Discovery of chloroplast capture in Juniperus excelsa complex by multi- locus phylogeny

Phytotaxa ◽  
2019 ◽  
Vol 413 (1) ◽  
pp. 11-26 ◽  
Author(s):  
FATEMEH HOJJATI ◽  
ROBERT P. ADAMS ◽  
RANDALL G. TERRY
Keyword(s):  
Concerted Evolution ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Single Copy ◽  
Species Level ◽  
Lineage Sorting ◽  
Chloroplast Capture ◽  
Juniperus Excelsa ◽  
Cp Genome

Previous studies of nrDNA (nuclear DNA) of Juniperus seravschanica indicated its nuclear DNA (ITS) was from an ancestor of J. polycarpos. However, analysis of cpDNA (chloroplast DNA) suggested the taxon had derived its chloroplast from an ancestor of J. foetidissima. That study has been viewed as putative, because the ITS region is sometimes unreliable for the detection of ancestral hybrids due to concerted evolution and lineage sorting. The recent availability of several single copy nuclear genes (SCNGs) with primers specifically designed for Juniperus presented an opportunity to fully investigate this case of putative chloroplast capture. Three phylogenetic analyses using five SCNGs (LHCA4, maldehy, myb, CnAIP3 and 4CL), ITS region, and four cpDNAs (petN- psbM, trnD-trnT, trnL-trnF and trnS-trnG) were performed on J. seravschanica, as well as other members of the J. excelsa complex: J. excelsa, J. polycarpos, and J. p. var. turcomanica. Analyses revealed incongruence between SCNGs, ITS region and cpDNA showing that J. seravschanica contains an ancestral J. foetidissima/ J. thruifera cp genome. In addition, the phylogenies indicate that the J. excelsa complex is composed of three distinct clades at the species level: J. excelsa, J. polycarpos and J. seravschanica and two varieties of J. polycarpos: J. p. var. polycarpos and J. p. var. turcomanica.

scholarly journals Identifying the North American Plum Species Phylogenetic Signal Using Nuclear, Mitochondrial, and Chloroplast DNA Markers

2016 ◽  
Vol 141 (6) ◽  
pp. 623-644 ◽  
Author(s):  
Dario J. Chavez ◽  
Thomas G. Beckman ◽  
José X. Chaparro
Keyword(s):  
Chloroplast Dna ◽  
Prunus Persica ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Its Region ◽  
Single Copy ◽  
Species Level ◽  
Species Relationships ◽  
The North

Prunus phylogeny has been extensively studied using chloroplast DNA (cpDNA) sequences. Chloroplast DNA has a slow rate of evolution, which is beneficial to determine species relationships at a deeper level. The chloroplast-based phylogenies have a limitation due to the transfer of this organelle by interspecific hybridization. This creates difficulties when studying species relationships. Interspecific hybrids in Prunus occur naturally and have been reported, which creates a problem when using cpDNA-based phylogenies to determine species relationships. The main goal of this project was to identify nuclear gene regions that could provide an improved phylogenetic signal at the species level in Prunus. A total of 11 species in Prunus and within section Prunocerasus were used. Two peach (Prunus persica) haploids were used to test the reliability of the molecular markers developed in this project to amplify single-copy genes. A total of 33 major genes associated with vernalization response, 16 with tree architecture, and 3 with isozymes, were tested. Similarly, 41 simple sequence repeat (SSR) markers, seven cpDNA regions, and the internal transcribed spacer (ITS) region, were used. Multiple gene regions were identified and provided the greatest number of characters, greatest variability, and improved phylogenetic signal at the species level in Prunus section Prunocerasus. Out of those, trnH-psbA, PGI, MAX4, AXR1, LFY, PHYE, and VRN1 are recommended for a phylogenetic analysis with a larger number of taxa. The use of potentially informative characters (PICS) as a measure of how informative a region will be for phylogenetic analyses has been previously reported beneficial in cpDNA regions and it clearly was important in this research. This will allow selecting the region(s), which can be used in phylogenetic studies with higher number of taxa.

scholarly journals Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kadriye Kahraman ◽  
Stuart James Lucas
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Single Copy ◽  
Corylus Avellana ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Complete Chloroplast Genome ◽  
A Genome ◽  
Cp Genome

Abstract Background Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar ‘Tombul’ with multiple annotation tools. Results Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales. Conclusion In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.

scholarly journals The genus Coprinellus (Basidiomycota; Agaricales) in Pakistan with the description of four new species

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 41-61 ◽  
Author(s):  
Shah Hussain ◽  
Muhammad Usman ◽  
Najam-ul-Sehar Afshan ◽  
Habib Ahmad ◽  
Junaid Khan ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Species Level ◽  
Rdna Its ◽  
The Family ◽  
Rdna Its Region ◽  
Morphological And Molecular Data ◽  
Species Descriptions

Mushrooms with a thin-fleshed pileus that becomes plicate on opening, deliquescent lamellae and dark brown to blackish basidiospores are commonly called coprinoid mushrooms. The genusCoprinellusis one of the important lineages of coprinoid mushroom in the family Psathyrellaceae. Species-level taxonomy inCoprinellusis based mainly on the presence or absence and the structure of veil and cystidia on the pileus, of cystidia on the lamellae and on basidiospore morphology. In this study, four new species ofCoprinellus(Co.campanulatus,Co.disseminatus-similis,Co.pakistanicusandCo.tenuis) are described from Pakistan. Species descriptions are based on morphological and molecular data. Phylogenetic analyses based on nuc rDNA ITS region show that the new speciesCo.campanulatusandCo.disseminatus-similisare clustered in a clade including members of section Micacei;Co.tenuisfalls in a clade with members of section Domestici; andCo.pakistanicusrecovered in a separate clade adjacent to other recently described clades of genusCoprinellus. Morpho-anatomical descriptions of the new species and comparison with closely allied taxa are provided. With this study, the number of known species ofCoprinellusin Pakistan has reached eight.

scholarly journals Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events

2021 ◽  
Author(s):  
Niklas Reichelt ◽  
Jun Wen ◽  
Claudia Paetzold ◽  
Marc Appelhans
Keyword(s):  
High Throughput Sequencing ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Single Copy ◽  
Reticulate Evolution ◽  
Gene Trees ◽  
Target Enrichment ◽  
Lineage Sorting ◽  
Phylogenetic Resolution

Background and aims: Zanthoxylum L. is the only pantropical genus within Rutaceae, with a few species native to temperate eastern Asia and North America. Efforts using Sanger sequencing failed to resolve the backbone phylogeny of Zanthoxylum. In this study, we employed target enrichment high-throughput sequencing to improve resolution. Gene trees were examined for concordance and sectional classifications of Zanthoxylum were evaluated. Off-target reads were investigated to identify putative single-copy markers for bait refinement, and low-copy markers for evidence of putative hybridization events. Methods: We developed a custom bait set for target enrichment of 745 exons in Zanthoxylum and applied it to 45 Zanthoxylum species and one Tetradium species as the outgroup. Illumina reads were processed via the HybPhyloMaker pipeline. Phylogenetic inferences were conducted using coalescent and concatenated methods. Concordance was assessed using quartet sampling. Off-target reads were assembled and putative single- and low-copy genes were extracted. Additional phylogenetic analyses were performed based on these alignments. Key results: Four major clades are supported within Zanthoxylum: the African clade, the Z. asiaticum clade, the Asian-Pacific-Australian clade, and the American-eastern Asian clade. While overall support has improved, regions of conflict are similar to those previously observed. Gene tree discordances indicate a hybridization event in the ancestor of the Hawaiian lineage, and incomplete lineage sorting for the American backbone. Off-target putative single-copy genes largely confirm on-target results, and putative low-copy genes provide additional evidence for hybridization in the Hawaiian lineage. Only two of the five sections of Zanthoxylum are resolved as monophyletic. Conclusion: Target enrichment is suitable to assess phylogenetic relationships in Zanthoxylum. Our phylogenetic analyses reveal that current sectional classifications need revision. Quartet tree concordance indicates several instances of reticulate evolution. Off-target reads are proven useful to identify additional phylogenetically informative regions for bait refinement or gene tree based approaches.

The complete plastome sequence of Gordonia penangensis Ridl. supports the transfer of Asian Gordonia into Polyspora (Theaceae)

Phytotaxa ◽  
2020 ◽  
Vol 458 (2) ◽  
pp. 159-166
Author(s):  
LE MIN CHOO ◽  
MATTI A. NIISSALO ◽  
PAUL K.F. LEONG ◽  
GILLIAN S. KHEW
Keyword(s):  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Peninsular Malaysia ◽  
Large Single Copy ◽  
Transfer Rnas ◽  
Dna Phylogeny ◽  
Small Single Copy ◽  
Unique Genes ◽  
Made In

Gordonia penangensis Ridl. is a rainforest tree native to Peninsular Malaysia and Singapore. Here we provide the complete plastome from a collection made in Singapore. The plastome sequence is 156,915 bp long with a large single copy, a small single copy and two inverted repeat regions of length 86,669, 18,200 and 26,023 bp, respectively. A total of 114 unique genes were identified, including 80 coding genes (seven in two copies), four ribosomal RNAs (all in two copies) and 30 transfer RNAs (seven in two copies). The plastome architecture and gene content are very similar to previously published plastomes from genus Polyspora, to which most Asian Gordonia species have been transferred. Phylogenetic analyses using maximum likelihood were carried out on CDS regions from complete plastomes of 88 taxa, including five out of the 43 species currently recognised to be from Polyspora. A nuclear DNA phylogeny based on ITS sequences was also generated. Our results support the view that all Asian species of Gordonia are best treated as Polyspora. Four new combinations, Polyspora penangensis (Ridl.) Niissalo & L.M.Choo, Polyspora singaporeana (Wall. ex Ridl.) Niissalo & L.M.Choo, Polyspora obtusa (Wall. ex Wight) Niissalo & L.M.Choo and Polyspora ovalis (Korth.) Niissalo & L.M.Choo are made. Three lectotypes are also designated here.

scholarly journals Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Lu Wang ◽  
Na He ◽  
Yao Li ◽  
Yanming Fang ◽  
Feilong Zhang
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Evolutionary Patterns ◽  
Closely Related Species ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Cp Genome ◽  
Rna Genes ◽  
Toxicodendron Vernicifluum

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

scholarly journals Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9132
Author(s):  
Shuilian He ◽  
Yang Yang ◽  
Ziwei Li ◽  
Xuejiao Wang ◽  
Yanbing Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Herbaceous Perennials ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Diversity Assessment ◽  
Cp Genome

The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.

scholarly journals Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Forests ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 861
Author(s):  
Huijuan Zhou ◽  
Xiaoxiao Gao ◽  
Keith Woeste ◽  
Peng Zhao ◽  
Shuoxin Zhang
Keyword(s):  
Comparative Analysis ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Species Hybrids ◽  
Rna Genes

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

scholarly journals Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12612
Author(s):  
Tian Zhang ◽  
Sipei Huang ◽  
Simin Song ◽  
Meng Zou ◽  
Tiechui Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Markers ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Medicinal Species ◽  
Protein Coding ◽  
Cp Genome ◽  
Rna Genes ◽  
Unique Genes

The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.

scholarly journals Internal Transcribed Spacer (ITS) as Dna Barcoding to Identify Fungal Species: a Review

2016 ◽  
Vol 11 (2) ◽  
pp. 37 ◽  
Author(s):  
Nurrahmi Dewi Fajarningsih
Keyword(s):  
Dna Barcoding ◽  
Internal Transcribed Spacer ◽  
Nuclear Dna ◽  
Dna Barcode ◽  
Its Region ◽  
Fungal Species ◽  
Species Level ◽  
Coding Region ◽  
Living Things ◽  
Fungal Identification

Despite the fact that fungi are important sources of both bioactive compounds and mycotoxins, and that they are very ubiquitous in our environment, their species identification is hampered by incomplete and often unclear literature. Fungi identification is primarily based on their phenotypic and physiological characteristics. Nowadays, many molecular methods to identify fungal species have been developed. One of the methods considered as a new concept to rapidly and accurately identify unknown fungal sample is DNA Barcoding. This literature review will outline the use of DNA barcoding approach to rapidly identify fungal species and the use of ITS region that recently has been designated as primary DNA barcode for fungal kingdom. “DNA barcode” is a short, highly variable and standardized DNA region with approximately 700 nucleotides in length, which is used as a unique pattern to identify living things. Internal Transcribed Spacer (ITS) region of nuclear DNA (rDNA) has become the most sequenced region to identify fungal taxonomy at species level, and even within species. ITS region is a highly polymorphic non-coding region with enough taxonomic units. Therefore, it is able to separate sequences into species level. Even though ribosomal ITS as a universal barcode marker for fungi is still hampered by few limitations, the ITS will remain as the key choice for fungal identification. The search for alternative regions as DNA marker to improve fungal identification, especially in specific heredities, has already started. 

Sign in / Sign up

Export Citation Format

Share Document