scholarly journals De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication

2019 ◽  
Vol 5 (6) ◽  
pp. eaav0547 ◽  
Author(s):  
Zelin Chen ◽  
Yoshihiro Omori ◽  
Sergey Koren ◽  
Takuya Shirokiya ◽  
Takuo Kuroda ◽  
...  
Keyword(s):  
Carassius Auratus ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
De Novo ◽  
Close Relative ◽  
Whole Genome ◽  
Draft Sequence ◽  
Goldfish Carassius Auratus ◽  
The Common ◽  
Conserved Noncoding Elements

For over a thousand years, the common goldfish (Carassius auratus) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp (Cyprinus carpio), goldfish share the recent genome duplication that occurred approximately 14 million years ago in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies provides an exciting opportunity to link genotype to phenotype and to understand the dynamics of genome evolution and speciation. We generated a high-quality draft sequence and gene annotations of a “Wakin” goldfish using 71X PacBio long reads. The two subgenomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged substantially across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression levels across all tissues, while loss of conserved noncoding elements determined expression variance between different tissues. This assembly provides an important resource for comparative genomics and understanding the causes of goldfish variants.

scholarly journals De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication

2018 ◽  
Author(s):  
Zelin Chen ◽  
Yoshihiro Omori ◽  
Sergey Koren ◽  
Takuya Shirokiya ◽  
Takuo Kuroda ◽  
...  
Keyword(s):  
Carassius Auratus ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
De Novo ◽  
Close Relative ◽  
Whole Genome ◽  
Draft Sequence ◽  
Zebrafish Model ◽  
Goldfish Carassius Auratus ◽  
The Common

SummaryFor over a thousand years throughout Asia, the common goldfish (Carassius auratus) was raised for both food and as an ornamental pet. Selective breeding over more than 500 years has created a wide array of body and pigmentation variation particularly valued by ornamental fish enthusiasts. As a very close relative of the common carp (Cyprinus carpio), goldfish shares the recent genome duplication that occurred approximately 14-16 million years ago (mya) in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies is an exciting opportunity to link genotype to phenotype as well as understanding the dynamics of genome evolution and speciation. Here we generated a high-quality draft sequence of a “Wakin” goldfish using 71X PacBio long-reads. We identified 70,324 coding genes and more than 11,000 non-coding transcripts. We found that the two sub-genomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, “ohnologous” genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged significantly across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression across all tissues, while loss of conserved, non-coding elements determined expression variance between different tissues. This draft assembly also provides an important resource for comparative genomics with the very commonly used zebrafish model (Danio rerio), and for understanding the underlying genetic causes of goldfish variants.

scholarly journals Genetic and Epigenetic Changes Are Rapid Responses of the Genome to the Newly Synthesized Autotetraploid Carassius auratus

2021 ◽  
Vol 11 ◽  
Author(s):  
Chongqing Wang ◽  
Yuwei Zhou ◽  
Huan Qin ◽  
Chun Zhao ◽  
Li Yang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Carassius Auratus ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Enrichment Analysis ◽  
Full Length ◽  
Aflp Analysis ◽  
Whole Genome ◽  
Epigenetic Alterations ◽  
Fish Genome

Whole genome duplication events have occurred frequently during the course of vertebrate evolution. To better understand the influence of polyploidization on the fish genome, we herein used the autotetraploid Carassius auratus (4n = 200, RRRR) (4nRR) resulting from the whole genome duplication of Carassius auratus (2n = 100, RR) (RCC) to explore the genomic and epigenetic alterations after polyploidization. We subsequently performed analyses of full-length transcriptome dataset, amplified fragment length polymorphism (AFLP) and methylation sensitive amplification polymorphism (MSAP) on 4nRR and RCC. By matching the results of 4nRR and RCC isoforms with reference genome in full-length transcriptome dataset, 649 and 1,971 novel genes were found in the RCC and 4nRR full-length geneset, respectively. Compared to Carassius auratus and Megalobrama amblycephala, 4nRR presented 3,661 unexpressed genes and 2,743 expressed genes. Furthermore, GO enrichment analysis of expressed genes in 4nRR revealed that they were enriched in meiosis I, whereas KEGG enrichment analysis displayed that they were mainly enriched in proteasome. Using AFLP analysis, we noted that 32.61% of RCC fragments had disappeared, while 32.79% of new bands were uncovered in 4nRR. Concerning DNA methylation, 4nRR exhibited a lower level of global DNA methylation than RCC. Additionally, 60.31% of methylation patterns in 4nRR were altered compared to RCC. These observations indicated that transcriptome alterations, genomic changes and regulation of DNA methylation levels and patterns had occurred in the newly established autotetraploid genomes, suggesting that genetic and epigenetic alterations were influenced by autotetraploidization. In summary, this study provides valuable novel insights into vertebrate genome evolution and generates relevant information for fish breeding.

scholarly journals A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Ao Li ◽  
Ai Liu ◽  
Xin Du ◽  
Jin-Yuan Chen ◽  
Mou Yin ◽  
...  
Keyword(s):  
Medicago Sativa ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genomic Sequence ◽  
Close Relative ◽  
Whole Genome ◽  
Forage Crops ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractAlfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.

scholarly journals Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shijing Feng ◽  
Zhenshan Liu ◽  
Jian Cheng ◽  
Zihe Li ◽  
Lu Tian ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Repetitive Sequences ◽  
Close Relative ◽  
Specific Gene ◽  
Gene Gain ◽  
Whole Genome ◽  
Genome Duplication Event ◽  
A Genome ◽  
The Impact

AbstractZanthoxylum bungeanum is an important spice and medicinal plant that is unique for its accumulation of abundant secondary metabolites, which create a characteristic aroma and tingling sensation in the mouth. Owing to the high proportion of repetitive sequences, high heterozygosity, and increased chromosome number of Z. bungeanum, the assembly of its chromosomal pseudomolecules is extremely challenging. Here, we present a genome sequence for Z. bungeanum, with a dramatically expanded size of 4.23 Gb, assembled into 68 chromosomes. This genome is approximately tenfold larger than that of its close relative Citrus sinensis. After the divergence of Zanthoxylum and Citrus, the lineage-specific whole-genome duplication event η-WGD approximately 26.8 million years ago (MYA) and the recent transposable element (TE) burst ~6.41 MYA account for the substantial genome expansion in Z. bungeanum. The independent Zanthoxylum-specific WGD event was followed by numerous fusion/fission events that shaped the genomic architecture. Integrative genomic and transcriptomic analyses suggested that prominent species-specific gene family expansions and changes in gene expression have shaped the biosynthesis of sanshools, terpenoids, and anthocyanins, which contribute to the special flavor and appearance of Z. bungeanum. In summary, the reference genome provides a valuable model for studying the impact of WGDs with recent TE activity on gene gain and loss and genome reconstruction and provides resources to accelerate Zanthoxylum improvement.

scholarly journals Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

2020 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akihiro Itai ◽  
Sachiko Isobe
Keyword(s):  
Related Species ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
De Novo ◽  
Genetic Maps ◽  
Japanese Pear ◽  
Pyrus Pyrifolia ◽  
Whole Genome ◽  
Protein Encoding ◽  
History Of

AbstractAimThe Japanese pear (P. pyrifolia) variety ‘Nijisseiki’ is valued for its superior flesh texture, which has led to its use as a breeding parent for most Japanese pear cultivars. However, in the absence of genomic resources for Japanese pear, the parents of the ‘Nijisseiki’ cultivar remain unknown, as does the genetic basis of its favorable texture. The genomes of pear and related species are complex due to ancestral whole genome duplication and high heterozygosity, and long-sequencing technology was used to address this.Methods and ResultsDe novo assembly of long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6□Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of whole genome duplication was observed, consistent with related species.Conclusion and PerspectiveThis is the first genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

scholarly journals A very recent whole genome duplication in Potamopyrgus antipodarum predates multiple origins of asexuality & associated polyploidy

2017 ◽  
Author(s):  
John Logsdon ◽  
Maurine Neiman ◽  
Jeffrey Boore ◽  
Joel Sharbrough ◽  
Laura Bankers ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Potamopyrgus Antipodarum ◽  
Recent Common Ancestor ◽  
Close Relative ◽  
Whole Genome ◽  
Evolutionary Trajectory ◽  
Initial Genome

Potamopyrgus antipodarum, a New Zealand freshwater snail, is a powerful system to study the maintenance of sexual reproduction. Obligate asexual P. antipodarum (herein, Pa) lineages include both triploids and tetraploids that are products of multiple separate transitions from diploid sexual ancestors. Distinct diploid sexual and polyploid asexual lineages coexist and compete; these separate lineages can be considered replicated natural experiments. We have shown that harmful mutations are accumulating at a higher rate in asexual than in sexual Pa, demonstrating the utility of this system as a model for investigating the evolution of sex at the genomic level. In order to better understand the causes and consequences of transitions to asexuality, we have sequenced multiple genomes and transcriptomes of Pa and a close relative, P. estuarinus (herein, Pe) a diploid sexual species. The diploid genome size of Pe is ~0.6X of the genome size of diploid Pa, inspiring us to investigate whether the most recent common ancestor of Pa had experienced a whole-genome duplication (WGD) event prior to the diversification of its many sexual and asexual lineages. In addition to its clear relevance to understanding the evolutionary history of this species, by being so recent, this apparent WGD will also be especially powerful in understanding events immediately following WGD. Our initial genome assembly of a model sexual Pa lineage was consistent with this possibility, indicating high fractions (~35%) of scaffolds containing extended, nearly identical, duplicated regions. This result also partly explains our general difficulty with assembling the genome, despite generating >100X genome coverage using multiple methodologies. Even considering the limitations of our current genome assembly, we used the assembly to test a series of predictions under the hypothesis of recent whole-genome duplication, all of which are consistent with WGD. These tests have shown: 1) a marked excess of duplicated copies of genes in Pa which are maintained in single copy in other animals, 2) implausibly high "heterozygosity" estimates in our model Pa sexual genome, presumably resulting from non-allelic comparisons, 3) higher sequence identity between thousands of Pa-specific paralogous genes, when compared to their Pe orthologs. These and additional lines of evidence will be presented and evaluated. Together, our results suggest that this initial genome-wide duplication event might have played a key role in the subsequent evolutionary trajectory of this species, potentially facilitating its repeated diversification into multiple asexual lineages. We are now generating additional long-range genome scaffolds for Pa using multiple methods, as well as improving the coverage and quality of the Pe genome. We will use these new data to conduct definitive phylogenomic tests of this especially remarkable whole genome duplication.

scholarly journals The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

2017 ◽  
Author(s):  
Evelyn E. Schwager ◽  
Prashant P. Sharma ◽  
Thomas Clarke ◽  
Daniel J. Leite ◽  
Torsten Wierschin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Hox Genes ◽  
Genome Duplication ◽  
Whole Genome ◽  
Parasteatoda Tepidariorum ◽  
Evolutionary Diversification ◽  
Horseshoe Crabs ◽  
The Common ◽  
House Spider

AbstractThe duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neofunctionalization and/or subfunctionalization since their duplication, and therefore may have contributed to the diversification of spiders and other pulmonate arachnids.

scholarly journals A very recent whole genome duplication in Potamopyrgus antipodarum predates multiple origins of asexuality & associated polyploidy

2017 ◽  
Author(s):  
John Logsdon ◽  
Maurine Neiman ◽  
Jeffrey Boore ◽  
Joel Sharbrough ◽  
Laura Bankers ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Potamopyrgus Antipodarum ◽  
Recent Common Ancestor ◽  
Close Relative ◽  
Whole Genome ◽  
Evolutionary Trajectory ◽  
Initial Genome

Potamopyrgus antipodarum, a New Zealand freshwater snail, is a powerful system to study the maintenance of sexual reproduction. Obligate asexual P. antipodarum (herein, Pa) lineages include both triploids and tetraploids that are products of multiple separate transitions from diploid sexual ancestors. Distinct diploid sexual and polyploid asexual lineages coexist and compete; these separate lineages can be considered replicated natural experiments. We have shown that harmful mutations are accumulating at a higher rate in asexual than in sexual Pa, demonstrating the utility of this system as a model for investigating the evolution of sex at the genomic level. In order to better understand the causes and consequences of transitions to asexuality, we have sequenced multiple genomes and transcriptomes of Pa and a close relative, P. estuarinus (herein, Pe) a diploid sexual species. The diploid genome size of Pe is ~0.6X of the genome size of diploid Pa, inspiring us to investigate whether the most recent common ancestor of Pa had experienced a whole-genome duplication (WGD) event prior to the diversification of its many sexual and asexual lineages. In addition to its clear relevance to understanding the evolutionary history of this species, by being so recent, this apparent WGD will also be especially powerful in understanding events immediately following WGD. Our initial genome assembly of a model sexual Pa lineage was consistent with this possibility, indicating high fractions (~35%) of scaffolds containing extended, nearly identical, duplicated regions. This result also partly explains our general difficulty with assembling the genome, despite generating >100X genome coverage using multiple methodologies. Even considering the limitations of our current genome assembly, we used the assembly to test a series of predictions under the hypothesis of recent whole-genome duplication, all of which are consistent with WGD. These tests have shown: 1) a marked excess of duplicated copies of genes in Pa which are maintained in single copy in other animals, 2) implausibly high "heterozygosity" estimates in our model Pa sexual genome, presumably resulting from non-allelic comparisons, 3) higher sequence identity between thousands of Pa-specific paralogous genes, when compared to their Pe orthologs. These and additional lines of evidence will be presented and evaluated. Together, our results suggest that this initial genome-wide duplication event might have played a key role in the subsequent evolutionary trajectory of this species, potentially facilitating its repeated diversification into multiple asexual lineages. We are now generating additional long-range genome scaffolds for Pa using multiple methods, as well as improving the coverage and quality of the Pe genome. We will use these new data to conduct definitive phylogenomic tests of this especially remarkable whole genome duplication.

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