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Typha angustifolia, commonly known as narrowleaf cattail, is a marginal, semi-aquatic, herbaceous perennial species with both ecological and edible values. In this study, the complete chloroplast (cp) genome of T. angustifolia was assembled using the next-generation sequencing technology. The whole cp genome was 161,597 bp in length, consisting of a large single copy (LSC, 89,119 bp) and a small single copy (SSC, 18,550 bp) separated by two copies of inverted region (IR, 26,964 bp). The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis showed that T. angustifolia is sister to Typha orientalis in the family Typhaceae. The cp genome of T. angustifolia is reported for the first time, which will provide essential and important genetic resources for future phylogenetic investigation within the genus Typha.

Typha angustifolia, commonly known as narrowleaf cattail, is a marginal, semi-aquatic, herbaceous perennial species with both ecological and edible values. In this study, the complete chloroplast (cp) genome of T. angustifolia was assembled using the next-generation sequencing technology. The whole cp genome was 161,597 bp in length, consisting of a large single copy (LSC, 89,119 bp) and a small single copy (SSC, 18,550 bp) separated by two copies of inverted region (IR, 26,964 bp). The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis showed that T. angustifolia is sister to Typha orientalis in the family Typhaceae. The cp genome of T. angustifolia is reported for the first time, which will provide essential and important genetic resources for future phylogenetic investigation within the genus Typha. [ABSTRACT FROM AUTHOR]

AbstractErasmia pulchella has brightly colored wings and releases toxic cyanide as a defense against predation. At present, the molecular phylogenetic status of this species is still unclear. Here, we presented the first complete mitochondrial genome of the genus Erasmia, which was assembled from data generated using a genome skimming method. The assembled mitogenome was 15,197 bp in length and consists of 37 genes, including 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. Phylogenetic analysis based on both maximum likelihood (ML) and Bayesian inference (BI) revealed that E. pulchella was most closely related to Amesia sanguiflua.

Erasmia pulchella has brightly colored wings and releases toxic cyanide as a defense against predation. At present, the molecular phylogenetic status of this species is still unclear. Here, we presented the first complete mitochondrial genome of the genus Erasmia, which was assembled from data generated using a genome skimming method. The assembled mitogenome was 15,197 bp in length and consists of 37 genes, including 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. Phylogenetic analysis based on both maximum likelihood (ML) and Bayesian inference (BI) revealed that E. pulchella was most closely related to Amesia sanguiflua. [ABSTRACT FROM AUTHOR]

Abstract Background Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches. Results EasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson–Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance 0.99) to those of trees inferred with the two pipelines. Conclusions EasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github ( https://github.com/zdf1987/EasyCGTree4 ).

Abstract Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation.

Background: Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches. Results: EasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson–Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines. Conclusions: EasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github (https://github.com/zdf1987/EasyCGTree4). [ABSTRACT FROM AUTHOR]

Veronica arvensis, which is an annual flowering plant in the plantain family Plantaginaceae, has commonly used as a Chinese herbal medicine to treat malaria in China. Here, the complete plastome of V. arvensis was successfully assembled based on genome skimming sequencing. The plastome of V. arvensis was 149,386 bp in length, comprising a pair of inverted repeats (IR; 24,946 bp) separated by a large single-copy (LSC) region (82,004 bp) and a small single-copy (SSC) region (17,490 bp). The plastid genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Six plastid hotspot regions (trnH-psbA, trnK-rps16, atpI-rps2, ndhF-rpl32, ccsA-ndhD and rps15-ycf1) were identified within Veronica. Phylogenetic analysis showed that the representative species from Veronica was monophyletic. V. persica and V. polita formed a maximum clade, followed by sister to V. arvensis.

Phylogenomics aims to infer the evolutionary relationships of organisms, and their genomes, genes, and proteins, from genomic data. Understanding the evolution of these components can provide clues about their biological functions. Here we describe minimal protocols for inferring families of genes (and the proteins they encode), and using them in phylogenomic analyses to infer species trees.

Veronica arvensis, which is an annual flowering plant in the plantain family Plantaginaceae, has commonly used as a Chinese herbal medicine to treat malaria in China. Here, the complete plastome of V. arvensis was successfully assembled based on genome skimming sequencing. The plastome of V. arvensis was 149,386 bp in length, comprising a pair of inverted repeats (IR; 24,946 bp) separated by a large single-copy (LSC) region (82,004 bp) and a small single-copy (SSC) region (17,490 bp). The plastid genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Six plastid hotspot regions (trnH-psbA, trnK-rps16, atpI-rps2, ndhF-rpl32, ccsA-ndhD and rps15-ycf1) were identified within Veronica. Phylogenetic analysis showed that the representative species from Veronica was monophyletic. V. persica and V. polita formed a maximum clade, followed by sister to V. arvensis. [ABSTRACT FROM AUTHOR]

Plantago asiatica, an herbaceous perennial species of Plantaginaceae, has been used as a traditional herbal medicine plant in China. In this study, the complete chloroplast (cp) genome of P. asiatica was sequenced and assembled using genome skimming data. The cp genome was 165,045 bp in length including the large single-copy (LSC, 82,964 bp) and small single-copy (SSC, 4,633 bp) regions separated by two copies of inverted region (IR, 38,724 bp). The cp genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, additionally with 27 duplicated genes in the IR regions. Phylogenetic analysis indicated that the representative species from Plantago was monophyletic and they were divided into four subgenera. P. asiatica belongs to the subgenus Plantago and was sister to P. rigida with high bootstrap value support.

Peltoboykinia tellimoides, which is distributed in Japan and China, is the type species of Peltoboykinia. In this study, we sequenced and assembled the complete chloroplast (cp) genome of P. tellimoides and reconstructed the phylogeny of Saxifragaceae based on the whole cp genome sequences. The cp genome of P. tellimoides was 156,274 bp in length, comprising a pair of inverted repeat regions (25,099 bp) separated by a large single copy region (88,109 bp) and a small single copy region (17,967 bp). The genome encoded 112 unique genes consisting of 78 different protein-coding genes, 30 transfer RNA and four ribosomal RNA genes, with 16 duplicated genes in the inverted repeats. Phylogenetic analysis indicated that P. tellimoides together with three Chrysosplenium species formed a high support clade, which was sister to Micranthes melanocentra.

Abstract Although scRNA-seq is now ubiquitously adopted in studies of intratumor heterogeneity, detection of somatic mutations and inference of clonal membership from scRNA-seq is currently unreliable. We propose DENDRO, an analysis method for scRNA-seq data that clusters single cells into genetically distinct subclones and reconstructs the phylogenetic tree relating the subclones. DENDRO utilizes transcribed point mutations and accounts for technical noise and expression stochasticity. We benchmark DENDRO and demonstrate its application on simulation data and real data from three cancer types. In particular, on a mouse melanoma model in response to immunotherapy, DENDRO delineates the role of neoantigens in treatment response.

Typha angustifolia , commonly known as narrowleaf cattail, is a marginal, semi-aquatic, herbaceous perennial species with both ecological and edible values. In this study, the complete chloroplast (cp) genome of T. angustifolia was assembled using the next-generation sequencing technology. The whole cp genome was 161,597 bp in length, consisting of a large single copy (LSC, 89,119 bp) and a small single copy (SSC, 18,550 bp) separated by two copies of inverted region (IR, 26,964 bp). The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis showed that T. angustifolia is sister to Typha orientalis in the family Typhaceae. The cp genome of T. angustifolia is reported for the first time, which will provide essential and important genetic resources for future phylogenetic investigation within the genus Typha ., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Zelkova sinica is a popular landscape plant in China because of its wide adaptation, strong disease resistance, large crown and beautiful fall color. Here, we assembled the complete chloroplast (cp) genome of Z. sinica based on genome skimming data. The cp genome is 158,924 bp in length including two copies of inverted region (IR, 26,427 bp) separated by the large single copy (LSC, 87,318 bp) and small single copy (SSC, 18,752 bp) regions. It encodes 111 unique genes, containing 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 18 duplicated genes in the IR regions. Phylogenetic analysis shows that Z. sinica is sister to Z. schneideriana in Ulmaceae family.

Plantago asiatica, an herbaceous perennial species of Plantaginaceae, has been used as a traditional herbal medicine plant in China. In this study, the complete chloroplast (cp) genome of P. asiatica was sequenced and assembled using genome skimming data. The cp genome was 165,045 bp in length including the large single-copy (LSC, 82,964 bp) and small single-copy (SSC, 4,633 bp) regions separated by two copies of inverted region (IR, 38,724 bp). The cp genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, additionally with 27 duplicated genes in the IR regions. Phylogenetic analysis indicated that the representative species from Plantago was monophyletic and they were divided into four subgenera. P. asiatica belongs to the subgenus Plantago and was sister to P. rigida with high bootstrap value support. [ABSTRACT FROM AUTHOR]

Peltoboykinia tellimoides, which is distributed in Japan and China, is the type species of Peltoboykinia. In this study, we sequenced and assembled the complete chloroplast (cp) genome of P. tellimoides and reconstructed the phylogeny of Saxifragaceae based on the whole cp genome sequences. The cp genome of P. tellimoides was 156,274 bp in length, comprising a pair of inverted repeat regions (25,099 bp) separated by a large single copy region (88,109 bp) and a small single copy region (17,967 bp). The genome encoded 112 unique genes consisting of 78 different protein-coding genes, 30 transfer RNA and four ribosomal RNA genes, with 16 duplicated genes in the inverted repeats. Phylogenetic analysis indicated that P. tellimoides together with three Chrysosplenium species formed a high support clade, which was sister to Micranthes melanocentra. [ABSTRACT FROM AUTHOR]

Verbascum phoeniceum, known as purple mullein or temptress purple, is a species native to Central Europe, Central Asia, and Western China. In the present study, the chloroplast (cp) genome of V. phoeniceum was assembled using genome skimming sequencing. The cp genome of V. phoeniceum is 153,348 bp in length comprising two copies of inverted regions (IR, 25,430 bp) separated by the large single-copy (LSC, 84,601 bp) and small single copy (SSC, 17,887 bp) regions. It encodes 114 unique genes, consisting of 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 20 duplicated genes in the IR regions. Phylogenetic analysis indicates that V. phoeniceum exhibits a closer relationship with Scrophularia rather than Buddleja.

Trophis caucana, which belongs to Moraceae, is a tree species lived in a humid climate at low and middle altitudes. The complete chloroplast (cp) genome of T. caucana was sequenced and assembled in this study. The cp genome is 161,445 bp in length with comprising two copies of inverted region (IR, 25,894 bp) separated by the large single copy (LSC, 89,633 bp) and small single copy (SSC, 20,024 bp) regions. It encodes 111 unique genes, consisting of 77 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis indicates that T. caucana is sister to Antiaris toxicaria in Moraceae family.

Lycium ferocissimum, known as African boxthorn or boxthorn, is a shrub in the Solanaceae family. In this study, we characterized the complete chloroplast (cp) genome sequence of L. ferocissimum using genome skimming data. It had a circular mapping molecular with the length of 155,894 bp, with a large single-copy region (LSC, 86,536 bp) and a small single-copy region (SSC, 18,406 bp) separated by a pair of inverted repeats (IRs, 25,476 bp). The cp genome encodes 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 20 duplicated genes in the IR regions. The phylogenetic analysis indicated that L. ferocissimum is sister to the other three Lycium species.

Erasmia pulchella has brightly colored wings and releases toxic cyanide as a defense against predation. At present, the molecular phylogenetic status of this species is still unclear. Here, we presented the first complete mitochondrial genome of the genus Erasmia , which was assembled from data generated using a genome skimming method. The assembled mitogenome was 15,197 bp in length and consists of 37 genes, including 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. Phylogenetic analysis based on both maximum likelihood (ML) and Bayesian inference (BI) revealed that E. pulchella was most closely related to Amesia sanguiflua ., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The identification of orthologous genes is relevant for comparative genomics, phylogenetic analysis, and functional annotation. There are many computational tools for the prediction of orthologous groups as well as web-based resources that offer orthology datasets for download and online analysis. This chapter presents a simple and practical guide to the process of orthologous group prediction, using a dataset of 10 prokaryotic proteomes as example. The orthology methods covered are OrthoMCL, COGtriangles, OrthoFinder2, and OMA. The authors compare the number of orthologous groups predicted by these various methods, and present a brief workflow for the functional annotation and reconstruction of phylogenies from inferred single-copy orthologous genes. The chapter also demonstrates how to explore two orthology databases: eggNOG6 and OrthoDB., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Osmanthus armatus (Oleaceae) is mainly distributed in the southwest of China and also planted in arboretums as an ornamental plant. In the present study, the plastome of O. armatus was reconstructed using genome skimming sequencing, and the phylogeny analysis was inferred based on whole plastome data. The plastome of O. armatus is 155,259 bp in length, comprising two copies of inverted regions (IR, 25,680 bp) separated by the large single copy (LSC, 86,534 bp) and small single copy (SSC, 17,365 bp) regions. The genome encodes 114 unique genes, including 80 different protein-coding genes, 30 tRNA genes, and four rRNA genes, with 20 duplicated genes in the IR regions. Phylogenetic analysis suggests that the representative species from Osmanthus is monophyletic, and O. armatus is sister to O. fragrans within this genus.

Paulownia elongata (Paulowniaceae) is an ornamental tree native to Asia. In this study, the chloroplast (cp) genome of P. elongata was assembled using genome skimming sequencing, and the phylogeny of Lamiales was reconstructed based on whole cp genome data. The cp genome of P. elongata is 154,670 bp in length, comprising two copies of inverted region (IR, 25,783 bp), regions separated by the large single copy (LSC, 85,370 bp) and small single copy (SSC, 17,734 bp) regions. The cp genome encodes 114 unique genes, including 80 different protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis indicates that P. elongata together with two other Paulownia species form a clade, which is sister to Triaenophora shennongjiaensis.

Crossostephium chinense is a common traditional Chinese medicinal plant used to cure arthralgia and rheumatism. The previous studies mainly focussed on its chemical compositions, with the genetic background and resources remaining scarce. Here, we conducted genome skimming for C. chinense, and using these data we not only assembled its complete chloroplast genome, but also reconstructed the phylogenetic relationship between C. chinense and Artemisia. The cp genomes of two C. chinense individuals ranged from 151,024 bp to 151,097 bp in length and had a typical quadripartite structure with a conserved genome arrangement. The cp genome encodes 114 unique genes, consisting of 80 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis indicates that C. chinense is sister to Artemisia annua and Artemisia fukudo.

Leontice incerta, which belongs to Berberidaceae, is an endangered species in China. In this study, the chloroplast (cp) genome of L. incerta was assembled using genome skimming sequencing and the phylogeny of Berberidaceae was reconstructed based on whole cp genome. The cp genome of L. incerta is 156,923 bp in length, comprising two copies of IR (26,121 bp) regions separated by the LSC (85,622 bp) and SSC (19,059 bp) regions. The cp genome encodes 112 unique genes, consisting of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis indicates that L. incerta is sister to Gymnospermium microrrhynchum, subsequently is sister to Nandia domestica.

Caryopteris mongholica, which belongs to the mint subfamily Ajugoideae (Lamiaceae), has high ornamental and medicinal value. Previously published phylogenetic studies strongly support the monophyly of Lamiaceae, but some major relationships within the family still remain unclear. In this study, we report the chloroplast (cp) genome of C. mongholica and take advantage of several previously reported cp genomes from related taxa to infer phylogeny in Lamiaceae. The cp genome of C. mongholica is 151,707 bp in length, comprising a pair of inverted repeat regions (25,634 bp) separated by a large single-copy region (83,203 bp) and a small single-copy region (17,236 bp). The genome encodes 114 unique genes consisting of 80 different protein-coding genes, 30 transfer RNA and four ribosomal RNA genes, with 19 duplicated genes in the inverted repeats. The phylogeny reconstruction based on the complete genome sequences of 20 mint species strongly supports the placement of Ajugoideae as sister to (Lamioideae + Scutellarioideae), as well as the sister relationship between Premnoideae and Tectona. [ABSTRACT FROM AUTHOR]

Cancer is a disease driven by evolutionary selection on somatic genetic and epigenetic alterations. Here, we propose Canopy, a method for inferring the evolutionary phylogeny of a tumor using both somatic copy number alterations and single-nucleotide alterations from one or more samples derived from a single patient. Canopy is applied to bulk sequencing datasets of both longitudinal and spatial experimental designs and to a transplantable metastasis model derived from human cancer cell line MDA-MB-231. Canopy successfully identifies cell populations and infers phylogenies that are in concordance with existing knowledge and ground truth. Through simulations, we explore the effects of key parameters on deconvolution accuracy and compare against existing methods. Canopy is an open-source R package available at https://cran.r-project.org/web/packages/Canopy/. [ABSTRACT FROM AUTHOR]

The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model, is known to be inapplicable under some conditions, ie, it leads to the inapplicability of the GTR model. Here, we simulate the evolution of DNA sequences along 12 trees characterized by different combinations of tree length, (non-)homogeneity of the substitution rate matrix R, and sequence length. We then evaluate both the frequency of the GTR model inapplicability for estimating distances and the accuracy of inferred alignments. Our results indicate that, inapplicability of the Waddel and Steel’s procedure can be considered a real practical issue, and illustrate that the probability of this inapplicability is a function of substitution rates and sequence length. We also discuss the implications of our results on the current implementations of maximum likelihood and Bayesian methods.

Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. [ABSTRACT FROM AUTHOR]

Zelkova sinica is a popular landscape plant in China because of its wide adaptation, strong disease resistance, large crown and beautiful fall color. Here, we assembled the complete chloroplast (cp) genome of Z. sinica based on genome skimming data. The cp genome is 158,924 bp in length including two copies of inverted region (IR, 26,427 bp) separated by the large single copy (LSC, 87,318 bp) and small single copy (SSC, 18,752 bp) regions. It encodes 111 unique genes, containing 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 18 duplicated genes in the IR regions. Phylogenetic analysis shows that Z. sinica is sister to Z. schneideriana in Ulmaceae family. [ABSTRACT FROM AUTHOR]

The field of computational biology encloses a wide range of optimization problems that show non-deterministic polynomial-time hard complexities. Nowadays, phylogeneticians are dealing with a growing amount of biological data that must be analyzed to explain the origins of modern species. Evolutionary relationships among organisms are often described by means of tree-shaped structures known as phylogenetic trees. When inferring phylogenies, two main challenges must be addressed. First, the inference of reliable evolutionary trees on data sets where different optimality principles support conflicting evolutionary hypotheses. Second, the processing of enormous tree searches spaces where traditional sequential strategies cannot be applied. In this sense, phylogenetic inference can benefit from the combination of high performance computing and evolutionary computation to carry out the reconstruction of complex evolutionary histories in reduced execution times. In this paper, we introduce multiobjective phylogenetics, a hybrid OpenMP/MPI approach to parallelize a well-known multiobjective metaheuristic, the fast non-dominated sorting genetic algorithm (NSGA-II). This algorithm has been designed to conduct phylogenetic analyses on multi-core clusters in accordance with two principles: maximum parsimony and maximum likelihood. The main goal is to combine the benefits of shared-memory and distributed-memory programming paradigms to efficiently infer a set of high-quality Pareto solutions. Experiments on six real nucleotide data sets and comparisons with other hybrid parallel approaches show that multiobjective phylogenetics is able to achieve significant performance in terms of parallel, multiobjective, and biological results. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Veronica arvensis , which is an annual flowering plant in the plantain family Plantaginaceae, has commonly used as a Chinese herbal medicine to treat malaria in China. Here, the complete plastome of V. arvensis was successfully assembled based on genome skimming sequencing. The plastome of V. arvensis was 149,386 bp in length, comprising a pair of inverted repeats (IR; 24,946 bp) separated by a large single-copy (LSC) region (82,004 bp) and a small single-copy (SSC) region (17,490 bp). The plastid genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Six plastid hotspot regions ( trn H- psb A, trn K- rps 16, atp I- rps 2, ndh F- rpl 32, ccs A- ndh D and rps 15- ycf 1) were identified within Veronica . Phylogenetic analysis showed that the representative species from Veronica was monophyletic. V. persica and V. polita formed a maximum clade, followed by sister to V. arvensis ., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Markov models of codon substitution naturally incorporate the structure of the genetic code and the selection intensity at the protein level, providing a more realistic representation of protein-coding sequences compared with nucleotide or amino acid models. Thus, for protein-coding genes, phylogenetic inference is expected to be more accurate under codon models. So far, phylogeny reconstruction under codon models has been elusive due to computational difficulties of dealing with high dimension matrices. Here, we present a fast maximum likelihood (ML) package for phylogenetic inference, CodonPhyML offering hundreds of different codon models, the largest variety to date, for phylogeny inference by ML. CodonPhyML is tested on simulated and real data and is shown to offer excellent speed and convergence properties. In addition, CodonPhyML includes most recent fast methods for estimating phylogenetic branch supports and provides an integral framework for models selection, including amino acid and DNA models. [ABSTRACT FROM PUBLISHER]

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns—similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author. [ABSTRACT FROM PUBLISHER]

Phylogeny inference is an importance issue in computational biology. Some early approaches based on characteristics such as the maximum parsimony algorithm and the maximum likelihood algorithm will become intractable when the number of taxonomic units is large. Recent algorithms based on distance data which adopt an agglomerative scheme are widely used for phylogeny inference. However, they have to recursively merge the nearest pair of taxa and estimate a distance matrix; this may enlarge the error gradually, and lead to an inaccurate tree topology. In this study, a splitting algorithm is proposed for phylogeny inference by using the spectral graph clustering (SGC) technique. The SGC algorithm splits graphs by using the maximum cut criterion and circumvents optimization problems through solving a generalized eigenvalue system. The promising features of the proposed algorithm are the following: (i) using a heuristic strategy for constructing phylogenies from certain distance functions, which are not even additive; (ii) distance matrices do not have to be estimated recursively; (iii) inferring a more accurate tree topology than that of the Neighbor-joining (NJ) algorithm on simulated datasets; and (iv) strongly supporting hypotheses induced by other methods for Baculovirus genomes. Our numerical experiments confirm that the SGC algorithm is efficient for phylogeny inference. [ABSTRACT FROM AUTHOR]

As models of sequence evolution become more and more complicated, many criteria for model selection have been proposed, and tools are available to select the best model for an alignment under a particular criterion. However, in many instances the selected model fails to explain the data adequately as reflected by large deviations between observed pattern frequencies and the corresponding expectation. We present MISFITS, an approach to evaluate the goodness of fit (http://www.cibiv.at/software/misfits). MISFITS introduces a minimum number of “extra substitutions” on the inferred tree to provide a biologically motivated explanation why the alignment may deviate from expectation. These extra substitutions plus the evolutionary model then fully explain the alignment. We illustrate the method on several examples and then give a survey about the goodness of fit of the selected models to the alignments in the PANDIT database. [ABSTRACT FROM PUBLISHER]

Verbascum phoeniceum, known as purple mullein or temptress purple, is a species native to Central Europe, Central Asia, and Western China. In the present study, the chloroplast (cp) genome of V. phoeniceum was assembled using genome skimming sequencing. The cp genome of V. phoeniceum is 153,348 bp in length comprising two copies of inverted regions (IR, 25,430 bp) separated by the large single-copy (LSC, 84,601 bp) and small single copy (SSC, 17,887 bp) regions. It encodes 114 unique genes, consisting of 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 20 duplicated genes in the IR regions. Phylogenetic analysis indicates that V. phoeniceum exhibits a closer relationship with Scrophularia rather than Buddleja. [ABSTRACT FROM AUTHOR]

Trophis caucana, which belongs to Moraceae, is a tree species lived in a humid climate at low and middle altitudes. The complete chloroplast (cp) genome of T. caucana was sequenced and assembled in this study. The cp genome is 161,445 bp in length with comprising two copies of inverted region (IR, 25,894 bp) separated by the large single copy (LSC, 89,633 bp) and small single copy (SSC, 20,024 bp) regions. It encodes 111 unique genes, consisting of 77 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis indicates that T. caucana is sister to Antiaris toxicaria in Moraceae family. [ABSTRACT FROM AUTHOR]

Lycium ferocissimum, known as African boxthorn or boxthorn, is a shrub in the Solanaceae family. In this study, we characterized the complete chloroplast (cp) genome sequence of L. ferocissimum using genome skimming data. It had a circular mapping molecular with the length of 155,894 bp, with a large single-copy region (LSC, 86,536 bp) and a small single-copy region (SSC, 18,406 bp) separated by a pair of inverted repeats (IRs, 25,476 bp). The cp genome encodes 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 20 duplicated genes in the IR regions. The phylogenetic analysis indicated that L. ferocissimum is sister to the other three Lycium species. [ABSTRACT FROM AUTHOR]

Osmanthus armatus (Oleaceae) is mainly distributed in the southwest of China and also planted in arboretums as an ornamental plant. In the present study, the plastome of O. armatus was reconstructed using genome skimming sequencing, and the phylogeny analysis was inferred based on whole plastome data. The plastome of O. armatus is 155,259 bp in length, comprising two copies of inverted regions (IR, 25,680 bp) separated by the large single copy (LSC, 86,534 bp) and small single copy (SSC, 17,365 bp) regions. The genome encodes 114 unique genes, including 80 different protein-coding genes, 30 tRNA genes, and four rRNA genes, with 20 duplicated genes in the IR regions. Phylogenetic analysis suggests that the representative species from Osmanthus is monophyletic, and O. armatus is sister to O. fragrans within this genus. [ABSTRACT FROM AUTHOR]

Maximum likelihood (ML) (Neyman, 1971) is an increasingly popular optimality criterion for selecting evolutionary trees. Finding optimal ML trees appears to be a very hard computational task — in particular, algorithms and heuristics for ML take longer to run than algorithms and heuristics for maximum parsimony (MP). However, while MP has been known to be NP-complete for over 20 years, no such hardness result has been obtained so far for ML. In this work we make a first step in this direction by proving that ancestral maximum likelihood (AML) is NP-complete. The input to this problem is a set of aligned sequences of equal length and the goal is to find a tree and an assignment of ancestral sequences for all of that tree's internal vertices such that the likelihood of generating both the ancestral and contemporary sequences is maximized. Our NP-hardness proof follows that for MP given in (Day, Johnson and Sankoff, 1986) in that we use the same reduction from VERTEX COVER; however, the proof of correctness for this reduction relative to AML is different and substantially more involved. [ABSTRACT FROM AUTHOR]