The Experts below are selected from a list of 312 Experts worldwide ranked by ideXlab platform

Roy H J Erkens - One of the best experts on this subject based on the ideXlab platform.

  • Chromosome-level reference genome of the soursop (Annona muricata): a new resource for Magnoliid research and tropical pomology.
    Molecular ecology resources, 2021
    Co-Authors: Joeri S. Strijk, Mareike Roeder, Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Herve Sauquet, Damien Daniel Hinsinger, Michael D Pirie, Daniel C. Thomas, Kun-fang Cao
    Abstract:

    The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676X sequencing depth) from PacBio and Illumina short-reads, in combination with 10XGenomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

  • Chromosome-level reference genome of the Soursop (Annona muricata), a new resource for Magnoliid research and tropical pomology
    2020
    Co-Authors: Joeri S. Strijk, Mareike Roeder, Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Herve Sauquet, Damien Daniel Hinsinger, Michael D Pirie, Daniel C. Thomas, Kun-fang Cao
    Abstract:

    Annonaceae contain important commercially grown tropical crops, but development of other promising species is hindered by a lack of genomic resources to build breeding programs. In addition, Annonaceae are part of the Magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades have remained unclear. To provide resources to both breeders and evolutionary researchers, we report the chromosome-level genome assembly of the soursop (Annona muricata). We assembled the soursop genome using a total of 444.32 Gb of DNA sequences that were generated using PacBio and Illumina short-reads, in combination with 10XGenomics, Bionano data and Hi-C sequencing. 949 scaffolds were assembled to a final size of 656.77Mb, with a scaffold N50 of 3.43 Mb. Repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size of A. muricata showed a slow but regular contraction of the population, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in Magnoliids, and providing an essential resource for delineating relationships of major lineages at the base of the angiosperms. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. The genome assembly as a community resource will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

  • Twelve new and exciting Annonaceae from the Neotropics.
    PhytoKeys, 2019
    Co-Authors: Paul J. M. Maas, Lars W Chatrou, Lubbert Y.th. Westra, Heimo Rainer, Nadja Verspagen, Nelson Zamora, Roy H J Erkens
    Abstract:

    As a result of concerted efforts of the community of Annonaceae taxonomists, increasingly detailed knowledge of the diversity of the Neotropical genera has been documented. With the exception of just two large genera, Annona and Xylopia, all Neotropical Annonaceae have been revised within the last 25 years. Subsequent to these publications, many new specimens have been collected and sent to us in Leiden for identification. These included a number that, despite the advanced state of taxonomic knowledge, proved to represent rarely collected, undescribed species. Here we describe 12 new species of Annona, Guatteria, Klarobelia, Tetrameranthus, and Xylopia. These species serve to illustrate the still underestimated diversity of the Neotropical flora, even in well studied plant groups like Annonaceae.

  • Data_Sheet_1_Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes.PDF
    2019
    Co-Authors: Thomas L P Couvreur, Herve Sauquet, Andrew J. Helmstetter, Erik J. M. Koenen, Rita D. Brandão, Stefan A. Little, Kevin Bethune, Roy H J Erkens
    Abstract:

    Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well-resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well-supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

  • Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes
    2018
    Co-Authors: Thomas L P Couvreur, Herve Sauquet, Andrew J. Helmstetter, Erik J. M. Koenen, Kevin Bethume, Rita D. Brandão, Stefan A. Little, Roy H J Erkens
    Abstract:

    Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 109 genera and ca. 2450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

Lars W Chatrou - One of the best experts on this subject based on the ideXlab platform.

  • Chromosome-level reference genome of the soursop (Annona muricata): a new resource for Magnoliid research and tropical pomology.
    Molecular ecology resources, 2021
    Co-Authors: Joeri S. Strijk, Mareike Roeder, Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Herve Sauquet, Damien Daniel Hinsinger, Michael D Pirie, Daniel C. Thomas, Kun-fang Cao
    Abstract:

    The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676X sequencing depth) from PacBio and Illumina short-reads, in combination with 10XGenomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

  • Chromosome-level reference genome of the Soursop (Annona muricata), a new resource for Magnoliid research and tropical pomology
    2020
    Co-Authors: Joeri S. Strijk, Mareike Roeder, Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Herve Sauquet, Damien Daniel Hinsinger, Michael D Pirie, Daniel C. Thomas, Kun-fang Cao
    Abstract:

    Annonaceae contain important commercially grown tropical crops, but development of other promising species is hindered by a lack of genomic resources to build breeding programs. In addition, Annonaceae are part of the Magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades have remained unclear. To provide resources to both breeders and evolutionary researchers, we report the chromosome-level genome assembly of the soursop (Annona muricata). We assembled the soursop genome using a total of 444.32 Gb of DNA sequences that were generated using PacBio and Illumina short-reads, in combination with 10XGenomics, Bionano data and Hi-C sequencing. 949 scaffolds were assembled to a final size of 656.77Mb, with a scaffold N50 of 3.43 Mb. Repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size of A. muricata showed a slow but regular contraction of the population, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in Magnoliids, and providing an essential resource for delineating relationships of major lineages at the base of the angiosperms. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. The genome assembly as a community resource will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

  • Twelve new and exciting Annonaceae from the Neotropics.
    PhytoKeys, 2019
    Co-Authors: Paul J. M. Maas, Lars W Chatrou, Lubbert Y.th. Westra, Heimo Rainer, Nadja Verspagen, Nelson Zamora, Roy H J Erkens
    Abstract:

    As a result of concerted efforts of the community of Annonaceae taxonomists, increasingly detailed knowledge of the diversity of the Neotropical genera has been documented. With the exception of just two large genera, Annona and Xylopia, all Neotropical Annonaceae have been revised within the last 25 years. Subsequent to these publications, many new specimens have been collected and sent to us in Leiden for identification. These included a number that, despite the advanced state of taxonomic knowledge, proved to represent rarely collected, undescribed species. Here we describe 12 new species of Annona, Guatteria, Klarobelia, Tetrameranthus, and Xylopia. These species serve to illustrate the still underestimated diversity of the Neotropical flora, even in well studied plant groups like Annonaceae.

  • A linear sequence to facilitate curation of herbarium specimens of Annonaceae
    Kew bulletin, 2018
    Co-Authors: Lars W Chatrou, Ian M. Turner, Bente B. Klitgaard, Paul J. M. Maas, Timothy M. A. Utteridge
    Abstract:

    This paper provides a linear sequence of four subfamilies, 15 tribes and 106 genera of the magnoliid family Annonaceae, based on state-of-the-art and stable phylogenetic relationships. The linear sequence facilitates the organisation of Annonaceae herbarium specimens.

  • Annonaceae substitution rates - a codon model perspective
    Revista Brasileira De Fruticultura, 2014
    Co-Authors: Lars W Chatrou, Michael D Pirie, Robin Van Velzen, Freek T. Bakker
    Abstract:

    The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

Thomas L P Couvreur - One of the best experts on this subject based on the ideXlab platform.

  • Chromosome-level reference genome of the soursop (Annona muricata): a new resource for Magnoliid research and tropical pomology.
    Molecular ecology resources, 2021
    Co-Authors: Joeri S. Strijk, Mareike Roeder, Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Herve Sauquet, Damien Daniel Hinsinger, Michael D Pirie, Daniel C. Thomas, Kun-fang Cao
    Abstract:

    The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676X sequencing depth) from PacBio and Illumina short-reads, in combination with 10XGenomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

  • Chromosome-level reference genome of the Soursop (Annona muricata), a new resource for Magnoliid research and tropical pomology
    2020
    Co-Authors: Joeri S. Strijk, Mareike Roeder, Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Herve Sauquet, Damien Daniel Hinsinger, Michael D Pirie, Daniel C. Thomas, Kun-fang Cao
    Abstract:

    Annonaceae contain important commercially grown tropical crops, but development of other promising species is hindered by a lack of genomic resources to build breeding programs. In addition, Annonaceae are part of the Magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades have remained unclear. To provide resources to both breeders and evolutionary researchers, we report the chromosome-level genome assembly of the soursop (Annona muricata). We assembled the soursop genome using a total of 444.32 Gb of DNA sequences that were generated using PacBio and Illumina short-reads, in combination with 10XGenomics, Bionano data and Hi-C sequencing. 949 scaffolds were assembled to a final size of 656.77Mb, with a scaffold N50 of 3.43 Mb. Repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size of A. muricata showed a slow but regular contraction of the population, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in Magnoliids, and providing an essential resource for delineating relationships of major lineages at the base of the angiosperms. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. The genome assembly as a community resource will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

  • Data_Sheet_1_Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes.PDF
    2019
    Co-Authors: Thomas L P Couvreur, Herve Sauquet, Andrew J. Helmstetter, Erik J. M. Koenen, Rita D. Brandão, Stefan A. Little, Kevin Bethune, Roy H J Erkens
    Abstract:

    Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well-resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well-supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

  • Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes
    2018
    Co-Authors: Thomas L P Couvreur, Herve Sauquet, Andrew J. Helmstetter, Erik J. M. Koenen, Kevin Bethume, Rita D. Brandão, Stefan A. Little, Roy H J Erkens
    Abstract:

    Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 109 genera and ca. 2450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

  • a new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics
    Botanical Journal of the Linnean Society, 2012
    Co-Authors: Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Michael D Pirie, Kurt M. Neubig, Richard J Abbott, Johan B Mols, Jan W Maas, Richard M K Saunders
    Abstract:

    The pantropical flowering plant family Annonaceae is the most species-rich family of Magnoliales. Despite long-standing interest in the systematics of Annonaceae, no authoritative classification has yet been published in the light of recent molecular phylogenetic analyses. Here, using the largest, most representative, molecular dataset compiled on Annonaceae to date, we present, for the first time, a robust family-wide phylogenetic tree and subsequent classification. We used a supermatrix of up to eight plastid markers sequenced from 193 ingroup and seven outgroup species. Some of the relationships at lower taxonomic levels are poorly resolved, but deeper nodes generally receive high support. Annonaceae comprises four major clades, which are here given the taxonomic rank of subfamily. The description of Annonoideae is amended, and three new subfamilies are described: Anaxagoreoideae, Ambavioideae and Malmeoideae. In Annonoideae, seven tribes are recognized, one of which, Duguetieae, is described as new. In Malmeoideae, seven tribes are recognized, six of which are newly described: Dendrokingstonieae, Fenerivieae, Maasieae, Malmeeae, Monocarpieae and Piptostigmateae. This new subfamilial and tribal classification is discussed against the background of previous classifications and characters to recognize subfamilies are reviewed. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 5–40.

Peter K. Endress - One of the best experts on this subject based on the ideXlab platform.

  • floral development and floral phyllotaxis in anaxagorea Annonaceae
    Annals of Botany, 2011
    Co-Authors: Peter K. Endress, Joseph E Armstrong
    Abstract:

    Background and Aims Anaxagorea is the phylogenetically basalmost genus in the large tropical Annonaceae (custard apple family) of Magnoliales, but its floral structure is unknown in many respects. The aim of this study is to analyse evolutionarily interesting floral features in comparison with other genera of the Annonaceae and the sister family Eupomatiaceae.

  • Regular ArticleGynoecium diversity and systematics of the Magnoliales and winteroids
    Botanical Journal of the Linnean Society, 1997
    Co-Authors: Anton Igersheim, Peter K. Endress
    Abstract:

    Carpel and ovule structure was compared in representatives of all 11 families of the Magnoliales (Annonaceae, Canellaceae, Degeneriaceae, Eupomatiaceae, Himantandraceae, Magnoliaceae, Myristicaceae) and winteroids (Austrobaileyaceae, Illiciaceae, Schisandraceae, Winteraceae). Special attention was paid to features that are constant at family level. Bisexual flowers are always protogynous. In all representatives studied the carpels are closed at anthesis. Carpel closure is attained in three different ways: (1) postgenital fusion of inner surfaces (Degeneriaceae, Eupomatiaceae, Winteraceae), or (2) occlusion by secretion (Austrobaileyaceae, Schisandraceae), or (3) a combination of (1) and (2): in Annonaceae, Canellaceae, Myristicaceae there is a conspicuous secretory canal in the innermost part of the ventral slit; in Illiciaceae and Magnoliaceae there is a narrow canal in the innermost part of the ventral slit; and in Himantandraceae the ventral slit is postgenitally fused in the style but completely open in the ovary. In most families the carpels have a double stigmatic crest or they have two tips in the transversal symmetry plane (i.e. at right angles to the median plane). Stigmas are unicellular papillate in most families but the papillae are bi- to multicellular (uniseriate) in Degeneriaceae and Eupomatiaceae. An unusual cryptic extracarpellary compitum was found in Himantandraceae and Schisandraceae. Intrusive oil cells were found in the carpel epidermis of Illiciaceae and Schisandraceae. Mature ovules vary in length between 0.15 and 1.1 mm. The outer integument is fully annular (not semiannular) in Degeneriaceae, Himantandraceae, Canellaceae, Myristicaceae, and Illiciaceae. A rudimentary aril occurs in Canellaceae, and originates at the same site as in arillate Annonaceae and Myristicaceae. The results most strongly support an Annonaceae-Myristicaceae-Canellaceae alliance, to some degree also an Eupomatiaceae-Degeneriaceae-Himantandraceae-Magnoliaceae alliance, and an Illiciaceae-Schisandraceae-Winteraceae-Austrobaileyaceae alliance.

  • Gynoecium diversity and systematics of the Magnoliales and winteroids
    Botanical Journal of the Linnean Society, 1997
    Co-Authors: Anton Igersheim, Peter K. Endress
    Abstract:

    Abstract Carpel and ovule structure was compared in representatives of all 11 families of the Magnoliales (Annonaceae, Canellaceae, Degeneriaceae, Eupomatiaceae, Himantandraceae, Magnoliaceae, Myristicaceae) and winteroids (Austrobaileyaceae, Illiciaceae, Schisandraceae, Winteraceae). Special attention was paid to features that are constant at family level. Bisexual flowers are always protogynous. In all representatives studied the carpels are closed at anthesis. Carpel closure is attained in three different ways: (1) postgenital fusion of inner surfaces (Degeneriaceae, Eupomatiaceae, Winteraceae), or (2) occlusion by secretion (Austrobaileyaceae, Schisandraceae), or (3) a combination of (1) and (2): in Annonaceae, Canellaceae, Myristicaceae there is a conspicuous secretory canal in the innermost part of the ventral slit; in Illiciaceae and Magnoliaceae there is a narrow canal in the innermost part of the ventral slit; and in Himantandraceae the ventral slit is postgenitally fused in the style but completely open in the ovary. In most families the carpels have a double stigmatic crest or they have two tips in the transversal symmetry plane (i.e. at right angles to the median plane). Stigmas are unicellular papillate in most families but the papillae are bi- to multicellular (uniseriate) in Degeneriaceae and Eupomatiaceae. An unusual cryptic extracarpellary compitum was found in Himantandraceae and Schisandraceae. Intrusive oil cells were found in the carpel epidermis of Illiciaceae and Schisandraceae. Mature ovules vary in length between 0.15 and 1.1 mm. The outer integument is fully annular (not semiannular) in Degeneriaceae, Himantandraceae, Canellaceae, Myristicaceae, and Illiciaceae. A rudimentary aril occurs in Canellaceae, and originates at the same site as in arillate Annonaceae and Myristicaceae. The results most strongly support an Annonaceae-Myristicaceae-Canellaceae alliance, to some degree also an Eupomatiaceae-Degeneriaceae-Himantandraceae-Magnoliaceae alliance, and an Illiciaceae-Schisandraceae-Winteraceae-Austrobaileyaceae alliance.

Michael D Pirie - One of the best experts on this subject based on the ideXlab platform.

  • Chromosome-level reference genome of the soursop (Annona muricata): a new resource for Magnoliid research and tropical pomology.
    Molecular ecology resources, 2021
    Co-Authors: Joeri S. Strijk, Mareike Roeder, Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Herve Sauquet, Damien Daniel Hinsinger, Michael D Pirie, Daniel C. Thomas, Kun-fang Cao
    Abstract:

    The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676X sequencing depth) from PacBio and Illumina short-reads, in combination with 10XGenomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

  • Chromosome-level reference genome of the Soursop (Annona muricata), a new resource for Magnoliid research and tropical pomology
    2020
    Co-Authors: Joeri S. Strijk, Mareike Roeder, Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Herve Sauquet, Damien Daniel Hinsinger, Michael D Pirie, Daniel C. Thomas, Kun-fang Cao
    Abstract:

    Annonaceae contain important commercially grown tropical crops, but development of other promising species is hindered by a lack of genomic resources to build breeding programs. In addition, Annonaceae are part of the Magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades have remained unclear. To provide resources to both breeders and evolutionary researchers, we report the chromosome-level genome assembly of the soursop (Annona muricata). We assembled the soursop genome using a total of 444.32 Gb of DNA sequences that were generated using PacBio and Illumina short-reads, in combination with 10XGenomics, Bionano data and Hi-C sequencing. 949 scaffolds were assembled to a final size of 656.77Mb, with a scaffold N50 of 3.43 Mb. Repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size of A. muricata showed a slow but regular contraction of the population, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in Magnoliids, and providing an essential resource for delineating relationships of major lineages at the base of the angiosperms. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. The genome assembly as a community resource will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

  • Annonaceae substitution rates - a codon model perspective
    Revista Brasileira De Fruticultura, 2014
    Co-Authors: Lars W Chatrou, Michael D Pirie, Robin Van Velzen, Freek T. Bakker
    Abstract:

    The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

  • a new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics
    Botanical Journal of the Linnean Society, 2012
    Co-Authors: Lars W Chatrou, Thomas L P Couvreur, Roy H J Erkens, Michael D Pirie, Kurt M. Neubig, Richard J Abbott, Johan B Mols, Jan W Maas, Richard M K Saunders
    Abstract:

    The pantropical flowering plant family Annonaceae is the most species-rich family of Magnoliales. Despite long-standing interest in the systematics of Annonaceae, no authoritative classification has yet been published in the light of recent molecular phylogenetic analyses. Here, using the largest, most representative, molecular dataset compiled on Annonaceae to date, we present, for the first time, a robust family-wide phylogenetic tree and subsequent classification. We used a supermatrix of up to eight plastid markers sequenced from 193 ingroup and seven outgroup species. Some of the relationships at lower taxonomic levels are poorly resolved, but deeper nodes generally receive high support. Annonaceae comprises four major clades, which are here given the taxonomic rank of subfamily. The description of Annonoideae is amended, and three new subfamilies are described: Anaxagoreoideae, Ambavioideae and Malmeoideae. In Annonoideae, seven tribes are recognized, one of which, Duguetieae, is described as new. In Malmeoideae, seven tribes are recognized, six of which are newly described: Dendrokingstonieae, Fenerivieae, Maasieae, Malmeeae, Monocarpieae and Piptostigmateae. This new subfamilial and tribal classification is discussed against the background of previous classifications and characters to recognize subfamilies are reviewed. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 5–40.

  • Dating clades with fossils and molecules: the case of Annonaceae
    Botanical Journal of the Linnean Society, 2012
    Co-Authors: Michael D Pirie, James A. Doyle
    Abstract:

    This article addresses the challenges involved in estimating the ages of clades using fossils and DNA sequences. We review the principles and problems of placing fossils in trees of extant taxa and using them to constrain the ages of nodes in molecular dating analyses. Endressinia and Futabanthus provide minimum ages of 112 Mya for the stem lineage and 89 Mya for the crown group of Annonaceae, and the diversity of endosperm ruminations in seeds from the London Clay indicates that the four main clades of Annonaceae had diverged by 50 Mya. Ages inferred using these minimum constraints and a plastid phylogenetic tree for Annonaceae, particularly crown ages of the two main clades (Malmeoideae and Annonoideae), depend on assumptions regarding the pattern of variation in rates of molecular evolution. Our results using methods that assume rate autocorrelation or log-normal distribution of rates suggest that neither assumption fits well the apparently abrupt changes in rates in Annonaceae. Instead of soft-bounded age constraints, we argue for the use of only well-substantiated fossil evidence by means of priors with hard bounds. Thus, we can infer ages that take into account both palaeontological and phylogenetic uncertainty, without confounding the different factors involved. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 84–116.