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 The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
José Ramón Pardos-Blas ◽  
Iker Irisarri ◽  
Samuel Abalde ◽  
Carlos M L Afonso ◽  
Manuel J Tenorio ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Duplication Event ◽  
Pomacea Canaliculata ◽  
Whole Genome ◽  
Genome Duplication Event ◽  
Whole Genome Duplication Event ◽  
Venomous Animals ◽  
Genes Encoding ◽  
Chromosome Level

Abstract Background Venoms are deadly weapons to subdue prey or deter predators that have evolved independently in many animal lineages. The genomes of venomous animals are essential to understand the evolutionary mechanisms involved in the origin and diversification of venoms. Results Here, we report the chromosome-level genome of the venomous Mediterranean cone snail, Lautoconus ventricosus (Caenogastropoda: Conidae). The total size of the assembly is 3.59 Gb; it has high contiguity (N50 = 93.53 Mb) and 86.6 Mb of the genome assembled into the 35 largest scaffolds or pseudochromosomes. On the basis of venom gland transcriptomes, we annotated 262 complete genes encoding conotoxin precursors, hormones, and other venom-related proteins. These genes were scattered in the different pseudochromosomes and located within repetitive regions. The genes encoding conotoxin precursors were normally structured into 3 exons, which did not necessarily coincide with the 3 structural domains of the corresponding proteins. Additionally, we found evidence in the L. ventricosus genome for a past whole-genome duplication event by means of conserved gene synteny with the Pomacea canaliculata genome, the only one available at the chromosome level within Caenogastropoda. The whole-genome duplication event was further confirmed by the presence of a duplicated hox gene cluster. Key genes for gastropod biology including those encoding proteins related to development, shell formation, and sex were located in the genome. Conclusions The new high-quality L. ventricosus genome should become a reference for assembling and analyzing new gastropod genomes and will contribute to future evolutionary genomic studies among venomous animals.

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 Retrotransposon proliferation coincident with the evolution of dioecy in Asparagus

2016 ◽  
Author(s):  
Alex Harkess ◽  
Francesco Mercati ◽  
Loredana Abbate ◽  
Michael McKain ◽  
J. Chris Pires ◽  
...  
Keyword(s):  
Genome Size ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Sex Chromosome ◽  
Duplication Event ◽  
Whole Genome ◽  
Dioecious Species ◽  
Genome Duplication Event ◽  
Chromosome Fusion ◽  
Whole Genome Duplication Event

AbstractCurrent phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or retrotransposon proliferation in dioecious species. We first estimate genome sizes or use published values for four hermaphrodites and four dioecious species distributed across the phylogeny and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements in particular have undergone a marked proliferation in dioecious species. In the absence of a detectable whole genome duplication event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species.

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 A chromosome‐level genome assembly of Brachymystax lenok tsinlingensis provides new insights into salmonids evolution

2021 ◽  
Author(s):  
Wenbo Zhu ◽  
Zhongkai Wang ◽  
Haorong Li ◽  
Hui Xiang ◽  
Ping Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gc Content ◽  
Gene Families ◽  
Whole Genome ◽  
Genome Duplication Event ◽  
Brachymystax Lenok Tsinlingensis ◽  
Brachymystax Lenok ◽  
Chromosome Level

The salmonid-specific fourth vertebrate whole-genome duplication (Ss4R) occurred ~80 million years ago in the ancestor of all salmonids and provides a unique opportunity to study the evolutionary history of the duplicated genome. Study of the genome of Brachymystax lenok tsinlingensis might be particularly insightful given that this is the only Brachymystax species with a published salmonid genome. Here, we present a high-quality chromosome-level genome assembly for B. l. tsinlingensis and found that the salmonids have a unique GC content and codon usage, have undergone a whole-genome duplication event and a burst of transposon-mediated repeat expansion, have a slower evolutionary rate, and possess specific expanded gene families and unique positively selected genes. Generally, the B. l. tsinlingensis genome could provide a valuable reference for the study of other salmonids as well as aid the conservation of this endangered species.

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