scholarly journals A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

2019 ◽  
Vol 11 (11) ◽  
pp. 3144-3157 ◽  
Author(s):  
Yutaka Satou ◽  
Ryohei Nakamura ◽  
Deli Yu ◽  
Reiko Yoshida ◽  
Mayuko Hamada ◽  
...  
Keyword(s):  
Genome Size ◽  
Inbred Line ◽  
Genome Assembly ◽  
Ciona Intestinalis ◽  
Type A ◽  
Chromosomal Evolution ◽  
Sequence Information ◽  
A Genome ◽  
Biological Studies ◽  
Wide Range

Abstract Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114–120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

scholarly journals Chromosome-level genome assembly of a regenerable maize inbred line A188

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guifang Lin ◽  
Cheng He ◽  
Jun Zheng ◽  
Dal-Hoe Koo ◽  
Ha Le ◽  
...  
Keyword(s):  
Inbred Line ◽  
Genome Assembly ◽  
Gene Function ◽  
Maize Inbred Line ◽  
Carotenoid Cleavage Dioxygenase ◽  
Structural Variations ◽  
Embryonic Callus ◽  
Network Analyses ◽  
A Genome ◽  
Chromosome Level

Abstract Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

scholarly journals Highly Contiguous Nanopore Genome Assembly of Chlamydomonas reinhardtii CC-1690

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Samuel O’Donnell ◽  
Frederic Chaux ◽  
Gilles Fischer
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Genome Size ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Content Type ◽  
Oxford Nanopore ◽  
A Genome ◽  
Reference Quality

ABSTRACT The current Chlamydomonas reinhardtii reference genome remains fragmented due to gaps stemming from large repetitive regions. To overcome the vast majority of these gaps, publicly available Oxford Nanopore Technology data were used to create a new reference-quality de novo genome assembly containing only 21 contigs, 30/34 telomeric ends, and a genome size of 111 Mb.

Marsupial chromosomics: bridging the gap between genomes and chromosomes

2019 ◽  
Vol 31 (7) ◽  
pp. 1189 ◽  
Author(s):  
Janine E. Deakin ◽  
Sally Potter
Keyword(s):  
Dna Sequence ◽  
Genome Assembly ◽  
Genome Architecture ◽  
Sequence Information ◽  
Full Potential ◽  
Tasmanian Devil ◽  
Sequencing Technology ◽  
A Genome ◽  
Devil Facial Tumour Disease ◽  
Chromosome Level

Marsupials have unique features that make them particularly interesting to study, and sequencing of marsupial genomes is helping to understand their evolution. A decade ago, it was a huge feat to sequence the first marsupial genome. Now, the advances in sequencing technology have made the sequencing of many more marsupial genomes possible. However, the DNA sequence is only one component of the structures it is packaged into: chromosomes. Knowing the arrangement of the DNA sequence on each chromosome is essential for a genome assembly to be used to its full potential. The importance of combining sequence information with cytogenetics has previously been demonstrated for rapidly evolving regions of the genome, such as the sex chromosomes, as well as for reconstructing the ancestral marsupial karyotype and understanding the chromosome rearrangements involved in the Tasmanian devil facial tumour disease. Despite the recent advances in sequencing technology assisting in genome assembly, physical anchoring of the sequence to chromosomes is required to achieve a chromosome-level assembly. Once chromosome-level assemblies are achieved for more marsupials, we will be able to investigate changes in the packaging and interactions between chromosomes to gain an understanding of the role genome architecture has played during marsupial evolution.

scholarly journals A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Martin Pippel ◽  
David Jebb ◽  
Franziska Patzold ◽  
Sylke Winkler ◽  
Heiko Vogel ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gene Annotation ◽  
Incomplete Lineage Sorting ◽  
Read Length ◽  
Ecological Niches ◽  
Average Read Length ◽  
General Applicability ◽  
Pacific Biosciences ◽  
A Genome ◽  
Wide Range

Abstract Background Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. Results Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations. Conclusions Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.

scholarly journals Intricacies of GABAA Receptor Function: The Critical Role of the β3 Subunit in Norm and Pathology

2021 ◽  
Vol 22 (3) ◽  
pp. 1457
Author(s):  
Sergey A. Menzikov ◽  
Sergey G. Morozov ◽  
Aslan A. Kubatiev
Keyword(s):  
Driving Forces ◽  
Expression Patterns ◽  
Critical Role ◽  
Reversal Potential ◽  
Type A ◽  
Aminobutyric Acid ◽  
Ontogenetic Changes ◽  
Acid Type ◽  
Biological Studies ◽  
Wide Range

Neuronal intracellular chloride ([Cl−]i) is a key determinant in γ-aminobutyric acid type A (GABA)ergic signaling. γ-Aminobutyric acid type A receptors (GABAARs) mediate both inhibitory and excitatory neurotransmission, as the passive fluxes of Cl− and HCO3− via pores can be reversed by changes in the transmembrane concentration gradient of Cl−. The cation–chloride co-transporters (CCCs) are the primary systems for maintaining [Cl−]i homeostasis. However, despite extensive electrophysiological data obtained in vitro that are supported by a wide range of molecular biological studies on the expression patterns and properties of CCCs, the presence of ontogenetic changes in [Cl−]i—along with the consequent shift in GABA reversal potential—remain a subject of debate. Recent studies showed that the β3 subunit possesses properties of the P-type ATPase that participates in the ATP-consuming movement of Cl− via the receptor. Moreover, row studies have demonstrated that the β3 subunit is a key player in GABAAR performance and in the appearance of serious neurological disorders. In this review, we discuss the properties and driving forces of CCCs and Cl−, HCO3−ATPase in the maintenance of [Cl−]i homeostasis after changes in upcoming GABAAR function. Moreover, we discuss the contribution of the β3 subunit in the manifestation of epilepsy, autism, and other syndromes.

scholarly journals Karyotype Diversity, Mode, and Tempo of the Chromosomal Evolution of Attina (Formicidae: Myrmicinae: Attini): Is There an Upper Limit to Chromosome Number?

Insects ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1084
Author(s):  
Danon Clemes Cardoso ◽  
Maykon Passos Cristiano
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Chromosomal Evolution ◽  
Upper Limit ◽  
Model Study ◽  
A Genome ◽  
Fungus Growing Ants ◽  
Evolutionary Paths ◽  
Limited Spectrum ◽  
Evolutionary Stasis

Ants are an important insect group that exhibits considerable diversity in chromosome numbers. Some species show only one chromosome, as in the males of the Australian bulldog ant Myrmecia croslandi, while some have as many as 60 chromosomes, as in the males of the giant Neotropical ant Dinoponera lucida. Fungus-growing ants are a diverse group in the Neotropical ant fauna, engaged in a symbiotic relationship with a basidiomycete fungus, and are widely distributed from Nearctic to Neotropical regions. Despite their importance, new chromosome counts are scarcely reported, and the marked variation in chromosome number across species has been poorly studied under phylogenetic and genome evolutionary contexts. Here, we present the results of the cytogenetic examination of fungus-farming ants and compile the cytogenetic characteristics and genome size of the species studied to date to draw insights regarding the evolutionary paths of karyotype changes and diversity. These data are coupled with a fossil-calibrated phylogenetic tree to discuss the mode and tempo of chromosomal shifting, considering whether there is an upper limit for chromosome number and genome size in ants, using fungus-farming ants as a model study. We recognize that karyotypes are generally quite variable across fungus-farming ant phylogeny, mostly between genera, and are more numerically conservative within genera. A low chromosome number, between 10 and 12 chromosomes, seems to present a notable long-term evolutionary stasis (intermediate evolutionary stasis) in fungus-farming ants. All the genome size values were inside a limited spectrum below 1 pg. Eventual departures in genome size occurred with regard to the mean of 0.38 pg, indicating that there is a genome, and likely a chromosome, number upper limit.

scholarly journals URMAP, an ultra-fast read mapper

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9338
Author(s):  
Robert Edgar
Keyword(s):  
Variant Calling ◽  
Mapping Algorithm ◽  
Sequencing Technologies ◽  
Mapping Software ◽  
A Genome ◽  
Biological Studies ◽  
Wide Range ◽  
Order Of Magnitude ◽  
Comparable Accuracy ◽  
Validation Tests

Mapping of reads to reference sequences is an essential step in a wide range of biological studies. The large size of datasets generated with next-generation sequencing technologies motivates the development of fast mapping software. Here, I describe URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased against repetitive regions which are difficult to map and may therefore pose an unrealistically easy challenge to read mappers and variant callers.

scholarly journals Genome Sequence of the Radiation-Resistant Bacterium Deinococcus radiophilus ATCC 27603T

2019 ◽  
Vol 8 (30) ◽  
Author(s):  
Claudia R. Maynard ◽  
Kyle S. MacLea
Keyword(s):  
Radiation Exposure ◽  
Genome Size ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Resistant Bacterium ◽  
Content Type ◽  
A Genome ◽  
Associated Proteins ◽  
Radiation Resistant ◽  
Deinococcus Radiophilus

The pigmented bacterium Deinococcus radiophilus, which is highly resistant to radiation exposure, was first isolated from irradiated lizardfish. We report a genome assembly of D. radiophilus UWO 1055T (=ATCC 27603T), with a predicted genome size of 2.7 Mbp (62.66% G+C content). A number of CRISPR-associated proteins and two CRISPR arrays were identified.

scholarly journals What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140331 ◽  
Author(s):  
Tyler A. Elliott ◽  
T. Ryan Gregory
Keyword(s):  
Genome Size ◽  
Developmental Rate ◽  
Rapid Expansion ◽  
Division Rate ◽  
Protein Coding ◽  
Genome Data ◽  
Pair Composition ◽  
A Genome ◽  
Wide Range ◽  
Size Diversity

Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.

scholarly journals Genome-based taxonomic classification

Genome ◽  
2019 ◽  
Vol 62 (2) ◽  
pp. 45-52 ◽  
Author(s):  
Bobby Paul ◽  
Gunjan Dixit ◽  
Thokur Sreepathy Murali ◽  
Kapaettu Satyamoorthy
Keyword(s):  
Genome Assembly ◽  
Bacterial Species ◽  
Sequence Information ◽  
Bacterial Identification ◽  
Biochemical Tests ◽  
Separate Species ◽  
Genome Database ◽  
Bacterial Populations ◽  
A Genome ◽  
Metadata Analysis

Bacterial populations are routinely characterized based on microscopic examination, colony formation, and biochemical tests. However, in the recent past, bacterial identification, classification, and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species, and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity. A genome assembly with a gANI score of <95% at the intraspecies level is generally considered indicative of a separate species. In this study, we have analysed 300 whole-genome sequences belonging to 26 different bacterial species available in the NCBI Genome database and calculated their similarity at the intraspecies level based on gANI score. At the intraspecies level, nine bacterial species showed less than 90% gANI and more than 10% of unaligned regions. We suggest the appropriate use of available bioinformatics resources after genome assembly to arrive at the proper bacterial identification, classification, and nomenclature to avoid erroneous species assignments and disparity due to diversity at the intraspecies level.

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