Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis

Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of A. sinensis using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished Carya species. We analyzed all 26 species’ chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that A. sinensis indeed belongs to the Carya genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that A. sinensis should be called C. sinensis.

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Morphometry and Phylogeny of the Different Populations of Selaginella tamariscina (P. Beauv.) Spring and S. pulvinata (Hook. & Grev.) Maxim. in Northern Thailand

Chiang Mai University Journal of Natural Sciences ◽

10.12982/cmujns.2021.077 ◽

2021 ◽

Vol 20 (4) ◽

Author(s):

Udon Pongkawong ◽

◽

Jatupol Kampuansai ◽

Rossarin Pollawatn ◽

Arunothai Jampeetong ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Southern China ◽

Phylogenetic Analyses ◽

Dna Barcode ◽

Morphological Characteristics ◽

Taxonomic Status ◽

Morphological Characters ◽

The Philippines ◽

Northern Thailand ◽

Selaginella Tamariscina

Abstract “Dok Hin” is the Thai local name for Selaginella species that form rosettes. They commonly distributes in Siberia, Manchuria, southern China, Japan, the Philippines and Thailand. Morphology of Dok Hin is very resemble leading to misidentification. So, exactly number of species of Dok Hin in Thailand and their differences in morphological characteristics is not well understood. Thus, revision of morphological characters and phylogenetic confirmation of the taxonomic identification are needed. This study aims to examine morphological charateristics and phylogenetic patterns in eight populations of the Dok Hin in Northern Thailand. Morphology of Dok Hin from each populations was quantitatively examined using 15 vegetative and 6 reproductive characters meanwhile phylogenetic analyses was explored by DNA barcode ITS2. The results of the phylogenetic analysis revealed the existence of two species of Dok Hin, S. tamariscina and S. pulvinata. Selaginella tamariscina can be distinguished from S. pulvinata by its presence of a pseudotrunk above ground and ridges of dorsal leaves. On the other hand, the results of phylogenetic analysis indicated the differences among populations of S. pulvinata as well. Chiang Mai populations of S. pulvinata was characterized by peculiar set of characters long leaves and leaf apices look like caudate, while the rest of their populations have shorter leaves and leaf apices look like aristate. It indicates that S. pulvinata has genetic and phenotypic divergence among populations. However, additional studies of Dok Hin populations in other parts of Thailand and studies on different genetic markers are necessary to confirm the taxonomic status of S. pulvinata. Keywords: Dok Hin, Morphometric, Phylogeny, Pseudotrunk, Resurrection plant

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Comparative analysis of chloroplast genomes indicated different origin for Indian Tea (Camellia assamica) cv TV-1 as compared to Chinese tea

10.1101/2020.07.13.199133 ◽

2020 ◽

Author(s):

Hukam C. Rawal ◽

Abhishek Mazumder ◽

Sangeeta Borchetia ◽

Biswajit Bera ◽

S. Soundararajan ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Comparative Analysis ◽

Morphological Characteristics ◽

African Countries ◽

Chloroplast Genomes ◽

Assam Tea ◽

Cp Genome ◽

Indian Tea ◽

Simple Sequence ◽

Different Origin

AbstractTea is an important plantation crop of some Asian and African countries. Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China joining area, yet specific origin of China and Assam tea are not yet clear. In the present study, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus. Cp genome based phylogenetic analysis indicated that Indian Assam Tea, TV-1 formed a different group from that of China tea, indicating that TV-1 might have undergone different domestication and hence owe different origin. The simple sequence repeats (SSRs) analysis and codon usage distribution pattern also supported the clustering order in the cp genome based phylogenetic tree.

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A Phylogenetic Analysis for Gene ITPK1

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.466-467.27 ◽

2012 ◽

Vol 466-467 ◽

pp. 27-30

Author(s):

Kun Luo ◽

Dong Hui Luo

Keyword(s):

Phylogenetic Analysis ◽

Protein Sequence ◽

Selection Pressure ◽

Phylogenetic Trees ◽

Essential Role ◽

Protein Sequences

Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK1) is a pivotal enzyme in producing IP6 , a moleculae that play an essential role in many biochemistry process in mammal cells. In this paper, two phylogenetic trees are constructed based on the mRNA sequences and the protein sequences, respectively. The results indicate that the protein sequences are more conserved than mRNA sequences in primates. Although both plant and animal have an abundant distribution of ITPK1 domain, there exists a great variation in protein sequence between plant and animal. The protein-based tree reflects an evolution orders that is consistent with that of organisms evolution. Z-test of selection indicates that evolution of protein ITPK1 is caused by selection pressure.

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Middle Pleistocene protein sequences from the rhinoceros genusStephanorhinusand the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae

PeerJ ◽

10.7717/peerj.3033 ◽

2017 ◽

Vol 5 ◽

pp. e3033 ◽

Cited By ~ 26

Author(s):

Frido Welker ◽

Geoff M. Smith ◽

Jarod M. Hutson ◽

Lutz Kindler ◽

Alejandro Garcia-Moreno ◽

...

Keyword(s):

Mass Spectrometry ◽

Phylogenetic Analysis ◽

Late Pleistocene ◽

Phylogenetic Relationships ◽

Protein Sequence ◽

Sequence Data ◽

Protein Sequences ◽

Middle Pleistocene ◽

Extant Species ◽

Protein Sequence Data

BackgroundAncient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genusStephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, includingStephanorhinusandDicerorhinus.MethodsZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genusStephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle PleistoceneStephanorhinusspecimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus,Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods.ResultsVarious ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae.Stephanorhinusis shown to be most closely related to the generaCoelodontaandDicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genusRhinoceros, opposed to forming a clade with the black and white rhinoceros species.DiscussionThe first biomolecular dataset available forStephanorhinusplaces this genus together with the extinct genusCoelodontaand the extant genusDicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genusDicerorhinusin a clade together with extantRhinocerosspecies. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.

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Pathogen-driven coevolution across CBP60 plant immune regulator subfamilies confers resilience on the regulator module

10.1101/2020.07.16.207134 ◽

2020 ◽

Author(s):

Qi Zheng ◽

Kristina Majsec ◽

Fumiaki Katagiri

Keyword(s):

Phylogenetic Analysis ◽

Euclidean Space ◽

Plant Species ◽

Protein Evolution ◽

Selection Pressure ◽

Protein Sequences ◽

Land Plant ◽

Strong Selection ◽

Pathogen Effectors ◽

Evolution Analysis

ABSTRACTAmong eight Arabidopsis CaM-Binding Protein (CBP) 60 family members, AtCBP60g and AtSARD1 are partially functionally redundant, major positive immune regulators while AtCBP60a is a negative immune regulator. Phylogenetic analysis of CBP60 protein sequences of 247 diverse land plant species indicated that the immune regulator CBP60a, CBP60g, and SARD1 subfamilies diversified at divergence of Angiosperms and have been evolving very fast, suggesting strong selection pressure from pathogen effectors. We developed the Protein Evolution Analysis in Euclidean Space (PEAES) approach to investigate effects of this potential selection. We detected significant coevolutionary interactions across the immune regulator subfamilies specific to different Core Eudicot lineages, which are consistent with hypothetical coevolutionary mechanisms that protect the positive immune regulator function from being targeted by pathogen effectors. Thus, fast coevolution across the subfamilies with overlapping or opposing functions appears crucial to maintain resilience of the CBP60 immune regulator module against fast-evolving pathogen effectors.

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Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy

International Journal of Molecular Sciences ◽

10.3390/ijms20071774 ◽

2019 ◽

Vol 20 (7) ◽

pp. 1774 ◽

Cited By ~ 1

Author(s):

Huan Zhu ◽

Yuxin Hu ◽

Feng Liu ◽

Zhengyu Hu ◽

Guoxiang Liu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Bacterial Genome ◽

Morphological Characteristics ◽

Rpob Gene ◽

Morphological Data ◽

Stalk Cell ◽

Free Standing ◽

Chloroplast Genomes ◽

Genome Origins

Trentepohliales is an aerial order of Chlorophyta with approximately 80 species distributed mainly in tropical and subtropical regions. The taxonomy of this genus is quite difficult and presents a challenge for many phycologists. Although plentiful molecular data is available, most of the sequences are not identified at the species level. In the present study, we described a new specimen with detailed morphological data and identified it as Trentepohlia odorata. A phylogenetic analysis showed T. odorata as a novel lineage in Trentepohliales. T. odorata has the closest relationship with T. annulata, which is expected since sporangia of both species are without stalk cell and with dorsal pore. Species with such morphological characteristics may represent deep lineages in Trentepohliales. Although an increasing number of chloroplast genomes of Ulvophyceae have been reported in recent years, the whole plastome of Trentepohliales has not yet been reported. Thus, the chloroplast genome of Trentepohlia odorata was reported in the present study. The whole plastome was 399,372 bp in length, with 63 predicted protein-coding genes, 31 tRNAs, and 3 rRNAs. Additionally, we annotated 95 free-standing open reading frames, of which seven were annotated with plastid origins, 16 with eukaryotic genome origins, and 33 with bacterial genome origins. Four rpo genes (rpoA, rpoB, rpoC1, and rpoC2) were annotated within ORF clusters. These four genes were fragmented into several (partial) ORFs by in-frame stop codons. Additionally, we detected a frame shift mutation in the rpoB gene. The phylogenetic analysis supported that Trentepohliales clustered with Dasycladales and nested into the BDT clade (Bryopsidales, Dasycladales and Trentepohliales). Our results present the first whole chloroplast genome of a species of Trentepohliales and provided new data for understanding the evolution of the chloroplast genome in Ulvophyceae.

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Comparison and Phylogenetic Analysis of Chloroplast Genomes of Three Medicinal and Edible Amomum Species

International Journal of Molecular Sciences ◽

10.3390/ijms20164040 ◽

2019 ◽

Vol 20 (16) ◽

pp. 4040 ◽

Cited By ~ 12

Author(s):

Yingxian Cui ◽

Xinlian Chen ◽

Liping Nie ◽

Wei Sun ◽

Haoyu Hu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Morphological Characteristics ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Edible Plant ◽

Protein Coding ◽

Chloroplast Genomes ◽

Cp Genome ◽

Pharmacologically Active

Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this study, therefore, is to mine genetic resources and improve molecular methods that could be used to distinguish these species. A total of eight complete chloroplasts (cp) genomes of these Amomum species which were collected from the main producing areas in China were determined to be 163,608–164,069 bp in size. All genomes displayed a typical quadripartite structure with a pair of inverted repeat (IR) regions (29,820–29,959 bp) that separated a large single copy (LSC) region (88,680–88,857 bp) from a small single copy (SSC) region (15,288–15,369 bp). Each genome encodes 113 different genes with 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. More than 150 SSRs were identified in the entire cp genomes of these three species. The Sanger sequencing results based on 32 Amomum samples indicated that five highly divergent regions screened from cp genomes could not be used to distinguish Amomum species. Phylogenetic analysis showed that the cp genomes could not only accurately identify Amomum species, but also provide a solid foundation for the establishment of phylogenetic relationships of Amomum species. The availability of cp genome resources and the comparative analysis is beneficial for species authentication and phylogenetic analysis in Amomum.

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Comparative chloroplast genomes and phylogenetic analysis of Aquilegia

Applications in Plant Sciences ◽

10.1002/aps3.11412 ◽

2021 ◽

Author(s):

Wei Zhang ◽

Huaying Wang ◽

Jianhua Dong ◽

Tengjiao Zhang ◽

Hongxing Xiao

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genomes

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Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽

10.3390/insects12080668 ◽

2021 ◽

Vol 12 (8) ◽

pp. 668

Author(s):

Tinghao Yu ◽

Yalin Zhang

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Strong Support ◽

Intergenic Spacer ◽

Taxonomic Status ◽

Start Codon ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

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