Embryology of the Irvingiaceae,a family with uncertain relationships among the Malpighiales

The Irvingiaceae, one of 40 families of the Malpighiales, comprise a small woody family of 10 species in three genera distributed in Old World tropics. Its relationships with other families are unclear, although recent molecular analyses suggest affinities with Linaceae, Caryocaraceae, Erythroxylaceae, and Rhizophoraceae. To gain insight into family relationships, we investigated 63 embryological characters of two previously unstudied African species, Irvingia gabonensis and I. smithii, and compared them with other Malpighiales and the sister group Oxalidales. Embryologically, Irvingia is characterized by the absence of an integumentary tapetum and by having a non-multiplicative inner integument, a multiplicative testa, many discrete fascicles of vascular bundles running in the testa from the raphe to antiraphe (each fascicle comprised several strands arranged in a concentric manner), and a fibrous exotegmen. Comparisons showed that Irvingia did not resemble any of the Linaceae, Caryocaraceae, Erythroxylaceae, Rhizophoraceae, or any of the other malpighialean families for which embryological data are available. The genus rather resembled Huaceae and Connaraceae (Oxalidales) in seed coat structure. However, 18 families (45%) of the Malpighiales are still poorly understood embryologically, and therefore additional studies are required for further critical comparisons.     

Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

Background  

The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales.     

Phylogeny of the eudicot order Malpighiales: analysis of a recalcitrant clade with sequences of the petD group II intron

Malpighiales are one of the most diverse orders of angiosperms. Molecular phylogenetic studies based on combined sequences of coding genes allowed to identify major lineages but hitherto were unable to resolve relationships among most families. Spacers and introns of the chloroplast genome have recently been shown to provide strong signal for inferring relationships among major angiosperm lineages and within difficult clades. In this study, we employed sequence data of the petD group II intron and the petB-petD spacer for a set of 64 Malpighiales taxa, representing all major lineages. Celastrales and Oxalidales served as outgroups. Sequence alignment was straightforward due to frequent microstructural changes with easily recognizable motifs (e.g., simple sequence repeats), and well defined mutational hotspots. The secondary structure of the complete petD intron was calculated for Idesia polycarpa as an example. Domains I and IV are the most length variable parts of the intron. They contain terminal A/T-rich stem-loop elements that are suggested to elongate independently in different lineages with a slippage mechanism earlier reported from the P8 stem-loop of the trnL intron. Parsimony and Bayesian analyses of the petD dataset yielded trees largely congruent with results from earlier multigene studies but statistical support of nodes was generally higher. For the first time a deep node of the Malpighiales backbone, a clade comprising Achariaceae, Violaceae, Malesherbiaceae, Turneraceae, Passifloraceae, and a Lacistemataceae–Salicaceae lineage received significant statistical support (83% JK, 1.00 PP) from plastid DNA sequences.     

Phylogenetic analyses of Malpighiales using plastid and nuclear DNA sequences, with particular reference to the embryology of Euphorbiaceae sens. str.

We present phylogenetic analyses of Malpighiales, which are poorly understood with respect to relationships within the order, using sequences from rbcL, atpB, matK and 18SrDNA from 103 genera in 23 families. From several independent and variously combined analyses, a four-gene analysis using all sequence data provided the best resolution, resulting in the single most parsimonious tree. In the Malpighiales [bootstrap support (BS) 100%], more than eight major clades comprising a family or group of families successively diverged, but no clade containing more than six families received over 50% BS. Instead, ten terminal clades that supported close relationships between and among families (>50% BS) were obtained, between, for example, Balanopaceae and Chrysobalanaceae; Lacistemataceae and Salicaceae; and Phyllanthaceae and Picrodendraceae. The monophyly of Euphorbiaceae sens. str. were strongly supported (BS 100%), but its sister group was unclear. Euphorbiaceae sens. str. comprised two basally diverging clades (BS 100%): one leading to the Clutia group (Chaetocarpus, Clutia, Pera and Trigonopleura), and the other leading to the rest of the family. The latter shared a palisadal, instead of a tracheoidal exotegmen as a morphological synapomorphy. While both Acalyphoideae (excluding Dicoelia and the Clutia group) and Euphorbioideae are monophyletic, Crotonoideae were paraphyletic, requiring more comprehensive analyses.     

Comparative floral structure and systematics of the clade of Lophopyxidaceae and Putranjivaceae (Malpighiales)

In molecular phylogenetic studies, Lophopyxidaceae and Putranjivaceae are well supported as sisters in the large rosid order Malpighiales. As the floral structure of both families is poorly known and the two families have never been compared, the present comparative study was carried out, as part of a larger project on the comparative floral structure of Malpighiales, using microtome section series and scanning electron microscopy (SEM) studies. Similar to other angiosperm clades, it appears that the structure of the ovules is a strong marker for suprafamilial relationships in Malpighiales. Both families have two collateral pendant antitropous ovules per carpel associated with obturators (as in some Euphorbiaceae s.l., to which Putranjivaceae belonged in earlier classifications). However, in contrast with Euphorbiaceae s.l., the ovules are not crassinucellar, but either incompletely tenuinucellar or only weakly crassinucellar with a long and conspicuously slender nucellus and an endothelium, and do not have a nucellar beak, but a normal micropyle, features they share with families other than Euphorbiaceae s.l. among Malpighiales. Other shared features of the two families include the following. The outer sepals tend to be smaller than the inner ones and the sepals do not protect the gynoecium in older buds. Sepals of some taxa have a single vascular trace. A short zone of synsepaly tends to be present. Stamens tend to be antesepalous in haplostemonous flowers. A short gynophore is present. The synascidiate zone extends up to above the placenta, but is restricted to the ovary in taxa with more than one carpel. The micropyle is formed by the inner integument. The ventral carpel slits extend down into the synascidiate zone as postgenitally fused furrows. The carpels have a broad dorsal band of vascular bundles in the style. The overall floral structure of the two families corroborates their sister position well and does not support the earlier association of Putranjivaceae with Euphorbiaceae s.l. or of Lophopyxidaceae with Geraniales–Sapindales–Celastrales, which rely on shared superficial floral similarities. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 404–448.     

Phylogenetic relationships of the enigmatic angiosperm family Podostemaceae inferred from 18S rDNA and rbcL sequence data

The phylogenetic relationships of some angiosperm families have remained enigmatic despite broad phylogenetic analyses of rbcL sequences. One example is the aquatic family Podostemaceae, the relationships of which have long been controversial because of major morphological modifications associated with their aquatic habit. Podostemaceae have variously been associated with Piperaceae, Nepenthaceae, Polygonaceae, Caryophyllaceae, Scrophulariaceae, Rosaceae, Crassulaceae, and Saxifragaceae. Two recent analyses of rbcL sequences suggest a possible sister-group relationship of Podostemaceae to Crassulaceae (Saxifragales). However, the branch leading to Podostemaceae was long, and use of different outgroups resulted in alternative placements. We explored the phylogenetic relationships of Podostemaceae using 18S rDNA sequences and a combined rbcL + 18S rDNA matrix representing over 250 angiosperms. In analyses based on 18S rDNA data, Podostemaceae are not characterized by a long branch; the family consistently appears as part of a Malpighiales clade that also includes Malpighiaceae, Turneraceae, Passifloraceae, Salicaceae, Euphorbiaceae, Violaceae, Linaceae, Chrysobalanaceae, Trigoniaceae, Humiriaceae, and Ochnaceae. Phylogenetic analyses based on a combined 18S rDNA + rbcL data set (223 ingroup taxa) with basal angiosperms as the outgroup also suggest that Podostemaceae are part of a Malpighiales clade. These searches swapped to completion, and the shortest trees showed enhanced resolution and increased internal support compared to those based on 18S rDNA or rbcL alone. However, when Gnetales are used as the outgroup, Podostemaceae appear with members of the nitrogen fixing clade (e.g., Elaeagnaceae, Ulmaceae, Rhamnaceae, Cannabaceae, Moraceae, and Urticaceae). None of the relationships suggested here for Podostemaceae receives strong bootstrap support. Our analyses indicate that Podostemaceae are not closely allied with Crassulaceae or with other members of the Saxifragales clade; their closest relatives, although still uncertain, appear to lie elsewhere in the rosids.     

Molecular phylogenetics of Linaceae with complete generic sampling and data from two plastid genes

The phylogeny of Linaceae is examined, with sampling from the 13 commonly recognized genera of the family and sequence data from the plastid genes matK and rbcL. Representatives of 24 additional families of the order Malpighiales are included in the analyses, with members of Celastrales, Fabales, Fagales, Oxalidales and Rosales used as outgroups. Linaceae and both subfamilies, the temperate Linoideae and the tropical Hugonioideae, are found to be monophyletic in likelihood‐ and parsimony‐based analyses, although the monophyly of Hugonioideae is not well supported. Average divergence time estimates using rbcL indicate that the subfamilies diverged from each other during the Palaeocene, approximately 60 million years ago. No sister group to Linaceae is consistently identified in these analyses, and relationships among families of Malpighiales are not well resolved. In accord with previous estimates of Linoideae phylogeny, Linum is shown to be nonmonophyletic, with several segregate genera nested within it, but the relationships of the south‐east Asian genera, Anisadenia, Reinwardtia and Tirpitzia, remain uncertain. In Hugonioideae, Indorouchera and Philbornea are found to be closely related to members of Hugonia section Durandea. Relationships of the neotropical genera Hebepetalum and Roucheria to the palaeotropical hugonioids are not consistently resolved. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 64–83.     

Mitochondrial genome characteristics of Somena scintillans (Lepidoptera: Erebidae) and comparation with other Noctuoidea insects

In this study, mitogenome of Somena scintillans (Lepidoptera: Erebidae) were sequenced and compared with other Noctuoidea species. The mitogenome is 15,410 base pairs in length. All 13 protein-coding genes (PCGs) are initiated by ATN codons except cox1 with CGA and all of PCGs terminate with TAA except nad4 with TAG. The codons ACG and CGC are absent. All the tRNA genes could be folded into the typical cloverleaf secondary structure except the trnS1 which not only loses dihydrouridine (DHU) arm but also mutates its anticodon into TCT. In the AT-rich region of the mitogenome the motif ‘ATAGA’ mutates to ‘ATATA’ and two copies of 161 bp-tandem repeats and two ‘TA’ short tandem repeats are founded. Phylogenetic analyses showed that S. scintillans is clustered into subfamily Lymatriinae. The phylogenetic relationships within Noctuoidea is (((Nolidae + (Euteliidae + Noctuidae)) + Erebidae) + Notodontidae)     

Comparative floral structure and systematics in Rhizophoraceae,Erythroxylaceae and the potentially related Ctenolophonaceae,Linaceae, Irvingiaceae and Caryocaraceae (Malpighiales)

Within the rosid order Malpighiales, Rhizophoraceae and Erythroxylaceae (1) are strongly supported as sisters in molecular phylogenetic studies and possibly form a clade with either Ctenolophonaceae (2) or with Linaceae, Irvingiaceae and Caryocaraceae (less well supported) (3). In order to assess the validity of these relationships from a floral structural point of view, these families are comparatively studied for the first time in terms of their floral morphology, anatomy and histology. Overall floral structure reflects the molecular results quite well and Rhizophoraceae and Erythroxylaceae are well supported as closely related. Ctenolophonaceae share some unusual floral features (potential synapomorphies) with Rhizophoraceae and Erythroxylaceae. In contrast, Linaceae, Irvingiaceae and Caryocaraceae are not clearly supported as a clade, or as closely related to Rhizophoraceae and Erythroxylaceae, as their shared features are probably mainly symplesiomorphies at the level of Malpighiales or a (still undefined) larger subclade of Malpighales, rather than synapomorphies. Rhizophoraceae and Erythroxylaceae share (among other features) conduplicate petals enwrapping stamens in bud, antepetalous stamens longer than antesepalous ones, a nectariferous androecial tube with attachment of the two stamen whorls at different positions: one whorl on the rim, the other below the rim of the tube, the ovary shortly and abruptly dorsally bulged and the presence of a layer of idioblasts (laticifers?) in the sepals and ovaries. Ctenolophonaceae share with Rhizophoraceae and/or Erythroxylaceae (among other features) sepals with less than three vascular traces, a short androgynophore, an ovary septum thin and severed or completely disintegrating during development, leading to a developmentally secondarily unilocular ovary, a zigzag‐shaped micropyle and seeds with an aril. Special features occurring in families of all three groupings studied here are, for example, synsepaly, petals not retarded and thus forming protective organs in floral bud, petals postgenitally fused or hooked together in bud, androecial tube and petals fusing above floral base, androecial corona, apocarpous unifacial styles, nucellus thin and long, early disintegrating (before embryo sac is mature), and nectaries on the androecial tube. Some of these features may be synapomorphies for the entire group, if it forms a supported clade in future molecular studies, or for subgroups thereof. Others may be plesiomorphies, as they also occur in other Malpighiales or also in Celastrales or Oxalidales (COM clade). The occurrence of these features within the COM clade is also discussed. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 166 , 331–416.     

Comparative floral structure and systematics in Celastrales (Celastraceae, Parnassiaceae, Lepidobotryaceae)

Floral morphology, anatomy and histology in the newly circumscribed order Celastrales, comprising Celastraceae, Parnassiaceae and Lepidobotryaceae are studied comparatively. Several genera of Celastraceae and Lepidobotrys (Lepidobotryaceae) were studied for the first time in this respect. Celastraceae are well supported as a group by floral structure (including genera that were in separate families in earlier classifications); they have dorsally bulged‐up locules (and thus apical septa) and contain oxalate druses in their floral tissues. The group of Celastraceae and Parnassiaceae is also well supported. They share completely syncarpous gynoecia with commissural stigmatic lobes (and strong concomitant development of the commissural vascular bundles but weak median carpel bundles), only weakly crassinucellar or incompletely tenuinucellar ovules with an endothelium, partly fringed sepals and petals, protandry in bisexual flowers combined with herkogamy by the movement of stamens and anther abscission, and stamens fused with the ovary. In contrast, Lepidobotryaceae are more distant from the other two families, sharing only a handful of features with Celastraceae (not Parnassiaceae), such as pseudohermaphroditic flowers, united stamen bases forming a collar around the gynoecium and seeds with a conspicuous aril. However, all three families together are also somewhat supported as a group and share petals that are not retarded in late floral bud development, 3‐carpellate gynoecia, ventral slits of carpels closed by long interlocking epidermal cells and pollen tube transmitting tissue encompassing several cell layers, both integuments usually more than two cell layers thick, and only weak or lacking floral indumentum. In some molecular analyses Celastrales form an unsupported clade with Malpighiales and Oxalidales. This association is supported by floral structure, especially between Celastrales and Malpighiales. Among Celastrales, Lepidobotryaceae especially share special features with Malpighiales, including a diplostemonous androecium with ten fertile stamens, epitropous ovules with an obturator and strong vascularization around the chalaza. © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society, 2005, 149 , 129–194.     

The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron

The complete sequence of the chloroplast genome of cassava (Manihot esculenta, Euphorbiaceae) has been determined. The genome is 161,453 bp in length and includes a pair of inverted repeats (IR) of 26,954 bp. The genome includes 128 genes; 96 are single copy and 16 are duplicated in the IR. There are four rRNA genes and 30 distinct tRNAs, seven of which are duplicated in the IR. The infA gene is absent; expansion of IRb has duplicated 62 amino acids at the 3′ end of rps19 and a number of coding regions have large insertions or deletions, including insertions within the 23S rRNA gene. There are 17 intron-containing genes in cassava, 15 of which have a single intron while two (clpP, ycf3) have two introns. The usually conserved atpF group II intron is absent and this is the first report of its loss from land plant chloroplast genomes. The phylogenetic distribution of the atpF intron loss was determined by a PCR survey of 251 taxa representing 34 families of Malpighiales and 16 taxa from closely related rosids. The atpF intron is not only missing in cassava but also from closely related Euphorbiaceae and other Malpighiales, suggesting that there have been at least seven independent losses. In cassava and all other sequenced Malphigiales, atpF gene sequences showed a strong association between C-to-T substitutions at nucleotide position 92 and the loss of the intron, suggesting that recombination between an edited mRNA and the atpF gene may be a possible mechanism for the intron loss.     

Comparative floral structure and systematics in Ochnaceae s.l. (Ochnaceae,Quiinaceae and Medusagynaceae; Malpighiales)

Ochnaceae s.l. (Ochnaceae, Quiinaceae and Medusagynaceae), one of the well‐supported subclades of the large order Malpighiales retrieved so far in molecular phylogenetic studies, were comparatively studied with regard to floral structure using microtome section series and scanning electron microscopy (SEM). Floral morphology, anatomy and histology also strongly reflect this close relationship. Potential synapomorphies of the subclade include: flowers nectarless, sepals of different sizes within a flower, petals not retarded in development and forming the protective organs of advanced floral buds, petal aestivation contort, petals with three vascular traces, petals reflexed over the sepals and directed toward the pedicel, polystemony, anthers almost or completely basifixed, gynoecium often with more than five carpels, short gynophore present, styles separate for at least their uppermost part and radiating outwards, suction‐cup‐shaped stigmas, vasculature forming a dorsal band of bundles in the upper stylar region, gynoecium epidermis with large, radially elongate cells, ovules either weakly crassinucellar or incompletely tenuinucellar with an endothelium, abundance of tanniferous tissues and sclerenchyma in floral organs. The most strongly supported subclade of two of the three families in molecular analyses, Quiinaceae and Medusagynaceae, is also particularly well supported by floral structural features, including the presence of functionally and morphologically unisexual flowers, a massive thecal septum that persists after anther dehiscence, styles radiating outward from the ovary, two lateral ovules per carpel, positioned one above the other, conspicuous longitudinal ribs on the ovary wall at anthesis, and a ‘false endothelium’ on the nucellus at anthesis. Additionally, the group fits well in Malpighiales and further emphasizes the relationship of Malpighiales with Celastrales and Oxalidales, and thus the unity of the COM clade. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 299–392.     

First steps towards a floral structural characterization of the major rosid subclades

A survey of our own comparative studies on several larger clades of rosids and over 1400 original publications on rosid flowers shows that floral structural features support to various degrees the supraordinal relationships in rosids proposed by molecular phylogenetic studies. However, as many apparent relationships are not yet well resolved, the structural support also remains tentative. Some of the features that turned out to be of interest in the present study had not previously been considered in earlier supraordinal studies. The strongest floral structural support is for malvids (Brassicales, Malvales, Sapindales), which reflects the strong support of phylogenetic analyses. Somewhat less structurally supported are the COM (Celastrales, Oxalidales, Malpighiales) and the nitrogen-fixing (Cucurbitales, Fagales, Fabales, Rosales) clades of fabids, which are both also only weakly supported in phylogenetic analyses. The sister pairs, Cucurbitales plus Fagales, and Malvales plus Sapindales, are structurally only weakly supported, and for the entire fabids there is no clear support by the present floral structural data. However, an additional grouping, the COM clade plus malvids, shares some interesting features but does not appear as a clade in phylogenetic analyses. Thus it appears that the deepest split within eurosids–that between fabids and malvids - in molecular phylogenetic analyses (however weakly supported) is not matched by the present structural data. Features of ovules including thickness of integuments, thickness of nucellus, and degree of ovular curvature, appear to be especially interesting for higher level relationships and should be further explored. Although features of interest are not necessarily stable at the level of a large clade, they do show a considerable concentration in particular clades and are rare or lacking in others. This may be viewed as a special trend for this feature to evolve in this group or to be conserved as a synapomorphy (or a combination of both).     

The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera

ABSTRACT: BACKGROUND: Lepidoptera encompasses more than 160,000 described species that have been classified into 45-48 superfamilies. The previously determined Lepidoptera mitochondrial genomes (mitogenomes) are limited to six superfamilies of the most derived lepidopteran lineage Ditrysia. Compared with the ancestral insect gene order, these mitogenomes all contain a tRNA rearrangement. To gain new insights into Lepidoptera mitogenome evolution, we sequenced the mitogenomes of two ghost moths that belong to primitive lepidopteran lineages and conducted a comparative mitogenomic analysis across Lepidoptera. RESULTS: The mitogenomes of Thitarodes renzhiensis and T. yunnanensis are 16,173 bp and 15,814 bp long with an A+T content of 81.28% and 82.33%, respectively. Different tandem repeats in the A+T-rich region mainly account for the size difference between the two mitogenomes. Both mitogenomes include 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. The 1,584-bp sequence from rrnS to nad2 was also determined for Thitarodes sp.QL, which has no repetitive sequence in the A+T-rich region. All three Thitarodes species possess the ancestral gene order with trnI-trnQ-trnM located between the A+T-rich region and nad2, which is different from the gene order trnM-trnI-trnQ in all previously sequenced Lepidoptera species. The formerly identified conserved elements of Lepidoptera mitogenomes (i.e. the motif 'ATAGA' and poly-T stretch in the A+T-rich region and the long intergenic spacer upstream of nad2) are absent in the Thitarodes mitogenomes. The phylogenetic analysis supports that Hepialoidea, represented by T. renzhiensis and T. yunnanensis, occupies a basal position in the currently sampled seven superfamilies. The relationships of the other six superfamilies are (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea). CONCLUSION: The mitogenomes of T. renzhiensis and T. yunnanensis exhibit unusual features compared with the previously determined Lepidoptera mitogenomes. Their ancestral gene order indicates that the tRNA rearrangement event occurred after Lepidoptera diverged from other holometabolous insect orders. Phylogenetic analysis based on mitogenome sequences is a power tool for addressing phylogenetic relationships among major Lepidoptera superfamilies. Characterization of the two ghost moth mitogenomes has enriched our knowledge of Lepidoptera mitogenomes and contributed to our understanding of the mechanisms underlying mitogenome evolution, especially gene rearrangements.     

Leaf structure of species from three closely related genera from tribe Crotoneae Dumort. (Euphorbiaceae s.s., Malpighiales)

Euphorbiaceae s.s. is one of the largest angiosperm families, comprising nine major lineages. Molecular analysis indicated a polyphyletic condition in the subfamily Crotonoideae s.l., with four lineages identified, including one termed inaperturate crotonoids, which encompasses the tribe Crotoneae. Anatomical data were obtained from 15 species of Croton sect. Cyclostigma (Griseb.) Müll. Arg., Brasiliocroton P. Berry & I. Cordeiro and Astraea Klotzsch, which belongs to this lineage. The presence and protodermal origin of the idioblasts with lipophilic content and the interruption of the palisade by collenchyma layers on the adaxial side of the mid vein are common to the Croton L. species analysed and Brasiliocroton. The presence of dorsiventrality, paracytic stomata, collateral vascular bundles, branched non-articulated laticifers and crystal idioblasts in the species studied indicates morphological similarities among the three genera. The interpretation of the stipite of the complex trichomes as emergences is a structural novelty for the group. Leaf anatomy provided an excellent source of characters for future studies of the tribe Crotoneae (Euphorbiaceae s.s., Malpighiales).