scholarly journals Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

2018 ◽  
Author(s):  
Matthew A. Conte ◽  
Rajesh Joshi ◽  
Emily C. Moore ◽  
Sri Pratima Nandamuri ◽  
William J. Gammerdinger ◽  
...  
Keyword(s):  
De Novo ◽  
Genome Structure ◽  
Structural Evolution ◽  
Lake Malawi ◽  
Genetic Maps ◽  
East African ◽  
High Coverage ◽  
African Cichlid ◽  
Structural Differences ◽  
Genetic Mechanisms

AbstractBackgroundAfrican cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to understand the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.ResultsWe re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage PacBio sequencing, and anchored contigs to linkage groups (LGs) using four different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes.Large intra-chromosomal structural differences (~2-28Mbp) among species are common, while inter-chromosomal differences are rare (< 10Mbp total). Placement of the centromeres within chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11 and LG20 are associated with reductions in recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element (TE) insertions compared to O. niloticus, suggesting that several TE families have a higher rate of insertion in the haplochromine cichlid lineage.ConclusionThis study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.

scholarly journals De Novo Genes are “Frozen Accidents” which Escaped Rapid Turnover of Pervasively Transcribed ORFs

2017 ◽  
Author(s):  
Jonathan Schmitz ◽  
Kristian Ullrich ◽  
Erich Bornberg-Bauer
Keyword(s):  
De Novo ◽  
Nucleotide Composition ◽  
Open Reading Frames ◽  
Evolutionary Time ◽  
High Coverage ◽  
De Novo Genes ◽  
Protein Properties ◽  
Genetic Mechanisms ◽  
Reading Frames ◽  
Gene Age

AbstractA recent surge of studies suggested that many novel genes arise de novo from previously non-coding DNA and not by duplication. However, since most studies concentrated on longer evolutionary time scales and rarely considered protein structural properties, it remains unclear how these properties are shaped by evolution, depend on genetic mechanisms and influence gene survival. Here we compare open reading frames (ORFs) from high coverage transcriptomes from mouse and another four mammals covering 160 million years of evolution. We find that novel ORFs pervasively emerge from intergenic and intronic regions but are rapidly lost again while relatively fewer arise from duplications but are retained over much longer times. Surprisingly, disorder and other protein properties of young ORFs do not change with gene age. Only length and nucleotide composition change, probably to avoid aggregation. Thus de novo genes resemble frozen accidents of randomly emerged ORFs which survived initial purging, likely because they are functional.

scholarly journals Personalized genome structure via single gamete sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruqian Lyu ◽  
Vanessa Tsui ◽  
Davis J. McCarthy ◽  
Wayne Crismani
Keyword(s):  
Single Cell ◽  
De Novo ◽  
Genome Structure ◽  
Genetic Maps ◽  
Evolutionary Processes ◽  
Short Read ◽  
Short Read Sequencing ◽  
New Space

AbstractGenetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an individual contain all of the information required to perform a de novo chromosome-scale assembly of an individual’s genome, which historically has been performed with populations and pedigrees. Here, we discuss how single-cell gamete sequencing offers the potential to merge the advantages of short-read sequencing with the ability to build personalized genetic maps and open up an entirely new space in personalized genetics.

scholarly journals RNA-Seq reveals divergent gene expression between larvae with contrasting trophic modes in the poecilogonous polychaete Boccardia wellingtonensis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Álvaro Figueroa ◽  
Antonio Brante ◽  
Leyla Cárdenas
Keyword(s):  
De Novo ◽  
Juvenile Stage ◽  
Type I ◽  
Rna Seq ◽  
Mrna Synthesis ◽  
De Novo Transcriptome ◽  
Larval Stages ◽  
Divergent Gene ◽  
Genetic Mechanisms ◽  
Planktotrophic Larvae

AbstractThe polychaete Boccardia wellingtonensis is a poecilogonous species that produces different larval types. Females may lay Type I capsules, in which only planktotrophic larvae are present, or Type III capsules that contain planktotrophic and adelphophagic larvae as well as nurse eggs. While planktotrophic larvae do not feed during encapsulation, adelphophagic larvae develop by feeding on nurse eggs and on other larvae inside the capsules and hatch at the juvenile stage. Previous works have not found differences in the morphology between the two larval types; thus, the factors explaining contrasting feeding abilities in larvae of this species are still unknown. In this paper, we use a transcriptomic approach to study the cellular and genetic mechanisms underlying the different larval trophic modes of B. wellingtonensis. By using approximately 624 million high-quality reads, we assemble the de novo transcriptome with 133,314 contigs, coding 32,390 putative proteins. We identify 5221 genes that are up-regulated in larval stages compared to their expression in adult individuals. The genetic expression profile differed between larval trophic modes, with genes involved in lipid metabolism and chaetogenesis over expressed in planktotrophic larvae. In contrast, up-regulated genes in adelphophagic larvae were associated with DNA replication and mRNA synthesis.

scholarly journals A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

2021 ◽  
Author(s):  
Guangtu Gao ◽  
Susana Magadan ◽  
Geoffrey C Waldbieser ◽  
Ramey C Youngblood ◽  
Paul A Wheeler ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Chromosome Number ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Structural Variations ◽  
High Coverage ◽  
Haploid Chromosome Number ◽  
Long Reads

Abstract Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.

scholarly journals Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in theChlamydomonas reinhardtiiplastid genome

2015 ◽  
Author(s):  
Rob W Ness ◽  
Susanne A Kraemer ◽  
Nick Colegrave ◽  
Peter D Keightley
Keyword(s):  
Mutation Rate ◽  
Genetic Drift ◽  
Plastid Genome ◽  
De Novo ◽  
Spontaneous Mutation ◽  
Genome Structure ◽  
Nuclear Genome ◽  
De Novo Mutation ◽  
Direct Estimate ◽  
Plastid Genomes

Plastids perform crucial cellular functions, including photosynthesis, across a wide variety of eukaryotes. Since endosymbiosis, plastids have maintained independent genomes that now display a wide diversity of gene content, genome structure, gene regulation mechanisms, and transmission modes. The evolution of plastid genomes depends on an input ofde novomutation, but our knowledge of mutation in the plastid is limited to indirect inference from patterns of DNA divergence between species. Here, we use a mutation accumulation experiment, where selection acting on mutations is rendered ineffective, combined with whole-plastid genome sequencing to directly characterize de novo mutation inChlamydomonas reinhardtii. We show that the mutation rates of the plastid and nuclear genomes are similar, but that the base spectra of mutations differ significantly. We integrate our measure of the mutation rate with a population genomic dataset of 20 individuals, and show that the plastid genome is subject to substantially stronger genetic drift than the nuclear genome. We also show that high levels of linkage disequilibrium in the plastid genome are not due to restricted recombination, but are instead a consequence of increased genetic drift. One likely explanation for increased drift in the plastid genome is that there are stronger effects of genetic hitchhiking. The presence of recombination in the plastid is consistent with laboratory studies inC. reinhardtiiand demonstrates that although the plastid genome is thought to be uniparentally inherited, it recombines in nature at a rate similar to the nuclear genome.

scholarly journals Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

2021 ◽  
Author(s):  
Myung-Shin Kim ◽  
Taeyoung Lee ◽  
Jeonghun Baek ◽  
Ji Hong Kim ◽  
Changhoon Kim ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Anthocyanin Biosynthesis ◽  
Genetic Maps ◽  
Soybean Cultivar ◽  
Gene Arrangement ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Crop Species ◽  
Satellite Repeats

AbstractMassive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel groups, we found that soybean contains four clearly separated groups of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

scholarly journals De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

2019 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akifumi Azuma ◽  
Fumiya Taniguchi ◽  
Toshiya Yamamoto ◽  
Akihiko Sato ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Genome Structure ◽  
Table Grape ◽  
Sequencing Analysis ◽  
Entire Genome ◽  
Table Grapes ◽  
Eukaryotic Genes

AbstractThis study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.

scholarly journals De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

2020 ◽  
Author(s):  
Jonathan R. Belyeu ◽  
Harrison Brand ◽  
Harold Wang ◽  
Xuefang Zhao ◽  
Brent S. Pedersen ◽  
...  
Keyword(s):  
De Novo ◽  
Genome Structure ◽  
Point Mutations ◽  
Large Family ◽  
Germline Mutations ◽  
Autism Spectrum ◽  
Parental Age ◽  
Single Nucleotide Variants ◽  
Multiple Testing Correction ◽  
Structural Mutations

AbstractEach human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. The germline mutation rate for single nucleotide variants and factors that significantly influence this rate, such as parental age, are now well established. However, far less is known about the frequency, distribution, and features that impact de novo structural mutations. We report a large, family-based study of germline mutations, excluding aneuploidy, that affect genome structure among 572 genomes from 33 families in a multigenerational CEPH-Utah cohort and 2,363 cases of non-familial autism spectrum disorder (ASD), 1,938 unaffected siblings, and both parents (9,599 genomes in total). We find that de novo structural mutations detected by alignment-based, short-read WGS occurred at an overall rate of at least 0.160 events per genome in unaffected individuals and was significantly higher (0.206 per genome) in ASD cases. In both probands and unaffected samples, nearly 73% of de novo structural mutations arose in paternal gametes, and predict most de novo structural mutations to be caused by mutational mechanisms that do not require sequence homology. After multiple testing correction we did not observe a statistically significant correlation between parental age and the rate of de novo structural variation in offspring. These results highlight that a spectrum of mutational mechanisms contribute to germline structural mutations, and that these mechanisms likely have markedly different rates and selective pressures than those leading to point mutations.

Explosive Speciation and Adaptive Radiation of East African Cichlid Fishes

2011 ◽  
pp. 333-362 ◽  
Author(s):  
Christian Sturmbauer ◽  
Martin Husemann ◽  
Patrick D. Danley
Keyword(s):  
Adaptive Radiation ◽  
East African ◽  
Cichlid Fishes ◽  
African Cichlid ◽  
Explosive Speciation
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