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Jinzhao Liu - One of the best experts on this subject based on the ideXlab platform.

Kun-fang Cao - 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.

  • Increasing axial parenchyma fraction in the Malagasy Magnoliids facilitated the co-optimisation of hydraulic efficiency and safety.
    The New phytologist, 2020
    Co-Authors: Amy Ny Aina Aritsara, Vonjisoa M. Razakandraibe, Tahiana Ramananantoandro, Sean M. Gleason, Kun-fang Cao
    Abstract:

    The evolution of angiosperms was accompanied by the segregation and specialisation of their xylem tissues. This study aimed to determine whether the fraction and arrangement of parenchyma tissue influence the hydraulic efficiency-safety trade-off in the basal angiosperms. We examined xylem anatomical structure and hydraulic functioning of 28 woody species of Magnoliids in a tropical rainforest of Madagascar and reported, for the first time, quantitative measurements that support the relationship between vessel-to-xylem parenchyma connectivity and the hydraulic efficiency-safety trade-off. We also introduced a new measurement - the distance of species from the trade-off limit - to quantify the co-optimisation of hydraulic efficiency and safety. Although the basal angiosperms in this study had low hydraulic conductivity and safety, species with higher axial parenchyma fraction (APf) had significantly higher hydraulic conductivity. Hydraulic efficiency-safety optimisation was accompanied by higher APf and vessel-to-axial parenchyma connectivity. Conversely, species exhibiting high ray parenchyma fraction and high vessel-to-ray connectivity had lower Ks and were further away from the hydraulic trade-off limit line. Our results provide evidence that axial parenchyma fraction and paratracheal arrangement are associated with both enhanced hydraulic efficiency and safety.

  • 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.

  • Termites amplify the effects of wood traits on decomposition rates among multiple bamboo and dicot woody species
    Journal of Ecology, 2015
    Co-Authors: Guofang Liu, William K. Cornwell, Kun-fang Cao, Richardus S. P. Van Logtestijn, Shi-jian Yang, Xiufang Xie, Ya-lin Zhang, Xu Pan
    Abstract:

    Wood decomposition is a key process in the terrestrial carbon cycle, controlling carbon storage with feedback to climate. In (sub) tropical forest, termites are major players in wood decomposition, but their role relative to that of microbial decomposers and wood traits of different tree species is poorly understood. The current literature also has strong bias towards dicot tree decomposition, while abundant woody monocots, particularly bamboos, also contribute greatly to (sub) tropical carbon cycling. Here, we present the first experiment to disentangle effects of dead wood traits and termite activity on decomposition of 66 angiosperm species of wide-ranging phylogenetic position: 31 bamboos, eight non-bamboo Poaceae, 18 eudicots and nine Magnoliids. We incubated dead stems of up to 4 size classes per species in a common garden' in tropical S China. We tested the hypotheses that (i) dead wood of bamboo (monocots) is less decomposable than dead wood of eudicots or Magnoliids; (ii) both microbial- and termite-driven decomposition show negative relationships with initial wood density and with dry matter content. Bamboo wood generally decomposed more slowly than dicot wood but only slightly slower at given wood density or diameter. Wood decomposition in both bamboo and dicot clades decreased with wood density or dry matter content. Termites contributed greatly to this pattern, explaining 53.4% of the variance in wood decomposition and preferentially attacking dead wood of lower initial density, which corresponded with thicker outer culm walls in the case of bamboo species. Thus, termites strongly strengthen the relationship between species' wood traits and litter decomposition as driven by microbial activity.Synthesis. These previously unknown relationships among dead wood quality, diameter, termites and decomposing microbes of both woody monocots and dicots will advance our understanding of the driving mechanisms of (sub) tropical wood decomposition and its contribution to the global carbon cycle.

  • Understanding the ecosystem implications of the angiosperm rise to dominance: leaf litter decomposability among Magnoliids and other basal angiosperms
    Journal of Ecology, 2014
    Co-Authors: Guofang Liu, William K. Cornwell, Xu Pan, Kun-fang Cao, Zhenying Huang, Ming Dong, Johannes H. C. Cornelissen
    Abstract:

    Litter decomposition has been a key driver of carbon and nutrient cycling in the present and past. Based on extant species data, there is a great deal of variation in litter decomposability among major plant lineages, suggesting potential shifts in plant effects on carbon and nutrient cycling during the early evolutionary history of angiosperms. Existing data suggest that eudicot species produce faster decomposing litter compared to gymnosperms, ferns and mosses. One of the missing puzzle pieces in this transition is the basal angiosperms, the functional role of which in past carbon and nutrient cycling has seldom been investigated. We hypothesized that owing to constraints on leaf and plant design related to hydraulic capacity, basal angiosperm trees should generally have resource conservative leaves of low decomposability and that fast-decomposing leaves may only be found in short-statured taxa. We performed a litterbag experiment with simultaneous outdoor incubation of leaf litters in a common environment, including 86 basal angiosperm species (including the magnoliid lineage), 33 eudicots, five gymnosperms and four ferns. We fit a nonlinear model to the decomposition data, and each speciesr decomposability was estimated using the proportional rate of mass loss through the experiment. The mass loss rates were 59.2% lower in basal angiosperms than in eudicot trees. There was one exceptional group within basal angiosperms: the Piperales had higher k values than other magnoliid lineages, but all of the free-standing species were short. Eudicots had higher k values overall and covered a range of plant statures from small-statured herbs to big woody trees. Synthesis. Understanding the ecosystem-level effects of the angiosperm rise to dominance is a crucial goal. Our results indicated that, among generally slow-decomposing magnoliid lineages, only the Piperales have fast decomposition rate associated with small plant statures. Thus it is unlikely that early magnoliid trees were both forest canopy dominants and produced resource acquisitive leaves turning into fast decomposable litter during the evolutionary history of angiosperms.

Veronique Daviero-gomez - One of the best experts on this subject based on the ideXlab platform.

  • Diversified fossil plant assemblages from the Maastrichtian in Isona (southeastern Pyrenees)
    Review of Palaeobotany and Palynology, 2014
    Co-Authors: Josep Marmi, Bernard Gomez, Caries Martin-closas, Sheila Villalba-breva, Veronique Daviero-gomez
    Abstract:

    At the end of the 1970s, several lower Maastrichtian localities with plant megafossil remains were reported near the village of Isona in the Tremp Syncline of the southeastern Pyrenees. These assemblages include conifers (taxodioids and cheirolepidiaceans), monocot angiosperms (Sabalites palms and likely Pandanaceans) and at least 15 types of magnoliid and eudicot angiosperm leaves. Conifers, Sabalites palms and some eudicots are shared with coeval localities in Portugal, France, Austria and Romania. In addition, Sabalites palms and at least five types of Magnoliids and eudicots found here are very similar to fossil leaves reported from Upper Cretaceous localities in North America, suggesting that the Isona flora possibly share some elements with North American floras. Data from the Isona locality also indicate that eudicots dominated the floodplain plant associations in fully continental-influenced terrestrial environments. (C) 2014 Elsevier B.V. All rights reserved.

  • Diversified fossil plant assemblages from the Maastrichtian in Isona (southeastern Pyrenees)
    Review of Palaeobotany and Palynology, 2014
    Co-Authors: Josep Marmi, Bernard Gomez, Caries Martin-closas, Sheila Villalba-breva, Veronique Daviero-gomez
    Abstract:

    Abstract At the end of the 1970s, several lower Maastrichtian localities with plant megafossil remains were reported near the village of Isona in the Tremp Syncline of the southeastern Pyrenees. These assemblages include conifers (taxodioids and cheirolepidiaceans), monocot angiosperms ( Sabalites palms and likely Pandanaceans) and at least 15 types of magnoliid and eudicot angiosperm leaves. Conifers, Sabalites palms and some eudicots are shared with coeval localities in Portugal, France, Austria and Romania. In addition, Sabalites palms and at least five types of Magnoliids and eudicots found here are very similar to fossil leaves reported from Upper Cretaceous localities in North America, suggesting that the Isona flora possibly share some elements with North American floras. Data from the Isona locality also indicate that eudicots dominated the floodplain plant associations in fully continental-influenced terrestrial environments.

Brandon T. Sinn - One of the best experts on this subject based on the ideXlab platform.

  • total duplication of the small single copy region in the angiosperm plastome rearrangement and inverted repeat instability in asarum
    American Journal of Botany, 2018
    Co-Authors: Lawrence M. Kelly, Brandon T. Sinn, Dylan D Sedmak, John V Freudenstein
    Abstract:

    PREMISE OF THE STUDY As more plastomes are assembled, it is evident that rearrangements, losses, intergenic spacer expansion and contraction, and syntenic breaks within otherwise functioning plastids are more common than was thought previously, and such changes have developed independently in disparate lineages. However, to date, the Magnoliids remain characterized by their highly conserved plastid genomes (plastomes). METHODS Illumina HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma henryi and those of representative species from each of the six taxonomic sections of Asarum. Sequenced plastomes were compared in a phylogenetic context provided by maximum likelihood and parsimony inferences made using an additional 18 publicly available plastomes from early-diverging angiosperm lineages. KEY RESULTS In contrast to previously published magnoliid plastomes and the newly sequenced Saruma henryi plastome published here, Asarum plastomes have undergone extensive disruption and contain extremely lengthy AT-repeat regions. The entirety of the small single copy region (SSC) of A. canadense and A. sieboldii var. sieboldii has been incorporated into the inverted repeat regions (IR), and the SSC of A. delavayi is only 14 bp long. All sampled Asarum plastomes share an inversion of a large portion of the large single copy region (LSC) such that trnE-UUC is adjacent to the LSC-IR boundary. CONCLUSIONS Plastome divergence in Asarum appears to be consistent with trends seen in highly rearranged plastomes of the monocots and eudicots. We propose that plastome instability in Asarum is due to repetitive motifs that serve as recombinatory substrates and reduce genome stability.

William E. Friedman - One of the best experts on this subject based on the ideXlab platform.

  • Arabinogalactan proteins mark stigmatic receptivity in the protogynous flowers of Magnolia virginiana (Magnoliaceae)
    American journal of botany, 2014
    Co-Authors: Juan M. Losada, Maria Herrero, José I. Hormaza, William E. Friedman
    Abstract:

    PREMISE OF THE STUDY Factors affecting floral receptivity in angiosperms remain opaque, but recent studies suggest that the acquisition of stigmatic receptivity associated with cell-wall-related arabinogalactan proteins (AGPs) may be a widespread feature of flowering plants. Here, the time during which a stigma is receptive is evaluated and related to the secretion of AGPs in Magnolia virginiana, a protogynous member of an early-divergent angiosperm clade (Magnoliids) with a clearly discernible female receptive phase. METHODS Magnolia virginiana flower phenology was documented, and histochemical changes in the stigma before and after pollination were examined. Stigmatic receptivity was evaluated in relation to the secretion of AGPs detected in whole mounts and immunolocalized in sectioned stigmas. KEY RESULTS Protogynous Magnolia flowers had a precise window of stigmatic receptivity, which is concomitant with the secretion of two AGPs labeled for different epitopes. After pollen germination and tube growth, these two AGPs could no longer be detected in the stigmas, suggesting that these AGPs interact with the growing male gametophytes and could be markers of stigmatic receptivity. CONCLUSIONS These results show that the period of stigmatic receptivity is finely coordinated with the secretion of two arabinogalactan proteins on stigmas of flowers of M. virginiana. This first report of AGP presence in stigmatic tissues in a member of the Magnoliids, together with recently described similar patterns in eudicots, monocots, and members of early-divergent lineages of flowering plants, suggests an ancient and widespread role for AGPs on stigmatic receptivity in angiosperms.

  • female gametophyte development in kadsura implications for schisandraceae austrobaileyales and the early evolution of flowering plants
    International Journal of Plant Sciences, 2003
    Co-Authors: William E. Friedman, William N Gallup, Joseph H Williams
    Abstract:

    Recent phylogenetic analyses of angiosperms have identified a set of “basal” angiosperm lineages (Amborella, Nymphaeales, and a clade that includes Illiciaceae, Schisandraceae, Trimeniaceae, and Austrobaileyaceae) that are central to the study of the origin and early diversification of flowering plants. Prior to this phylogenetic revelation, much of the work on the embryology of ancient angiosperm lineages focused on core Magnoliids (e.g., Magnoliales, Winterales). It is now apparent that little is known about the basic embryological features of the most ancient extant lineages of flowering plants, particularly with respect to the nature and development of the female gametophyte and the ploidy and genetics of the endosperm. Here, we report that Kadsura japonica (Schisandraceae) develops a four‐celled female gametophyte with an egg cell, two synergids, and a uninucleate central cell. The pattern of free‐nuclear divisions in the female gametophyte of Kadsura precisely matches what has recently been reported...