged from 2.57 to 3.22 pg demonstrating 1.25-fold variation. The mean amount of 2C nuclear DNA of the cardamom was calculated as 2.87 pg which is equivalent of 2806 Mbp as the diploid genome size. The chromosome number was found to be 2n = 48. Among the thirty accessions of cardamom studied using ISSR markers, C53 (feral from Bonacaud) showed a very prominent level of genetic diversity and was lowest for C96 (Avinash-I, a released variety from Indian Institute of Spices Research, Kozhikode).ConclusionThese analyses revealed the existence of genetic variability within the studied cardamom accessions. The plant specimens also differed significantly in their genome size. However, the genetic variability parameters did not show any correlation with genome size.

Molecular cytogenetic study in Octopus (Amphioctopus) areolatus from Japan

Octopus (Amphioctopus) areolatus is an important marine cephalopod in Japan. We examined its diploid chromosome number, karyotype, and genome size (C value), and performed fluorescence in situ hybridization (FISH) using a vertebrate telomeric probe. The diploid chromosome number was 60 in embryonic cells, with 24 pairs of metacentric chromosomes, four pairs of metacentric/submetacentric chromosomes, and two pairs of submetacentric chromosomes. The mean C value was estimated to be 5.47 pg. From these findings, and those reported previously for other octopus species, we suggest that the factor causing the quantum change of C value in O. (A.) areolatus was genome duplication, and not polyploidy. In telomeric FISH analysis, hybridization signals were clearly observed in the telomeric regions of the chromosomes. This is the first report of FISH analysis of cephalopod chromosomes, and our findings suggest that the telomere sequence of O. (A.) areolatus is (TTAGGG)n, which may allow gene mapping in the future.

Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana.

Arabidopsis thaliana became the model organism for plant studies because of its small diploid genome, rapid lifecycle and short adult size. Its genome was the first among plants to be sequenced, becoming the reference in plant genomics. However, the Arabidopsis genome is characterized by an inherently complex organization, since it has undergone ancient whole genome duplications, followed by gene reduction, diploidization events and extended rearrangements, which relocated and split up the retained portions. These events, together with probable chromosome reductions, dramatically increased the genome complexity, limiting its role as a reference. The identification of paralogs and single copy genes within a highly duplicated genome is a prerequisite to understand its organization and evolution and to improve its exploitation in comparative genomics. This is still controversial, even in the widely studied Arabidopsis genome. This is also due to the lack of a reference bioinformatics pipeline that could exhaustively identify paralogs and singleton genes. We describe here a complete computational strategy to detect both duplicated and single copy genes in a genome, discussing all the methodological issues that may strongly affect the results, their quality and their reliability. This approach was used to analyze the organization of Arabidopsis nuclear protein coding genes, and besides classifying computationally defined paralogs into networks and single copy genes into different classes, it unraveled further intriguing aspects concerning the genome annotation and the gene relationships in this reference plant species. Since our results may be useful for comparative genomics and genome functional analyses, we organized a dedicated web interface to make them accessible to the scientific community

Reticulate evolution in the Crepidomanes minutum species complex (Hymenophyllaceae)

Hybridization is an important mechanism of speciation in plants and often results in complexes that comprise multiple sexual diploids and their hybrid offspring. However, the intricacy of these systems has prevented a thorough understanding of many groups. The Crepidomanes minutum species complex (Hymenophyllaceae) is a widely distributed, morphologically variable fern species complex. Although prior reports of apogamy and polyploidy suggest hybridization, it has never been the focus of a phylogenetic study. Morphology, nuclear (gapCp), and chloroplast (rbcL) DNA sequences, cytology, field observation, and spore counts were used to infer phylogeny and trace hybrid origins. The C. minutum species complex is composed of at least three major clades: the African clade, clade 1 (East Asia and the Pacific), and clade 2 (Southeast Asia and the South Pacific). Clades 1 and 2 differ strikingly in morphological variation (uniform in clade 1 vs. highly variable in clade 2) and occurrence of hybrids (rare in clade 1 vs. frequent in clade 2). Apogamy and polyploidy were confirmed as likely mechanisms of hybrid stabilization in clade 2. Despite the large genetic distance between clades 1 and 2, several specimens were observed with gapCp sequences from both; diploid genome size and sexual reproduction indicate maintenance of genetic diversity via introgression or incomplete lineage sorting, rather than ongoing hybridization, in these specimens. The C. minutum species complex is a reticulate network including multiple diploid lineages and their stabilized hybrid crosses. Additional sampling focused on reproductive mode and ploidy level is needed to delimit diploid species and hybrids.

Correlations of geographic distribution and temperature of embryonic development with the nuclear DNA content in the Salamandridae (Urodela, Amphibia)

We used flow cytometry to measure the nuclear DNA content in erythrocytes of 27 salamandrid species. Across these species, diploid genome size varied more than 2 fold (51.3-104.4 pg). According to genome size and geographic distribution, 3 groups of newt species were recognized: West Palearctics with smaller amounts of nuclear DNA; Nearctic, with intermediate values; and East Asiatic, with higher genome sizes. Viviparous West Palearctic salamanders differed from most of the oviparous West Palearctic newts in possessing larger genome sizes. The nuclear DNA content strongly correlates with species range limits. At the same temperature, embryos of salamandrid species with larger genome sizes have a markedly longer developmental time than those with smaller genomes. We present an analysis of the relationships between the amount of nuclear DNA and water temperature at the breeding sites.

DNA-Feulgen cytophotometric determination of genome size for the freshwater-invading copepod Eurytemora affinis.

Variation in nuclear DNA content within some eukaryotic species is well documented, but causes and consequences of such variation remain unclear. Here we report genome size of an estuarine and salt-marsh calanoid copepod, Eurytemora affinis, which has recently invaded inland freshwater habitats independently and repeatedly in North America, Europe, and Asia. Adults and embryos of E. affinis from the St. Lawrence River drainage were examined for somatic cell DNA content and the presence or absence of embryonic chromatin diminution, using Feulgen-DNA cytophotometry to determine a diploid or 2C genome size of 0.6-0.7 pg DNA/cell. The majority of somatic cell nuclei, however, have twice this DNA content (1.3 pg/nucleus) in all of the adults examined and possibly represent a population of cells arrested at the G2 stage of the cell cycle or associated with some degree of endopolyploidy. Both suggestions contradict assumptions that DNA replication does not occur in adult tissues during the determinate growth characteristic of copepods. Absence of germ cell nuclei with markedly elevated DNA values, commonly found for species of cyclopoid copepods that show chromatin diminution, indicates that E. affinis lacks this trait. The small genome size and presumed absence of chromatin diminution increase the potential utility of E. affinis as a model for genomic studies on mechanisms of adaptation during freshwater invasions.

Tripsacum dactyloides (Poaceae): a natural model system to study parthenogenesis

Diplosporous apomeiosis, formation of unreduced embryo sacs primarily of the Antennaria type, followed by parthenogenetic embryo development and pseudogamy (fertilization of the central cell) describe gametophytic apomixis within the Tripsacum agamic complex. Tripsacum dactyloides (Eastern gamagrass) is a close relative of domesticated maize and was chosen as a natural model system to investigate gene expression patterns associated with parthenogenesis. The genome size of diploid sexual and polyploid apomictic T. dactyloides was estimated by flow cytometry to be 7.37pg (2C), 14.74pg (4C) and 22.39pg (6C), respectively. The diploid genome size is thus approximately 1.35× larger than that of maize. The apomeiotic-pseudogamous pathway of seed formation was demonstrated at a rate of 92% by the flow cytometric seed screen (FCSS) with single mature seeds in tetraploid accessions. This number includes twin embryos which were detected in 13% of the seeds analyzed. Fertilization of unreduced egg cells (BIII hybrids) was measured in 10% of apomictic seeds. Autonomous (fertilization-independent) embryo development and fertilization-dependent endosperm formation were confirmed by pollination of tetraploid T. dactyloides with a diploid transgenic maize line carrying an actin:: β -glucuronidase (GUS) reporter construct. GUS expression was detected after pollination in the developing endosperm, but not in the embryo. In similar intraspecific crossing experiments with maize, GUS expression was detected in both the embryo and endosperm. A protocol was established for microdissection of embryo sacs and early parthenogenetic embryos of T. dactyloides. Together, these techniques provide new tools for future studies aimed at comparing gene expression patterns between sexual maize and sexual or apomictic T. dactyloides.

CYTOGENETICS OF THE AMPHIPOD JASSA MARMORATA (COROPHIOIDEA: ISCHYROCERIDAE): KARYOTYPE MORPHOLOGY, CHROMOSOME BANDING, FLUORESCENTIN SITUHYBRIDIZATION, AND NUCLEAR DNA CONTENT

Abstract Developing embryos proved to be a suitable source of cells for advanced cytological investigations on Amphipods. Conventional karyotyping, Ag- and fluorochrome-staining, C-banding, endonuclease digestion, fluorescent in situ hybridization (FISH) and nuclear DNA flow cytometric assay were tested in the Ischyroceridae Jassa marmorata. The karyotype consists of 6 chromosome pairs of which 5 are metacentric and 1 subtelocentric. The rDNA/FISH revealed that major ribosomal cistrons are located on the telomeric regions in the short arm of pair 6. A marked size variation of hybridization signals was observed. Silver and fluorochrome staining enhanced no chromosome regions. Constitutive heterochromatin was scarce and limited to tiny, pericentromeric blocks as revealed by C-banding and three different restriction enzymes. The diploid genome size (1.90 pg) and the Adenine-Thymine base-pair nuclear DNA relative amount (28.85%) of J. marmorata are by far the lowest encountered in Amphipoda and Crustacea, res...

Genome size variations are related to X‐chromosome heterochromatin polymorphism in Arvicanthis sp. from Benin (West Africa)

The African grass rat, Arvicanthis sp., from Benin shows sex‐chromosome polymorphism for the presence in the karyotype of three X‐chromosome forms: subtelocentric (Xst), submetacentric (Xsm), and metacentric (Xm). Here we report statistically significant differences of diploid genome size (g.s.) among individuals, from 6.22 ± 0.06 pg to 6.80 ± 0.10 pg, depending on the X‐chromosome form. The evaluation of the total and X‐chromosome heterochromatin content alone (Xst: 2.16 ± 0.22%; Xsm: 5.02 ± 0.22%; Xm: 6.54 ± 0.28%), supports this suggestion. DNA base‐pair preferential staining revealed that heterochromatin of both autosome and sex chromosomes is AT‐rich. Digestion of genomic DNA with sixteen restriction enzymes produced DNA bands representing the repetitive fraction of the genome. When these were used as probes for fluorescence in situ hybridization (FISH), two hybridization patterns were found: a) FISH positive signals localized in the pericentromeric areas of every chromosome of the complement and b) chromosome specific signals co‐localizing with both the pericentromeric regions of every chromosome and the heterochromatic regions of Xsm and Xm, but not on the Xst chromosome. FISH performed with a (TTAGGG)n probe revealed a telomere‐only pattern.

Chloroplast DNA Sequence Homologies among Vascular Plants

The extent of sequence conservation in the chloroplast genome of higher plants has been investigated. Supercoiled chloroplast DNA, prepared from pea seedlings, was labeled in vitro and used as a probe in reassociation experiments with a high concentration of total DNAs extracted from several angiosperms, gymnosperms, and lower vascular plants. In each case the probe reassociation was accelerated, demonstrating that some chloroplast sequences have been highly conserved throughout the evolution of vascular plants. Only among the flowering plants were distinct levels of cross-reaction with the pea chloroplast probe evident; broad bean and barley exhibited the highest and lowest levels, respectively. With the hydroxylapatite assay these levels decreased with a decrease in probe fragment length (from 1,860 to 735 bases), indicating that many conserved sequences in the chloroplast genome are separated by divergent sequences on a rather fine scale. Despite differences observed in levels of homology with the hydroxylapatite assay, S1 nuclease analysis of heteroduplexes showed that outside of the pea family the extent of sequence relatedness between the probe and various heterologous DNAs is approximately the same: 30%. In our interpretation, the fundamental changes in the chloroplast genome during angiosperm evolution involved the rearrangement of this 30% with respect to the more rapidly changing sequences of the genome. These rearrangements may have been more extensive in dicotyledons than in monocotyledons. We have estimated the amount of conserved and divergent DNA interspersed between one another.From the reassociation experiments, determinations were made of the percentage of chloroplast DNA in total DNA extracts from different higher plants; this value remained relatively constant when compared with the large variation in the diploid genome size of the plants.