scholarly journals Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yongxia Zhang ◽  
Guo-Qiang Zhang ◽  
Diyang Zhang ◽  
Xue-Die Liu ◽  
Xin-Yu Xu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Gene Loss ◽  
Genome Duplication ◽  
Gene Families ◽  
Ethylene Biosynthesis ◽  
Whole Genome ◽  
Mads Box Genes ◽  
Orchid Species ◽  
Medicinal Orchid ◽  
High Quality Genome

AbstractAs one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.

scholarly journals Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Wenyan Nong ◽  
Zhe Qu ◽  
Yiqian Li ◽  
Tom Barton-Owen ◽  
Annette Y. P. Wong ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Horseshoe Crab ◽  
Genome Duplication ◽  
Population Level ◽  
Gene Families ◽  
Whole Genome ◽  
Horseshoe Crabs ◽  
The Individual ◽  
Evolutionary Consequences ◽  
High Quality Genome

AbstractWhole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7 Gb, N50 = 90.2 Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7 Gb, N50 = 109.7 Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C. rotundicauda and T. tridentatus genomes from populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for improving our understanding of invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both the individual and population level. We also provide improved genomic resources for horseshoe crabs, of applied value for breeding programs and conservation of this fascinating and unusual invertebrate lineage.

scholarly journals Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication

2020 ◽  
Author(s):  
Wenyan Nong ◽  
Zhe Qu ◽  
Yiqian Li ◽  
Tom Barton-Owen ◽  
Annette Y.P. Wong ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Horseshoe Crab ◽  
Genome Duplication ◽  
Gene Families ◽  
Whole Genome ◽  
Breeding Programs ◽  
Horseshoe Crabs ◽  
The Common ◽  
Evolutionary Consequences ◽  
High Quality Genome

AbstractWhole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7Gb, N50 = 90.2Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7Gb, N50 = 109.7Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD, and that these WGD events are shared with spiders. Comparison of the genomes of C. rotundicauda and T. tridentatus populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for a better understanding of the consequences of invertebrate WGD events on evolutionary fates of genes and microRNAs at individual and population levels, and highlights the genetic diversity with practical values for breeding programs and conservation of horseshoe crabs.

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

scholarly journals Giant African snail genomes provide insights into molluscan whole-genome duplication and aquatic-terrestrial transition

2020 ◽  
Author(s):  
Conghui Liu ◽  
Yuwei Ren ◽  
Zaiyuan Li ◽  
Qi Hu ◽  
Lijuan Yin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Terrestrial Ecosystems ◽  
Gene Families ◽  
Gene Clusters ◽  
Immune Defense ◽  
Whole Genome ◽  
Genomic Plasticity ◽  
Ecological Adaptability ◽  
Chromosome Level

AbstractWhole-genome duplication (WGD) has been observed across a wide variety of eukaryotic groups, contributing to evolutionary diversity and environmental adaptability. Mollusks are the second largest group of animals, and are among the organisms that have successfully adapted to the nonmarine realm through aquatic-terrestrial (A-T) transition, and no comprehensive research on WGD has been reported in this group. To explore WGD and the A-T transition in Mollusca, we assembled a chromosome-level reference genome for the giant African snail Achatina immaculata, a global invasive species, and compared the genomes of two giant African snails (A. immaculata and Achatina fulica) to the other available mollusk genomes. The chromosome-level macrosynteny, colinearity blocks, Ks peak and Hox gene clusters collectively suggested the occurrence of a WGD event shared by A. immaculata and A. fulica. The estimated timing of this WGD event (∼70 MYA) was close to the speciation age of the Sigmurethra-Orthurethra (within Stylommatophora) lineage and the Cretaceous-Tertiary (K-T) mass extinction, indicating that the WGD reported herein may have been a common event shared by all Sigmurethra-Orthurethra species and could have conferred ecological adaptability and genomic plasticity allowing the survival of the K-T extinction. Based on macrosynteny, we deduced an ancestral karyotype containing 8 conserved clusters for the Gastropoda-Bivalvia lineage. To reveal the mechanism of WGD in shaping adaptability to terrestrial ecosystems, we investigated gene families related to the respiration, aestivation and immune defense of giant African snails. Several mucus-related gene families expanded early in the Stylommatophora lineage, functioning in water retention, immune defense and wound healing. The hemocyanins, PCK and FBP families were doubled and retained after WGD, enhancing the capacity for gas exchange and glucose homeostasis in aestivation. After the WGD, zinc metalloproteinase genes were highly tandemly duplicated to protect tissue against ROS damage. This evidence collectively suggests that although the WGD may not have been the direct driver of the A-T transition, it provided an important legacy for the terrestrial adaptation of the giant African snail.

scholarly journals Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants

2020 ◽  
Vol 11 ◽  
Author(s):  
Zhe Yu ◽  
Chunfang Zheng ◽  
Victor A. Albert ◽  
David Sankoff
Keyword(s):  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Duplicate Genes ◽  
Whole Genome ◽  
Coding Sequence ◽  
Genome Doubling ◽  
Whole Genome Doubling ◽  
Synteny Blocks ◽  
Genomic Divergence

We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost—there are few if any relics of the missing sequence. Pseudogenes are rare or extremely transient in this context. The potential exceptions lie exclusively with a few examples of speciation, where the synteny blocks in some larger genomes tolerate degenerate sequence during genomic divergence of two species, but not after whole genome doubling in the same species where fractionation pressure eliminates virtually all non-coding sequence.

scholarly journals Comparative Genomics of Six Juglans Species Reveals Patterns of Disease-associated Gene Family Contractions

2019 ◽  
Author(s):  
Alex Trouern-Trend ◽  
Taylor Falk ◽  
Sumaira Zaman ◽  
Madison Caballero ◽  
David B. Neale ◽  
...  
Keyword(s):  
Gene Family ◽  
Whole Genome Duplication ◽  
Common Ancestor ◽  
Genome Duplication ◽  
Gene Prediction ◽  
Gene Families ◽  
Whole Genome ◽  
High Quality ◽  
Gene Models ◽  
Genome Annotations

ABSTRACTJuglans (walnuts), the most speciose genus in the walnut family (Juglandaceae) represents most of the family’s commercially valuable fruit and wood-producing trees and includes several species used as rootstock in agriculture for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional in-house developed tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multiexonic and monoexonic putative genes to yield between 27,000 and 44,000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 89.6%. We utilized these high quality annotations to assess gene family evolution within Juglans and among Juglans and selected Eurosid species, which revealed significant contractions in several gene families in J. hindsii including disease resistance-related Wall-associated Kinase (WAK) and Catharanthus roseus Receptor-like Kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.SIGNIFICANCEHigh-quality full genome annotations for six species of walnut (Juglans) and a wingnut (Pterocarya) outgroup were constructed using semi-unsupervised gene prediction followed by gene model filtering and functional characterization. These annotations represent the most comprehensive set for any hardwood genus to date. Comparative analyses based on the gene models uncovered rapid evolution in multiple gene families related to disease-response and a whole genome duplication in a Juglandaceae common ancestor.

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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