Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes

Abstract Background and Aims Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. Methods A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Key Results Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Conclusions Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

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Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes

PeerJ ◽

10.7717/peerj.7480 ◽

2019 ◽

Vol 7 ◽

pp. e7480 ◽

Cited By ~ 5

Author(s):

Qi Chen ◽

Xiaobo Wu ◽

Dequan Zhang

Keyword(s):

Chloroplast Genome ◽

Related Species ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Gc Content ◽

Closely Related Species ◽

Complete Chloroplast Genome ◽

Plastid Genomes ◽

Chloroplast Genomes ◽

Fritillaria Cirrhosa

Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.

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

10.21203/rs.3.rs-304635/v1 ◽

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.

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Development of Plastid Genomic Resources for Discrimination and Classification of Epimedium wushanense (Berberidaceae)

International Journal of Molecular Sciences ◽

10.3390/ijms20164003 ◽

2019 ◽

Vol 20 (16) ◽

pp. 4003 ◽

Cited By ~ 4

Author(s):

Guo ◽

Ren ◽

Xu ◽

Liao ◽

Song ◽

...

Keyword(s):

Related Species ◽

Phylogenetic Trees ◽

Morphological Characteristics ◽

Rrna Genes ◽

Closely Related Species ◽

Protein Coding ◽

Important Species ◽

Plastid Genomes ◽

First Time

Epimedium wushanense (Berberidaceae) is recorded as the source plant of Epimedii Wushanensis Folium in the Chinese Pharmacopoeia. However, controversies exist on the classification of E. wushanense and its closely related species, namely, E. pseudowushanense, E. chlorandrum, E. mikinorii, E. ilicifolium, and E. borealiguizhouense. These species are often confused with one another because of their highly similar morphological characteristics. This confusion leads to misuse in the medicinal market threatening efficiency and safety. Here, we studied the plastid genomes of these Epimedium species. Results show that the plastid genomes of E. wushanense and its relative species are typical circular tetramerous structure, with lengths of 156,855–158,251 bp. A total of 112 genes were identified from the Epimedium plastid genomes, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A loss of rpl32 gene in E. chlorandrum was found for the first time in this study. The phylogenetic trees constructed indicated that E. wushanense can be distinguished from its closely related species. E. wushanense shows a closer relationship to species in ser. Dolichocerae. In conclusion, the use of plastid genomes contributes useful genetic information for identifying medicinally important species E. wushanense and provides new evidence for understanding phylogenetic relationships within the Epimedium genus.

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Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Scientific Reports ◽

10.1038/s41598-021-83664-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Maria Alejandra Serna-Sánchez ◽

Oscar A. Pérez-Escobar ◽

Diego Bogarín ◽

María Fernanda Torres-Jimenez ◽

Astrid Catalina Alvarez-Yela ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Divergence Times ◽

Molecular Clocks ◽

Phylogenetic Placement ◽

Plastid Genomes ◽

Phylogenetic Reconstructions ◽

A Genome ◽

Tree Models ◽

Phylogenomic Analyses ◽

First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

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Genealogical inference of closely related species based on microsatellites

Genetics Research ◽

10.1017/s0016672301005444 ◽

2001 ◽

Vol 78 (3) ◽

pp. 209-212 ◽

Cited By ~ 31

Author(s):

CHRISTIAN SCHLÖTTERER

Keyword(s):

Population Genetics ◽

Related Species ◽

Phylogenetic Relationships ◽

Microsatellite Analysis ◽

Closely Related Species ◽

Research Areas

Despite their unmatched popularity in many research areas, microsatellites have not yet become a major tool for the inference of genealogical relationships of closely related species. Recent studies have successfully extended the repertoire of microsatellite analysis beyond population genetics and demonstrate that phylogenetic relationships of closely related species can be inferred accurately with fewer loci than previously assumed.

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The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

Forests ◽

10.3390/f11111179 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1179

Author(s):

Ueric José Borges de Souza ◽

Luciana Cristina Vitorino ◽

Layara Alexandre Bessa ◽

Fabiano Guimarães Silva

Keyword(s):

Plastid Genome ◽

Structural Characteristics ◽

Gc Content ◽

Single Copy ◽

Chloroplast Genes ◽

Artocarpus Heterophyllus ◽

Plastid Genomes ◽

The Family ◽

High Degree ◽

Degree Of Similarity

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.

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Phylogeny and Comparative Analysis of Chinese Chamaesium Species Revealed by the Complete Plastid Genome

Plants ◽

10.3390/plants9080965 ◽

2020 ◽

Vol 9 (8) ◽

pp. 965 ◽

Cited By ~ 1

Author(s):

Xian-Lin Guo ◽

Hong-Yi Zheng ◽

Megan Price ◽

Song-Dong Zhou ◽

Xing-Jin He

Keyword(s):

Plastid Genome ◽

Molecular Phylogenetics ◽

Genome Structure ◽

Gc Content ◽

Plastid Genomes ◽

Second Generation Sequencing ◽

Ssr Loci ◽

Small Genus ◽

Generation Sequencing ◽

Simple Sequence

Chamaesium H. Wolff (Apiaceae, Apioideae) is a small genus mainly distributed in the Hengduan Mountains and the Himalayas. Ten species of Chamaesium have been described and nine species are distributed in China. Recent advances in molecular phylogenetics have revolutionized our understanding of Chinese Chamaesium taxonomy and evolution. However, an accurate phylogenetic relationship in Chamaesium based on the second-generation sequencing technology remains poorly understood. Here, we newly assembled nine plastid genomes from the nine Chinese Chamaesium species and combined these genomes with eight other species from five genera to perform a phylogenic analysis by maximum likelihood (ML) using the complete plastid genome and analyzed genome structure, GC content, species pairwise Ka/Ks ratios and the simple sequence repeat (SSR) component. We found that the nine species’ plastid genomes ranged from 152,703 bp (C. thalictrifolium) to 155,712 bp (C. mallaeanum), and contained 133 genes, 34 SSR types and 585 SSR loci. We also found 20,953–21,115 codons from 53 coding sequence (CDS) regions, 38.4–38.7% GC content of the total genome and low Ka/Ks (0.27–0.43) ratios of 53 aligned CDS. These results will facilitate our further understanding of the evolution of the genus Chamaesium.

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Evolutionary characterization of a Y chromosomal sequence conserved in the genus Mus

Genetics Research ◽

10.1017/s001667230002752x ◽

1988 ◽

Vol 52 (2) ◽

pp. 145-150 ◽

Cited By ~ 5

Author(s):

Yutaka Nishioka

Keyword(s):

Related Species ◽

Rattus Norvegicus ◽

Phylogenetic Relationships ◽

Repetitive Sequence ◽

Repetitive Sequences ◽

Closely Related Species ◽

Specific Hybridization ◽

Male Specific ◽

Chromosomal Sequence

SummaryThe extent of accumulation of mouse Y chromosomal repetitive sequences generally correlates with the known phylogenetic relationships in the genus Mus. However, we describe here a M. musculus Y chromosomal repetitive sequence, designated as ACClfl, whose accumulation patterns among eight Mus species do not correspond to their phylogenetic relationships. Although male-specific hybridization bands were present in all the species examined, significant accumulation (> 200 copies) in the Y chromosomes was found in M. minutoides (subgenus Nannomys), M. pahari (subgenus Coelomys) and M. saxicola (subgenus Pyromys) as well as in the three closely related species M. hortulanus, M. musculus and M. spretus that belong to the subgenus Mus. Unexpectedly, the Y chromosomes of M. caroli and M. cookii (both subgenus Mus) had considerably reduced amounts of ACClfl-related sequences. Furthermore, in rats (Rattus norvegicus) the major accumulation sites appear to be autosomal. These observations suggest that caution must be taken in the interpretation of data obtained with repetitive sequences that have evolved quickly.

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Morphological and molecular evidence for a new species of Russula (Russulaceae) from southern China

Phytotaxa ◽

10.11646/phytotaxa.202.2.2 ◽

2015 ◽

Vol 202 (2) ◽

pp. 94 ◽

Cited By ~ 8

Author(s):

Yang Kun Li ◽

Xin Zhang ◽

Ye Yuan ◽

Zheng Cao ◽

Jun Feng Liang

Keyword(s):

New Species ◽

Related Species ◽

Phylogenetic Relationships ◽

Internal Transcribed Spacer ◽

Southern China ◽

Its Region ◽

Molecular Evidence ◽

Closely Related Species ◽

A New Species

Russula subrutilans sp. nov., a new species of Russula is described from southern China. It is unique for having buff pink to light congo-pink pileus, distant ventricose to subventricose lamellae with rare lamellulae, globose to broadly ellipsoid spores with bluntly conical warts forming a partial reticulum, and narrowly clavate to clavate cheilocystidia and pleurocysitidia with variable tips. Phylogenetic relationships among the new species and other closely related species in the genus are inferred based on the internal transcribed spacer (ITS) region.

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Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances

10.1101/2021.04.23.441144 ◽

2021 ◽

Author(s):

Belen Escobari ◽

Thomas Borsch ◽

Taylor S. Quedensley ◽

Michael Gruenstaeudl

Keyword(s):

Dna Sequence ◽

Phylogenetic Trees ◽

Plastid Genome ◽

Intergenic Spacer ◽

Genetic Distances ◽

Sequence Alignments ◽

Multiple Sequence ◽

Plastid Genomes ◽

Tree Inference ◽

The Impact

ABSTRACTPREMISEThe genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it.METHODSWe sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference.RESULTSOur results indicate that the inclusion of all plastid genome partitions is needed to infer fully resolved phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia.CONCLUSIONSThe concatenation and combined analysis of all plastid genome partitions and the construction of manually curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of strongly supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence datasets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.

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