scholarly journals Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1338
Author(s):  
JiYoung Yang ◽  
Koji Takayama ◽  
Jin-Suk Youn ◽  
Jae-Hong Pak ◽  
Seung-Chul Kim
Keyword(s):  
Sequence Similarity ◽  
East Asian ◽  
Geographic Origin ◽  
Gc Content ◽  
European Beech ◽  
Protein Coding ◽  
Ulleung Island ◽  
Usage Patterns ◽  
Phylogenomic Analyses ◽  
Close Relatives

Beech trees of the genus Fagus (Fagaceae) are monoecious and distributed in the Northern Hemisphere. They represent an important component of mixed broad-leaved evergreen–deciduous forests and are an economically important source of timber. Despite their ecological and economical importance, however, little is known regarding the overall plastome evolution among Fagus species in East Asia. In particular, the taxonomic position and status of F. multinervis, a beech species endemic to Ulleung Island of Korea, remains unclear even today. Therefore, in this study, we characterized four newly completed plastomes of East Asian Fagus species (one accession each of F. crenata and F. multinervis and two accessions of F. japonica). Moreover, we performed phylogenomic analyses comparing these four plastomes with F. sylvatica (European beech) plastome. The four plastomes were highly conserved, and their size ranged from 158,163 to 158,348 base pair (bp). The overall GC content was 37.1%, and the sequence similarity ranged from 99.8% to 99.99%. Codon usage patterns were similar among species, and 7 of 77 common protein-coding genes were under positive selection. Furthermore, we identified five highly variable hotspot regions of the Fagus plastomes (ccsA/ndhD, ndhD/psaC, ndhF/rpl32, trnS-GCU/trnG-UCC, and ycf1). Phylogenetic analysis revealed the monophyly of Fagus as well as early divergence of the subgenus Fagus and monophyletic Engleriana. Finally, phylogenetic results supported the taxonomic distinction of F. multinervis from its close relatives F. engleriana and F. japonica. However, the sister species and geographic origin of F. multinervis on Ulleung Island could not be determined.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

2016 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals Mitochondrial genome evolution of placozoans: gene rearrangements and repeat expansions

2020 ◽  
Author(s):  
Hideyuki Miyazawa ◽  
Hans-Jürgen Osigus ◽  
Sarah Rolfes ◽  
Kai Kamm ◽  
Bernd Schierwater ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gc Content ◽  
Distribution Patterns ◽  
Sister Group ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Inverted Repeats ◽  
Protein Coding ◽  
Group I ◽  
Phylogenomic Analyses

Abstract Placozoans, non-bilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNA are circular chromosomes of 32-43 kbp in size, which encode 12 protein-coding genes, 24 tRNAs, and 2 rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon-intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Since P. mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.

scholarly journals Characterization of Haemophilus parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China

2018 ◽  
Vol 13 (1) ◽  
pp. 217-226
Author(s):  
Yongliang Che ◽  
Longbai Wang ◽  
Xuemin Wu ◽  
Rujing Chen ◽  
Chenyan Wang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Genomic Sequence ◽  
Virulent Strain ◽  
Sequence Similarity ◽  
Gc Content ◽  
Trna Genes ◽  
Haemophilus Parasuis ◽  
Protein Coding ◽  
Query Cover ◽  
Genes Encoding

AbstractHaemophilus parasuisis an important bacterium affecting pigs, causing Glässer’s disease. To further characterize this species, we determined the complete genomic sequence ofH. parasuisCL120103, which was isolated from diseased pigs. The strainH. parasuisCL120103 was identified as serovar 2. The size of the largest scaffold is 2,326,318 bp and contains 145 large contigs, with the N50 contig being 20,573 bp in length. The complete genome ofH. parasuisCL120103 is 2,305,354 bp in length with 39.97% GC content and contains 2227 protein-coding genes, 19 ribosomal rRNA operons and 60 tRNA genes. Sequence similarity of the genome ofH. parasuisCL120103 to the previously sequenced genome ofH. parasuiswas up to 96% and query cover to 86%. Annotation of the genome ofH. parasuisCL120103 identified a number of genes encoding potential virulence factors. These virulence factors are involved in metabolism, adhesion, secretion and LPS biosynthesis. These related genes pave the way to better understand mechanisms underlying metabolic capabilities. The comprehensive genetic and phylogenetic analysis shows thatH. parasuisis closely related toActinobacillus pleuropneumoniaeand provides a foundation for future experimental confirmation of the virulence and pathogen-host interactions inH. parasuis.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2463 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V. Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

2016 ◽  
Author(s):  
Mei Fang Lin ◽  
Wen Hwa Chou ◽  
Marcelo V Kitahara ◽  
Chao Lun Allen Chen ◽  
David John Miller ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Single Copy ◽  
Scleractinian Corals ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Nuclear Markers ◽  
Protein Coding ◽  
Mitochondrial Sequences ◽  
Phylogenomic Analyses ◽  
Close Relatives

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

scholarly journals Complete plastid genome of Angelica, Ostericum and related species (Apiaceae): genomic evolution and phylogenetic implications

2021 ◽  
Author(s):  
Qiu-Ping Jiang ◽  
Megan Price ◽  
Xian-Lin Guo ◽  
Wei Gou ◽  
Song-Dong Zhou ◽  
...  
Keyword(s):  
Related Species ◽  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Protein Coding ◽  
Next Generation Sequencing Technology ◽  
Plastid Genomes ◽  
Phylogenetic Implications ◽  
Usage Patterns ◽  
Intergenic Regions

Abstract Background Subtribe Angelicinae is a large and taxonomically complex group of Apiaceae, encompassing Angelica, Archangelica, Coelopleurum, Conioselinum, Czernaevia, Glehnia, Levisticum and Ostericum that are distributed in the Northern Hemisphere, and whether this taxa is natural is debatable, especially between Angelica and Ostericum. To determine genommic evolution and phylogenetic relationships between Angelica, Ostericum, and related species, we newly assembled the complete plastid genome sequences of eight subtribe Angelicinae species and Melanosciadium pimpinelloideum using next-generation sequencing technology. Results The nine plastid genomes we sequenced were conserved, and their size ranged from 146765 bp to 164329 bp, showing the typical quadripartite circular structure with an overall GC content of 37.5–37.8%. IR boundary analyses showed that the genes in the LSC region transfer into the IR regions and the SSC region was relatively stable. Codon usage patterns were similar among these species and we identified 66–86 SSRs, with the most abundant SSR being mononucleotide. The Pi analyses showed that petA-psbJ(0.02778), atpI-atpH(0.17333) and petA-psbJ(0.04726) intergenic regions had the highest Pi values in Angelica, Ostericum, and ten species, respectively. Conclusions Ostericum exhibited significant differences in size of genomes, content of genes and tRNAs, GC content, some type of SSRs, and IR boundaries to Angelica, and phylogenetic analyses found the relatedness between Angelica and Ostericum is more distant in protein-coding genes of the plastid genomes trees and nrITS trees.

scholarly journals From de novo to ‘de nono’: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

2018 ◽  
Author(s):  
Claudio Casola
Keyword(s):  
De Novo ◽  
Sequence Similarity ◽  
Gc Content ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Gene Sets ◽  
De Novo Genes ◽  
De Novo Gene ◽  
Similarity Searches ◽  
Novel Protein

AbstractThe evolution of novel protein-coding genes from noncoding regions of the genome is one of the most compelling evidence for genetic innovations in nature. One popular approach to identify de novo genes is phylostratigraphy, which consists of determining the approximate time of origin (age) of a gene based on its distribution along a species phylogeny. Several studies have revealed significant flaws in determining the age of genes, including de novo genes, using phylostratigraphy alone. However, the rate of false positives in de novo gene surveys, based on phylostratigraphy, remains unknown. Here, I re-analyze the findings from three studies, two of which identified tens to hundreds of rodent-specific de novo genes adopting a phylostratigraphy-centered approach. Most of the putative de novo genes discovered in these investigations are no longer included in recently updated mouse gene sets. Using a combination of synteny information and sequence similarity searches, I show that about 60% of the remaining 381 putative de novo genes share homology with genes from other vertebrates, originated through gene duplication, and/or share no synteny information with non-rodent mammals. These results led to an estimated rate of ∼12 de novo genes per million year in mouse. Contrary to a previous study (Wilson et al. 2017), I found no evidence supporting the preadaptation hypothesis of de novo gene formation. Nearly half of the de novo genes confirmed in this study are within older genes, indicating that co-option of preexisting regulatory regions and a higher GC content may facilitate the origin of novel genes.

scholarly journals Comparative Analysis and Phylogenetic Implications of Plastomes of Five Genera in Subfamily Amyridoideae (Rutaceae)

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 277
Author(s):  
Kuo Sun ◽  
Qiao-Yun Liu ◽  
Ao Wang ◽  
Yong-Wei Gao ◽  
Liang-Cheng Zhao ◽  
...  
Keyword(s):  
East Asian ◽  
Structural Variations ◽  
Phylogenetic Implications ◽  
Phylogenetic Hypotheses ◽  
Recent Classification ◽  
Toddalia Asiatica ◽  
Phylogenomic Analyses ◽  
Close Relatives ◽  
Varia Tions

In the most recent classification of Rutaceae, Amyridoideae is the largest and most diverse subfamily. In Amyridoideae, the genera Phellodendron, Tetradium, Toddalia and Zanthoxylum were proposed as “proto-Rutaceae”due to substantial phytochemical similarities. In this study, we investigated the plastome varia-tions in eight species representing these four genera and Melicope. All plastomes exhibited a typical quadripartite structure with four regions (LSC, SSC, IRa and IRb). The whole chloroplast genome size ranged from 158,383 bp to 159,014 bp and the gene number ranged from 115 to 116. By comparative analyses, we found that there were structural variations at the LSC/IR and SSC/IR borders of the plastomes in the five genera, especially in Melicope. Three most divergent regions (trnH-psbA, trnE-trnT and psaB) were found from the LSC region, which had great potential for developing effective genetic markers. In addition, we conducted a phylogenomic analyses of the “proto-Rutaceae”and related taxa with plastomes data from 36 species. Our results showed that (1) Phellodendron, Tetradium, Toddalia and Zanthoxylum were confirmed as close relatives and grouped together as the ‘proto-Rutaceae’, (2) Phellodendron was sister to Tetradium, and Toddalia was deeply nested within Zanthoxylum, and (3) Toddalia asiatica was closely related to the Southwest Pacific and East Asian species of Zanthoxylum, and Melicope pteleifolia was more closely related to Acronychia than it is to Tetradium. This study provided new insights into the plastome structural varia-tions in subfamily Amyridoideae, and demonstrated that the plastomes data were sufficiently robust to explore implications of the phylogeny for the previous phylogenetic hypotheses.

scholarly journals The Chloroplast Genome Comparative Characteristic of Artificial Breeding Tree, a Case About Broussonetia Kazinoki × Broussonetia Papyifera

2020 ◽  
Author(s):  
Wan zhang ◽  
Guiyan Yang ◽  
Yunlin Zhao ◽  
Zhenggang Xu ◽  
Huimin Huang ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Genome Structure ◽  
Gc Content ◽  
Hybrid Origin ◽  
Comparative Characteristic ◽  
Protein Coding ◽  
Species Ranges ◽  
Artificial Breeding ◽  
Cp Genome ◽  
High Degree

Abstract Background: Broussonetia kazinoki × Broussonetia papyifera (ZJGS) is a hybrid species, which has a very complicated hybrid origin. Its excellent characteristics make it both ecological benefits and economically valuable.Results: This study aimes to further understand ZJGS and Moraceae taxa through the ZJGS chloroplast (cp) genome structure and the comparative with 12 closely related Moraceae species, especially the cross parent B. kazinoki and B. papyrifera. The analyses show that ZJGS cp genome is 160,903 bp in length. Among the 13 Moraceae species, the cp genome length of seven Broussonetia species (ranges from 160,239 bp to 162,594 bp) is larger than that of six Morus species (ranges from 158,459 bp to 159,265 bp). However, the average GC content of Broussonetia species is lower than that of Morus species, which is 35.72% and 36.26%, respectively. Compared with Moraceae species, the ZJGS cp genome has a high degree of sequence similarity with B. kazinoki and B. monoica. In the comparison of repeated sequences, ZJGS and its maternal species B. kazinoki shows similar simple sequence repeats (SSRs) frequency. Among the 77 shared protein-coding genes (PCGs) in Moraceae species, the obvious positive selection of Ka/Ks ratios acted on petD and rpl16 genes of B. kazinoki and B. papyrifera, respectively, and the Ka/Ks ratio > 3. Phylogenetic analysis based on shared PCGs from 28 species shows that ZJGS is closely related to maternal B. kazinoki.Conclusions: These findings provide data support for the origin of ZJGS hybridization, and provide genomic resources for future ZJGS resource development and molecular breeding.

scholarly journals Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees

Insects ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 652
Author(s):  
Hongwei Tan ◽  
Muhammad Naeem ◽  
Hussain Ali ◽  
Muhammad Shakeel ◽  
Haiou Kuang ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Genome Sequence ◽  
Apis Cerana ◽  
Gc Content ◽  
Protein Domain ◽  
Pollination Services ◽  
Protein Coding ◽  
Close Relationship ◽  
Genome Scale ◽  
Asian Honeybee

In Pakistan, Apis cerana, the Asian honeybee, has been used for honey production and pollination services. However, its genomic makeup and phylogenetic relationship with those in other countries are still unknown. We collected A. cerana samples from the main cerana-keeping region in Pakistan and performed whole genome sequencing. A total of 28 Gb of Illumina shotgun reads were generated, which were used to assemble the genome. The obtained genome assembly had a total length of 214 Mb, with a GC content of 32.77%. The assembly had a scaffold N50 of 2.85 Mb and a BUSCO completeness score of 99%, suggesting a remarkably complete genome sequence for A. cerana in Pakistan. A MAKER pipeline was employed to annotate the genome sequence, and a total of 11,864 protein-coding genes were identified. Of them, 6750 genes were assigned at least one GO term, and 8813 genes were annotated with at least one protein domain. Genome-scale phylogeny analysis indicated an unexpectedly close relationship between A. cerana in Pakistan and those in China, suggesting a potential human introduction of the species between the two countries. Our results will facilitate the genetic improvement and conservation of A. cerana in Pakistan.

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