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 Comparative Inference of Duplicated Genes Produced by Polyploidization in Soybean Genome

2013 ◽  
Vol 2013 ◽  
pp. 1-4
Author(s):  
Yanmei Yang ◽  
Jinpeng Wang ◽  
Jianyong Di
Keyword(s):  
Statistical Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Duplication Event ◽  
Plant Evolution ◽  
Soybean Genome ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Genome Duplication Event ◽  
Scientific Value

Soybean (Glycine max) is one of the most important crop plants for providing protein and oil. It is important to investigate soybean genome for its economic and scientific value. Polyploidy is a widespread and recursive phenomenon during plant evolution, and it could generate massive duplicated genes which is an important resource for genetic innovation. Improved sequence alignment criteria and statistical analysis are used to identify and characterize duplicated genes produced by polyploidization in soybean. Based on the collinearity method, duplicated genes by whole genome duplication account for 70.3% in soybean. From the statistical analysis of the molecular distances between duplicated genes, our study indicates that the whole genome duplication event occurred more than once in the genome evolution of soybean, which is often distributed near the ends of chromosomes.

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 A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

GigaScience ◽  
2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Zheng Fan ◽  
Tao Yuan ◽  
Piao Liu ◽  
Lu-Yu Wang ◽  
Jian-Feng Jin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Hox Genes ◽  
Genome Duplication ◽  
Duplication Event ◽  
Whole Genome ◽  
High Quality ◽  
Genome Duplication Event ◽  
Whole Genome Duplication Event ◽  
Chromosome Level

Abstract Background The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event. Results We present a chromosome-level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi-C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes. Conclusions The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species’ adaptation to the environment.

scholarly journals Identity and divergence of protein domain architectures after the yeast whole-genome duplication event

2010 ◽  
Vol 6 (11) ◽  
pp. 2305 ◽  
Author(s):  
Luigi Grassi ◽  
Diana Fusco ◽  
Alessandro Sellerio ◽  
Davide Corà ◽  
Bruno Bassetti ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Duplication Event ◽  
Protein Domain ◽  
Whole Genome ◽  
Genome Duplication Event ◽  
Whole Genome Duplication Event

scholarly journals Exploring whole-genome duplicate gene retention with complex genetic interaction analysis

Science ◽  
2020 ◽  
Vol 368 (6498) ◽  
pp. eaaz5667 ◽  
Author(s):  
Elena Kuzmin ◽  
Benjamin VanderSluis ◽  
Alex N. Nguyen Ba ◽  
Wen Wang ◽  
Elizabeth N. Koch ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genetic Interaction ◽  
Interaction Analysis ◽  
Quantitative Measure ◽  
Duplicate Gene ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Genome Duplication Event ◽  
Genetic Interaction Analysis

Whole-genome duplication has played a central role in the genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated, and factors that influence the retention of persisting duplicates remain poorly understood. We describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping of digenic interactions for a deletion mutant of each paralog, and of trigenic interactions for the double mutant, provides insight into their roles and a quantitative measure of their functional redundancy. Trigenic interaction analysis distinguishes two classes of paralogs: a more functionally divergent subset and another that retained more functional overlap. Gene feature analysis and modeling suggest that evolutionary trajectories of duplicated genes are dictated by combined functional and structural entanglement factors.

scholarly journals Evolution after whole genome duplication: teleost microRNAs

2021 ◽  
Author(s):  
Thomas Desvignes ◽  
Jason Sydes ◽  
Jerôme Montfort ◽  
Julien Bobe ◽  
John H Postlethwait
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Retention Rates ◽  
Phenotypic Change ◽  
Whole Genome ◽  
Protein Coding ◽  
Mirna Genes ◽  
Evolutionary Features ◽  
Mirna Evolution

Abstract microRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the Teleost Genome Duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than non-clustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3’ complementary regions, compared to minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multi-species analysis of the mechanisms influencing metazoan miRNA evolution after whole genome duplication.

Sign in / Sign up

Export Citation Format

Share Document