scholarly journals Integrating transcriptomes to investigate genes associated with adaptation to aquatic environments, and assess phylogenetic conflict and whole-genome duplications in Alismatales

2021 ◽  
Author(s):  
Lingyun Chen ◽  
Bei Lu ◽  
Diego F. Morales-Briones ◽  
Michael L. Moody ◽  
Fan Liu ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Incomplete Lineage Sorting ◽  
Recent Common Ancestor ◽  
Aquatic Environments ◽  
Whole Genome ◽  
Freshwater Species ◽  
Freshwater Algae ◽  
Terrestrial Plants ◽  
Most Recent Common Ancestor

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times beyond. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptation to aquatic environments by including 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptation, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as ((Tofieldiaceae, Araceae), core Alismatids). There is phylogenetic conflict among the backbone of the three main clades that could be due to incomplete lineage sorting and introgression. We identified 18 putative WGD events. One of them had occurred at the most recent common ancestor of core Alismatids, and four occurred at seagrass lineages. Other events are distributed in terrestrial, emergent, and submersed life-forms and seagrasses across Alismatales. We also found that lineage and life-form were each important for different evolutionary patterns for the genes related to freshwater/marine adaptation. For example, some light or ethylene-related genes were lost in the seagrass Zosteraceae, but present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments, phylogeny, and whole-genome duplication of Alismatales.

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 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.

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 Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gareth B. Gillard ◽  
Lars Grønvold ◽  
Line L. Røsæg ◽  
Matilde Mengkrog Holen ◽  
Øystein Monsen ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Whole Genome Duplication ◽  
Genome Stability ◽  
Genome Duplication ◽  
Gene Dosage ◽  
Whole Genome ◽  
Specific Expression ◽  
Tissue Specific ◽  
Genome Doubling ◽  
Expression Evolution

Abstract Background Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80–100 million years ago. Results We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of “toxic mutations”. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. Conclusions Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

scholarly journals Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amit Rai ◽  
Hideki Hirakawa ◽  
Ryo Nakabayashi ◽  
Shinji Kikuchi ◽  
Koki Hayashi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Experimental Validation ◽  
Genome Duplication ◽  
Indole Alkaloids ◽  
Whole Genome ◽  
Comparative Genome Analysis ◽  
Plant Genomes ◽  
Genome Triplication ◽  
Chromosome Level

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

scholarly journals Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Nishiki ◽  
Kenichi Lee ◽  
Mizue Kanai ◽  
Shu-ichi Nakayama ◽  
Makoto Ohnishi
Keyword(s):  
Genetic Difference ◽  
Phylogenetic Analyses ◽  
Treponema Pallidum ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Global Perspectives ◽  
Most Recent Common Ancestor ◽  
Sex With Men

AbstractJapan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.

Whole-genome analysis-based phylogeographic investigation of Streptococcus pneumoniae serotype 19A sequence type 320 isolates in Japan.

2021 ◽  
Author(s):  
Satoshi Nakano ◽  
Takao Fujisawa ◽  
Bin Chang ◽  
Yutaka Ito ◽  
Hideki Akeda ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Sampling Bias ◽  
Health Concern ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Identification Rate ◽  
Most Recent Common Ancestor ◽  
The Common ◽  
The U.S

After the introduction of the seven-valent pneumococcal conjugate vaccine, the global spread of multidrug resistant serotype 19A-ST320 strains became a public health concern. In Japan, the main genotype of serotype 19A was ST3111, and the identification rate of ST320 was low. Although the isolates were sporadically detected in both adults and children, their origin remains unknown. Thus, by combining pneumococcal isolates collected in three nationwide pneumococcal surveillance studies conducted in Japan between 2008 and 2020, we analyzed 56 serotype 19A-ST320 isolates along with 931 global isolates, using whole-genome sequencing to uncover the transmission route of the globally distributed clone in Japan. The clone was frequently detected in Okinawa Prefecture, where the U.S. returned to Japan in 1972. Phylogenetic analysis demonstrated that the isolates from Japan were genetically related to those from the U.S.; therefore, the common ancestor may have originated in the U.S. In addition, Bayesian analysis suggested that the time to the most recent common ancestor of the isolates form Japan and the U.S. was approximately the 1990s to 2000, suggesting the possibility that the common ancestor could have already spread in the U.S. before the Taiwan 19F-14 isolate was first identified in a Taiwanese hospital in 1997. The phylogeographical analysis supported the transmission of the clone from the U.S. to Japan, but the analysis could be influenced by sampling bias. These results suggested the possibility that the serotype 19A-ST320 clone had already spread in the U.S. before being imported into Japan.

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