scholarly journals Complete plastome sequence of Iodes cirrhosa Turcz., the first in the Icacinaceae, comparative genomic analyses and possible split of Idoes species in response to climate changes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6663 ◽  
Author(s):  
Liqiang Wang ◽  
Hui Zhang ◽  
Mei Jiang ◽  
Haimei Chen ◽  
Linfang Huang ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Sequence Similarity ◽  
Divergence Time ◽  
Single Copy ◽  
Late Eocene ◽  
Rrna Genes ◽  
Phylogenetic Study ◽  
Comparative Genomic ◽  
Variable Regions ◽  
Next Generation Sequencing Technology

Plastome-based phylogenetic study has largely resolved the phylogeny of Icacinaceae. However, no single complete plastome sequence is available for Icacinaceae species, thereby limiting the further phylogenomics analysis of the members of this family. Here, we obtained the complete plastome sequence of Iodes cirrhosa Turcz., which is the first in Icacinaceae, by using the next-generation sequencing technology. The genome was annotated and compared with other closely related plastomes by using mVISTA. The divergence time of six Iodes species was analyzed using the BEAST software. The plastome of I. cirrhosa was 151,994 bp long, with a pair of inverted repeats (IRs, 24,973 bp) separated by a large single-copy (LSC, 84,527 bp) region and a small single-copy (SSC, 17,521 bp) region. The plastome encoded 112 unique genes, including 80 protein-coding, 28 tRNA, and four rRNA genes. Approximately 59 repeat sequences and 188 simple sequence repeats were identified. Four pairs of partially overlapped genes, namely, psbD/psbC, ndhF/Ψycf1, atpB/atpE, and rpl22/rps3, were observed. A comparison of the boundaries of the LSC, SSC, and IR regions with four other plastomes from Aquifoliales and Sapindales exhibited a high overall degree of sequence similarity. Four most highly variable regions, namely, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbJ, and rps16/trnQ-UUG, were found. Using the plastome of I. cirrhosa as reference, we reassembled the plastomes of five Iodes species. Ka/Ks ratio analyses revealed that 27 genes and 52 amino acid residue sites from 11 genes had undergone strong positive selection in the Iodes branch, with the most abundant proteins being the NDH and ribosomal proteins. Divergence-time analysis indicated that Iodes species were first formed 34.40 million years ago. Results revealed that the ancestor of the six species was likely to have split in the late Eocene epoch. In summary, the first complete plastome sequence of I. cirrhosa provided valuable information regarding the evolutionary processes of Iodes species.

scholarly journals The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1692
Author(s):  
Li Gu ◽  
Ting Su ◽  
Ming-Tai An ◽  
Guo-Xiong Hu
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Similarity ◽  
Single Copy ◽  
Structural Features ◽  
Rrna Genes ◽  
Trna Genes ◽  
Sequencing Data ◽  
High Sequence Similarity ◽  
Plastid Genomes ◽  
Cp Genome

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.

scholarly journals Comparative genome analysis revealed gene inversions, boundary expansion and contraction, and gene loss in Stemona sessilifolia (Miq.) Miq. chloroplast genome

2021 ◽  
Author(s):  
Jingting Liu ◽  
Mei Jiang ◽  
Haimei Chen ◽  
Yu Liu ◽  
Chang Liu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gene Loss ◽  
Herbal Medicines ◽  
Single Copy ◽  
Asparagus Officinalis ◽  
Accurate Identification ◽  
Protein Coding ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Next Generation Sequencing Technology

AbstractStemona sessilifolia (Miq.) Miq., commonly known as Baibu, is one of the most popular herbal medicines in Asia. In Chinese Pharmacopoeia, Baibu has multiple authentic sources, and there are many homonym herbs sold as Baibu in the herbal medicine market. The existence of the counterfeits of Baibu brings challenges to its identification. To assist the accurate identification of Baibu, we sequenced and analyzed the complete chloroplast genome of Stemona sessilifolia using next-generation sequencing technology. The genome was 154,039 bp in length, possessing a typical quadripartite structure consisting of a pair of inverted repeats (IRs: 27,094 bp) separating by a large single copy (LSC: 81,950 bp) and a small single copy (SSC: 17,901 bp). A total of 112 unique genes were identified, including 80 protein-coding, 28 transfer RNA, and four ribosomal RNA genes. Besides, 45 tandem, 27 forward, 23 palindromic, and 72 simple sequence repeats were detected in the genome by repeat analysis. Compared with its counterfeits (Asparagus officinalis and Carludovica palmate), we found that IR expansion and SSC contraction events of Stemona sessilifolia resulted in two copies of the rpl22 gene in the IR regions and partial duplication of the ndhF gene in the SSC region. Secondly, an approximately 3-kb-long inversion was identified in the LSC region, leading to the petA and cemA gene presented in the complementary strand of the chloroplast DNA molecule. Comparative analysis revealed some highly variable regions, including trnF-GAA_ndhJ, atpB_rbcL, rps15_ycf1, trnG-UCC_trnR-UCU, ndhF_rpl32. Finally, gene loss events were investigated in the context of phylogenetic relationships. In summary, the complete plastome of Stemona sessilifolia will provide valuable information for the molecular identification of Baibu and assist in elucidating the evolution of Stemona sessilifolia.

scholarly journals Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8450 ◽  
Author(s):  
Sunan Huang ◽  
Xuejun Ge ◽  
Asunción Cano ◽  
Betty Gaby Millán Salazar ◽  
Yunfei Deng
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Variable Regions ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

scholarly journals The First Transcriptome Assembly of Yenyuan Stream Salamander (Batrachuperus yenyuanensis) Provides Novel Insights into Its Molecular Evolution

2019 ◽  
Vol 20 (7) ◽  
pp. 1529 ◽  
Author(s):  
Jianli Xiong ◽  
Yunyun Lv ◽  
Yong Huang ◽  
Qiangqiang Liu
Keyword(s):  
Sequence Similarity ◽  
Transcriptome Assembly ◽  
Repetitive Sequences ◽  
Divergence Time ◽  
Gene Families ◽  
Single Copy ◽  
Phylogenetic Position ◽  
Interesting Insight ◽  
Chinese Giant Salamander ◽  
Lineage Divergence

The Yenyuan stream salamander (Batrachuperus yenyuanensis) has been previously evaluated with regards to phylogeny, population genetics, and hematology, but genomic information is sparse due to the giant genome size of salamanders which contain highly repetitive sequences, thus resulting in the lack of a complete reference genome. This study evaluates the encoding genetic sequences and provides the first transcriptome assembly of Yenyuan stream salamander based on mixed samples from the liver, spermary, muscle and spleen tissues. Using this transcriptome assembly and available encoding sequences from other vertebrates, the gene families, phylogenetic status, and species divergence time were compared or estimated. A total of 13,750 encoding sequences were successfully obtained from the transcriptome assembly of Yenyuan stream salamander, estimated to contain 40.1% of the unigenes represented in tetrapod databases. A total of 88.79% of these genes could be annotated to a biological function by current databases. Through gene family clustering, we found multiple possible isoforms of the Scribble gene—whose function is related to regeneration—based on sequence similarity. Meanwhile, we constructed a robust phylogenetic tree based on 56 single-copy orthologues, which indicates that based on phylogenetic position, the Yenyuan stream salamander presents the closest relationship with the Chinese giant salamander (Andrias davidianus) of the investigated vertebrates. Based on the fossil-calibrated phylogeny, we estimated that the lineage divergence between the ancestral Yenyuan stream salamander and the Chinese giant salamander may have occurred during the Cretaceous period (~78.4 million years ago). In conclusion, this study not only provides a candidate gene that is valuable for exploring the remarkable capacity of regeneration in the future, but also gives an interesting insight into the understanding of Yenyuan stream salamander by this first transcriptome assembly.

scholarly journals Molecular phylogenetics of stream treefrogs of the Hyloscirtus larinopygion group (Anura: Hylidae), and description of two new species from Ecuador

Zootaxa ◽  
2012 ◽  
Vol 3364 (1) ◽  
pp. 1 ◽  
Author(s):  
LUIS A. COLOMA ◽  
SOFÍA CARVAJAL-ENDARA ◽  
JUAN F. DUEÑAS ◽  
ARTURO PAREDES-RECALDE ◽  
MANUEL MORALES-MITE ◽  
...  
Keyword(s):  
New Species ◽  
Molecular Phylogenetics ◽  
Divergence Time ◽  
Late Eocene ◽  
Sister Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
12S Rrna ◽  
Locality Record ◽  
Minimum Age

We review the systematics of frogs of the Hyloscirtus larinopygion group. A new phylogenetic tree inferred frommitochondrial DNA (partial sequences of 12S rRNA, valine-tRNA, and 16S rRNA genes; ~2.3 kb) of eleven species ofthe H. larinopygion group is provided, based on maximum parsimony, maximum likelihood, and Bayesian analyses. Ourphylogeny confirms the close relationship of members of the H. larinopygion group with Andean relatives of the H.armatus group, which also occurs in the Andes. Hyloscirtus tapichalaca is placed as sister species to the rest of the H.larinopygion group, in which two clades (A+B) are evident. Although ingroup relationships are well supported, themonophyly of the H. larinopygion group and placement of H. tapichalaca require additional testing. Genetic divergencesamong species of the H. larinopygion group are shallow compared to those observed in many other anurans, with geneticdistance among sister species (H. princecharlesi and H. ptychodactylus) as low as 1.31%. However, this pattern isconcordant with radiations in other highland Andean lineages of anurans that show marked morphological or behavioraldifferentiation, but low divergence in mitochondrial markers. Divergence-time analyses (using BEAST) indicate that theHyloscirtus clade is a relatively ancient lineage that appeared in the Eocene, at a minimum age of 51.2 million years ago(MYA), while the H. larinopygion group originated in the Middle-Late Eocene at a minimum age of 40.9 MYA. Ourresults might suggest a rapid radiation of Hyloscirtus starting in the Miocene into the Pliocene, from at least 14.2 MYA tothe most recent divergence between sister taxa at ~2.6 MYA. We also describe two sympatric new species of Hyloscirtusfrom northwestern Ecuador: H. criptico sp. nov. and H. princecharlesi sp. nov. We diagnose them by their phylogeneticposition (they are not sister to each other), genetic divergence, and a unique combination of color patterns, and othermorphological features. Additionally, we describe the suctorial tadpoles and the extreme ontogenic color changes in H.larinopygion, H. lindae, H. pantostictus, H. princecharlesi, H. psarolaimus, and H. tigrinus. Furthermore, we describe theosteology of H. criptico, H. lindae, H. pacha, H. pantostictus, H. princecharlesi, H. psarolaimus, H. ptychodactylus, andH. staufferorum. We describe vocalizations of H. lindae, H. pacha, H. pantostictus, H. pasarolaimus, H. staufferorum, andH. tapichalaca. Hyloscirtus tigrinus is recorded for the first time in Ecuador and its range is extended 62.4 km (airlinedistance), from its southernmost locality record in Departamento de Nariño, Colombia. Most species of the H.larinopygion group are currently severely threatened by extinction, after surviving the catastrophic extinctions in the1980s and 1990s that led to the disappearance of many other sympatric anurans that bred in swiftly flowing water and hadlotic water tadpoles in the Andean highlands. Research and conservation actions are urgently needed for these species. Inorder to better call attention to these conservation issues, we name one of the new species in honor of Prince Charles ofWales, who is contributing significantly to the growth of awareness in the battle against tropical deforestation, climate change, and the catastrophic extinction of rainforest amphibians.

Comparative genomic analyses reveal functional insights into key determinants of the pathogenesis of Pectobacterium actinidiae to kiwifruit

2020 ◽  
Author(s):  
Qi Lu ◽  
Fuhua Yan ◽  
Yuanyuan Liu ◽  
Qiaohong Li ◽  
Meng Yang ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Bacterial Species ◽  
Soft Rot ◽  
Single Copy ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Virulence Determinants ◽  
Secretion Systems ◽  
Genome Level ◽  
Functional Analyses

The Gram-negative (G-) bacterial species Pectobacterium actinidiae causes summer canker in kiwifruit plants. However, little is known about its virulence factors and the mechanisms of genetic adaptation. We aimed to identify the key determinants that control the virulence of P. actinidiae to kiwifruit by genomic and functional analyses. Within four P. actinidiae isolates, low genetic variability displayed and shared an average 98.7% and 82% in genome-level sequence similarity and coding genes. Phylogenetic analysis, based on both the bulk of single nucleotide polymorphisms (SNPs) and genomes single-copy genes, revealed that P. actinidiae strains cluster into a sole clade, whichclosly related to the clades of P. odoriferum, the pathogen of vegetable soft rot from a completely different host range. By comparison with these two clades of genomes, 746 unique core orthologs/genes were enriched in the clades of P. actinidiae, especially for the key virulence determinants involved in the biosynthesis of secretion systems (type III, III and IV), iron, flagellar and the quorum-sensing system. Our results provide insights into the pathogenomics basis underlying the genetic diversification and evolution of pathogenicity in the species of P. actinidiae.

scholarly journals Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ju Namgung ◽  
Hoang Dang Khoa Do ◽  
Changkyun Kim ◽  
Hyeok Jae Choi ◽  
Joo‑Hwan Kim
Keyword(s):  
Middle Eocene ◽  
Ornamental Plants ◽  
Divergence Time ◽  
Late Eocene ◽  
Molecular Dating ◽  
Rrna Genes ◽  
Phylogenomic Analysis ◽  
South American ◽  
Long Distance ◽  
Chloroplast Genomes

AbstractAllioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, five of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein-coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA, psbA upstream, rpl32-trnL-UAG, ycf1, rpl22, matK, and ndhF, were identified in the studied Allium species. Additionally, we present the first phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, five species of Amaryllidoideae, one species of Agapanthoideae, and five species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae-Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by differentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for Allioideae and subsequent spread to Eurasia during the middle Eocene. Cool and arid conditions during the late Eocene led to isolation between African and Eurasian species. African Allioideae may have diverged to South American taxa in the late Oligocene. Rather than vicariance, long-distance dispersal is the most likely explanation for intercontinental distribution of African and South American Allioideae species.

scholarly journals Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 474 ◽  
Author(s):  
Dong-Mei Li ◽  
Chao-Yi Zhao ◽  
Xiao-Fei Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Species Identification ◽  
Single Copy ◽  
Rrna Genes ◽  
Genome Sequences ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Kaempferia Galanga ◽  
Chloroplast Genomes

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

scholarly journals Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1332
Author(s):  
Kai Jiang ◽  
Li-Yuan Miao ◽  
Zheng-Wei Wang ◽  
Zi-Yi Ni ◽  
Chao Hu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Single Copy ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Protein Coding ◽  
Variable Regions ◽  
Sequencing Platform ◽  
Close Relationship

Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa.

scholarly journals The small ribosomal subunit RNA isoforms in Plasmodium cynomolgi.

Genetics ◽  
1994 ◽  
Vol 136 (3) ◽  
pp. 857-865 ◽  
Author(s):  
V Corredor ◽  
V Enea
Keyword(s):  
Ribosomal Subunit ◽  
Plasmodium Species ◽  
Single Copy ◽  
Small Subunit ◽  
Rrna Genes ◽  
Last Common Ancestor ◽  
Small Subunit Rrna ◽  
Specific Sequence ◽  
Variable Regions ◽  
Plasmodium Cynomolgi

Abstract We report the isolation, characterization and analysis of the small subunit rRNA genes in Plasmodium cynomolgi (Ceylon). As in other Plasmodium species, these genes are present in low copy number, are unlinked and form two types that are distinct in sequence and are expressed stage specifically. The asexually expressed (type A) genes are present in four copies in the Ceylon- and in five copies in the Berok-strain. Surprisingly, the sexually expressed (type B) gene is present in a single copy. The vast majority of the differences between gene types is confined to the variable regions. The pattern of divergence is different from that observed in Plasmodium berghei or in Plasmodium falciparum. Analysis of the small subunit rRNA sequences of P. cynomolgi, P. berghei and P. falciparum, indicates that the two gene types do not evolve independently but rather interact (through gene conversion or some form of recombination) to such an extent as to erase whatever stage-specific sequence signatures they may have had in the last common ancestor.

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