DNA barcoding of Corydalis,the most taxonomically complicated genus of Papaveraceae

The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya–Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA‐trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P‐distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia‐recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well‐supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.     

Pollen evolution and its taxonomic significance in Cuscuta (dodders, Convolvulaceae)

The pollen morphology of 148 taxa (135 species and 13 varieties) of the parasitic plant genus Cuscuta (dodders, Convolvulaceae) was examined using scanning electron microscopy. Six quantitative characters were coded using the gap-weighting method and optimized onto a consensus tree constructed from three large-scale molecular phylogenies of the genus based on nuclear internal transcribed spacer (ITS) and plastid trn-LF sequences. The results indicate that 3-zonocolpate pollen is ancestral, while grains with more colpi (up to eight) have evolved only in two major lineages of Cuscuta (subg. Monogynella and clade O of subg. Grammica). Complex morphological intergradations occur between species when their tectum is described using the traditional qualitative types—imperforate, perforate, and microreticulate. This continuous variation is better expressed quantitatively as “percent perforation,” namely the proportion of perforated area (puncta or lumina) from the total tectum surface. Tectum imperforatum is likely the ancestral condition, while pollen grains with increasingly larger perforation areas have evolved multiple times. The reticulated tectum, unknown in other Convolvulaceae, has evolved in Cuscuta only in two lineages (subg. Monogynella, and clade O of subg. Grammica). Overall, the morphology of pollen supports Cuscuta as a sister to either the “bifid-style” Convolvulaceae clade (Dicranostyloideae) or to one of the members of this clade. Pollen characters alone are insufficient to reconstruct phylogenetic relationships; however, palynological information is useful for the species-level taxonomy of Cuscuta.     

Diversity and evolution of the gynoecium in Cuscuta (dodders, Convolvulaceae) in relation to their reproductive biology: two styles are better than one

The gynoecium of 122 species and 14 varieties of Cuscuta (dodders) was investigated by light and scanning electron microscopy to assess its diversity and evolution and to provide a morphological foundation for understanding the different reproductive strategies encountered in the genus. Data were optimized into a consensus tree constructed from three large-scale molecular phylogenies of the genus based on nuclear ITS and plastid trnL-F sequences. The number of styles combined with the stigma shape are the only floral/fruit characters that enable the separation of Cuscuta subgenera. In addition, gynoecium morphology is useful for delimiting species in some clades. The one-style gynoecium of subg. Monogynella is mostly likely ancestral whereas gynoecia with two styles are derived in subgenera Cuscuta and Grammica. Gynoecia with two styles encountered in the latter subgenera provide a greater morphological complexity and flexibility for various reproductive strategies. In subg. Cuscuta, both the equal styles and stigmas continue to elongate and modify their position after the flowers open, until pollination occurs. In subg. Grammica, the two unequal styles may cause a spatial separation of the sexes in the flower, herkogamy, while the two stigmas mature sequentially and have a differential timing of their receptivity for pollen. A nectary consisting of a ring of modified stomata at the base of the ovary, the equivalent of the hypogynous nectary disc present in many Convolvulaceae, was observed for the first time in all Cuscuta species. The vasculature of the styles is reduced, represented mostly by phloem; xylem is present only in subg. Monogynella. Some gynoecial characters, for example papillae diameter, stigma surface area, stigma width, and style width were moderately correlated with pollen volume, pollen polar?Cequatorial ratio and tectum perforation. Gynoecium features suggest that Cuscuta is allied with the ??bifid clade?? (Dicranostyloideae) in Convolvulaceae.     

Molecular phylogenetics of Paphiopedilum (Cypripedioideae; Orchidaceae) based on nuclear ribosomal ITS and plastid sequences

Phylogenetic relationships in the genus Paphiopedilum were studied using nuclear ribosomal internal transcribed spacer (ITS) and plastid sequence data. The results confirm that the genus Paphiopedilum is monophyletic, and the division of the genus into three subgenera Parvisepalum, Brachypetalum and Paphiopedilum is well supported. Four sections of subgenus Paphiopedilum (Pardalopetalum, Cochlopetalum, Paphiopedilum and Barbata) are recovered as in a recent infrageneric treatment, with strong support. Section Coryopedilum is also recovered, with low bootstrap but high posterior probability values for support of monophyly. Relationships in section Barbata remain unresolved, and short branch lengths and the narrow geographical distribution of many species in the section suggest that it possibly underwent rapid radiation. Mapping chromosome and genome size data (including some new genome size measurements) onto the phylogenetic framework shows that there is no clear trend in increase in chromosome number in the genus. However, the diploid chromosome number of 2n = 26 in subgenera Parvisepalum and Brachypetalum suggests that this is the ancestral condition, and higher chromosome numbers in sections Cochlopetalum and Barbata suggest that centric fission has possibly occurred in parallel in these sections. The trend for genome size evolution is also unclear, although species in section Barbata have larger genome sizes than those in other sections. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 176–196.     

Genome size and plastid trnK-matK markers give new insights into the evolutionary history of the genus Lavandula L.

The genus Lavandula L. consists of 39 species distributed from the North Atlantic Islands, across the Mediterranean Basin to India. We analysed 36 taxa of the genus Lavandula representing two of the three subgenera and six of the eight sections according to the most recent classification (Upson & Andrews 2004). We achieved a phylogenetic reconstruction from partial sequences from plastid trnK and matK genes; the genome size was estimated by flow cytometer measurements. The primary aim was to track phylogenetic patterns through the maternal inherited marker at the sectional level and identify possible genome duplications. The cpDNA tree shows the phylogenetic relationships between subgenus, sections and also elucidates for the first time the relationships between the endemic species of Macaronesia, Morocco and Arabia. The ancestral split between the two subgenera could be explained by dispersal followed by an early vicariance event. The C-value shows genome up-sizing within several phylogenetic clades and geographical areas. An ancestral genome-up sizing is characterized at the node of section Dentatae and Lavandula. The cpDNA tree suggests that the taxa L. angustifolia subsp. pyrenaica (DC.) Guinea and L. stoechas subsp. luiseiri are best treated as a distinct species.     

Supraspecific division of the genusJuncus (Juncaceae)

A new classification of the genusJuncus (Juncaceae) is presented. The genus is divided into two subgenera, characterized by the presence/absence of bracteoles and the structure of inflorescence. Lower rank subdivisions, sections, generally correspond to the traditionally recognized subgenera introduced by Buchenau. A new name is introduced for what has been called subg. (sect.)Ensifolii, Juncus sect.Iridifolii. A checklist of supraspecific names inJuncus, with typification and references to the sectional names accepted, is presented in the Appendix.     

A new infrageneric classification and phylogenetic trends in the genusRhododendron (Ericaceae)

Recent studies have improved the infrageneric classification ofRhododendron, including my own investigations on flavonoids and anthocyanins as chemosystematic markers. From a synoptical comparison of morphological, anatomical and phytochemical characters a new system for the genus is proposed. Phylogenetic character progressions and relationships among subgenera, sections and subsections are discussed and illustrated. Key positions for subg.Candidastrum between chori subgenerumRhododendron andNomazalea, and for subg.Choniastrum between chori subgenerumHymenanthes andNomazalea are suggested.     

Analysis of phylogenetic relationships in the genus Solanum (Solanaceae) as revealed by RAPD markers

Phylogenetic relationships and genetic variation were examined in the genus Solanum based on the random amplified polymorphic DNA (RAPD) technique. Genetic distances were estimated for 42 accessions from five subgenera [Archaesolanum, Minon (Syn. Brevantherum), Leptostemonum, Potatoe, and Solanum]. This investigation provided new information and reinforced some suggestions from previous phylogenetic studies. Analysis with random markers from the total genome clearly separated Solanum sect. Dulcamara, from the other members of Solanum subg. Potatoe, and indicated that among the analysed Solanum subgenera subg. Solanum is most closely related to it. The results suggest that Solanum sect. Dulcamara should be excluded from Solanum subg. Potatoe. The subclusters formed by S. rostratum and S. citrullifolium appear to be distinct from the subcluster formed by the two accessions of S. sisymbriifolium. This topology indicates that Solanum sect. Androceras and Solanum sect. Cryptocarpum are fairly closely related, although the data suggest that the two sections should not be maintained.     

Karyological studies of Iranian <Emphasis Type="Italic">Allium</Emphasis> L. (Amaryllidaceae) species with focus on sect. <Emphasis Type="Italic">Acanthoprason</Emphasis>. 1. Mitotic chromosomes

Eighteen species and subspecies (34 accessions) of Allium sect. Acanthoprason and 11 species (17 accessions) belonging to other subgenera and sections of Allium were karyologically investigated and include first reports for 12 species. The examined plants of 47 accessions were diploid, three accessions of two species were tetraploid, and in the A. bisotunense accession, we found a mix of di- and triploid individuals. B chromosomes were found in 10 accessions. A basic chromosome number of x = 8 was confirmed for all investigated members of subg. Melanocrommyum and subg. Allium, and x = 9 for Allium tripedale of subg. Nectaroscordum. Idiograms were drawn for each accession, and metaphase images are presented illustrating observed chromosomal variations. Also, karyotype features and asymmetry parameters were calculated for all accessions. Chromosomal aberrations, e.g. aneuploid cells or loss of whole or parts of chromosome arms, were rarely observed. In general, the karyotypes showed low variation in inter- and intrachromosomal asymmetry especially inside of the taxonomic groups, though satellited chromosomes were good markers for subgenera and even specific for two studied sections of subg. Allium. Six different types of satellites were recognized, two of them were newly described: Type P was prevalent in subg. Melanocrommyum, and type O in sect. Codonoprasum. Statistical analyses were performed on five karyological parameters to test correct relationships and also to test previous grouping hypotheses. Although our data confirm distinct karyological characters for the subgenera investigated, the remarkable morphological diversity inside of subg. Melanocrommyum is not mirrored by striking karyological differences.     

Molecular phylogeny of <Emphasis Type="Italic">Nassauvia</Emphasis> (Asteraceae,Mutisieae) based on nrDNA ITS sequences

The phylogeny of the genus Nassauvia and closely related genera was reconstructed using sequences from the internal transcribed spacer regions (ITS) of nuclear ribosomal DNA. The genus Triptilion is nested within Nassauvia, making the latter genus paraphyletic. Neither of the two subgenera Nassauvia and Strongyloma is resolved as monophyletic, and none of the sections of subgenus Nassauvia is recovered as monophyletic. The evolution of the compound secondary inflorescences has been complex in Nassauvia, with the highly aggregated forms representing the original condition in the genus. However, the ancestral condition is equivocal in several clades, and there are alternative reconstructions for the gains–losses of the variously aggregated conditions. There has been at least one gain of solitary capitula in Nassauvia. The evolution of flavonoid chemistry has been complex in Nassauvia, and flavonoids are of limited phylogenetic-taxonomic utility in the genus. Gains–losses of flavonols occur only on terminals whereas changes in flavones and C-glycosyl flavones occur at various levels in the tree. Gains–losses of methylation of flavones and flavonols occur only on terminals.     

Infrageneric Phylogeny and Temporal Divergence of Sorghum (Andropogoneae,Poaceae) Based on Low-Copy Nuclear and Plastid Sequences

The infrageneric phylogeny and temporal divergence of Sorghum were explored in the present study. Sequence data of two low-copy nuclear (LCN) genes, phosphoenolpyruvate carboxylase 4 (Pepc4) and granule-bound starch synthase I (GBSSI), from 79 accessions of Sorghum plus Cleistachne sorghoides together with those from outgroups were used for maximum likelihood (ML) and Bayesian inference (BI) analyses. Bayesian dating based on three plastid DNA markers (ndhA intron, rpl32-trnL, and rps16 intron) was used to estimate the ages of major diversification events in Sorghum. The monophyly of Sorghum plus Cleistachne sorghoides (with the latter nested within Sorghum) was strongly supported by the Pepc4 data using BI analysis, and the monophyly of Sorghum was strongly supported by GBSSI data using both ML and BI analyses. Sorghum was divided into three clades in the Pepc4, GBSSI, and plastid phylograms: the subg. Sorghum lineage; the subg. Parasorghum and Stiposorghum lineage; and the subg. Chaetosorghum and Heterosorghum lineage. Two LCN homoeologous loci of Cleistachne sorghoides were first discovered in the same accession. Sorghum arundinaceum, S. bicolor, S. x drummondii, S. propinquum, and S. virgatum were closely related to S. x almum in the Pepc4, GBSSI, and plastid phylograms, suggesting that they may be potential genome donors to S. almum. Multiple LCN and plastid allelic variants have been identified in S. halepense of subg. Sorghum. The crown ages of Sorghum plus Cleistachne sorghoides and subg. Sorghum are estimated to be 12.7 million years ago (Mya) and 8.6 Mya, respectively. Molecular results support the recognition of three distinct subgenera in Sorghum: subg. Chaetosorghum with two sections, each with a single species, subg. Parasorghum with 17 species, and subg. Sorghum with nine species and we also provide a new nomenclatural combination, Sorghum sorghoides.     

Giants and dwarfs: molecular phylogenies reveal multiple origins of annual spurges within Euphorbia subg. Esula

Euphorbia (Euphorbiaceae) comprises over 2150 species and is thus the second-largest genus of flowering plants. In Europe, it is represented by more than 100 species with highest diversity in the Mediterranean area; the majority of taxa belong to subgenus Esula Pers., including about 500 taxa. The few available phylogenetic studies yielded contrasting results regarding the monophyly of subg. Esula, and the phylogenetic relationships among its constituents remain poorly understood. We have sampled DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and the plastid trnT-trnF region from about 100, predominantly European taxa of subg. Esula in order to infer its phylogenetic history. The plastid data support monophyly of subg. Esula whereas the ITS phylogeny, which is generally less resolved, is indecisive in this respect. Although some major clades have partly incongruent positions in the ITS and plastid phylogenies, the taxonomic content of the major terminal clades is congruent in both trees. As traditional sectional delimitations are largely not corroborated, an improved classification is proposed. Character state reconstruction illustrates that the annual life form developed independently several times in different clades of subgenus Esula from perennial ancestors, and that several morphological traits used in previous classifications of Euphorbia developed in parallel in different lineages.     

A molecular phylogenetic study of Hemsleya (Cucurbitaceae) based on ITS, rpl16, trnH-psbA, and trnL DNA sequences

This paper presents the first molecular phylogeny of the genus Hemsleya using nuclear ITS and plastid trnH-psbA, rpl16, and trnL DNA sequences to examine the relationships among Hemsleya species. Phylogenetic relationships were elucidated using a combined analysis of all four datasets, however, the number of parsimony-informative characters was still insufficient to resolve all relationships. Parsimony and Bayesian trees were highly congruent. Twenty-three species of Hemsleya split into two major clades corresponding to two subgenera, i.e., subg. Graciliflorae and subg. Hemsleya. These results are partly in agreement with Li’s sectional classification. However, the molecular data are inconsistent with Li’s classification at the subsectional level. The molecular phylogeny revealed a striking overall correlation between the phylogenetic relationships of the species and their geographical distribution. The Kangdian ancient landmass could be the center of origin of the genus.     

Phylogeny,biogeography, and morphological ancestral character reconstruction in the Mediterranean genus Fumana (Cistaceae)

Fumana is a diverse genus of the Cistaceae family, consisting of 21 currently accepted species. In this study, nuclear (ITS) and plastid (matK, trnT‐L) molecular markers were used to reconstruct the phylogeny and to estimate divergence times, including 19 species of Fumana. Phylogenetic analyses (Bayesian Inference, Maximum Parsimony and Maximum Likelihood) confirmed the monophyly of Fumana and did not support the infrageneric divisions previously established. The results support four main clades that group species that differ in vegetative and reproductive characters. Given the impossibility to define morphological characters common to all species within the clades, our proposal is to reject infrageneric divisions. Molecular dating and ancestral area analyses provide evidence for a Miocene diversification of the genus in the north‐western Mediterranean. Ancestral state reconstructions revealed ancestral character states for some traits related to xeric and arid habitats, suggesting a preadaptation to the Mediterranean climate.     

Development and Function of the Elaiosome in Knautia (Dipsacaceae)

The fruits of the genus Knautia differ from those of all other Dipsacaceae by the possession of a white, ± hemispherical basal appendage (elaiosome). In a series of field experiments Sernander (1906) demonstrated that, due to this elaiosome, the fruits of Knautia are dispersed by ants. Sernander (1906) assumed that the elaiosome is built from fused bracts (forming the epicalyx) whereas Bresinsky (1963) interpreted it as part of the perianth. In the present study the elaiosome development was investigated in four species of all three subgenera of Knautia: subg. Trichera (K. drymeia, K. dipsacifolia), subg. Tricheranthes (K. integrifolia) and subg. Knautia (K. orientalis). A comparison with early stages of the fruit development in other Dipsacaceae (e.g., Lomelosia graminifolia) indicates that the elaiosome is of epicalyx origin. In all species of Knautia the development of the elaiosome begins prior to anthesis and independently of fertilization. The growth of the elaiosome tissue in K. orientalis is mainly caused by periclinal cell divisions in the subepidermal layers of the epicalyx base. In K. dipsacifolia and K. drymeia a meristem around the base of the central bundle, which supplies epicalyx and flower, becomes active and develops cells in cascade-like rows. The elaiosome cells of ripe fruits are filled with numerous oil droplets. Moreover the central bundle increases by the formation of additional phloem cells. In addition, other important morphological adaptations to ant dispersal are demonstrated: the hair-cover of the fruit and strongly lignified horizontal vascular bundles between elaiosome and seed prevent the seed from being eaten; a lignified cramp anchors the elaiosome to the fruit; and thickened and strongly cutinized walls of the epidermis protect the elaiosome during dispersal. In regard to germination, a correlation between the removal of the elaiosome and germination speed and rate was found; fruits with dissected elaiosomes germinate faster and with a higher germination rate than fruits with elaiosomes.     

RAD sequencing resolved phylogenetic relationships in European shrub willows (Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs

The large and diverse genus Salix L. is of particular interest for decades of biological research. However, despite the morphological plasticity, the reconstruction of phylogenetic relationships was so far hampered by the lack of informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) and taller shrubs (subg. Vetrix), while previous phylogenetic studies placed species of these two subgenera just in one largely unresolved clade. Here we want to test the utility of genomic RAD sequencing markers for resolving relationships at different levels of divergence in Salix. Based on a sampling of 15 European species representing 13 sections of the two subgenera, we used five different RAD sequencing datasets generated by Ipyrad to conduct phylogenetic analyses. Additionally we reconstructed the evolution of growth form and analyzed the genetic composition of the whole clade. The results showed fully resolved trees in both ML and BI analysis with high statistical support. The two subgenera Chamaetia and Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within the Vetrix/Chamaetia clade, a division into three major subclades could be observed. All species were confirmed to be monophyletic. Based on our data, arctic‐alpine dwarf shrubs evolved four times independently. The structure analysis showed five mainly uniform genetic clusters which are congruent in sister relationships observed in the phylogenies. Our study confirmed RAD sequencing as a useful genomic tool for the reconstruction of relationships on different taxonomic levels in the genus Salix.     

Fates of Evolutionarily Distinct,Plastid‐type Glyceraldehyde 3‐phosphate Dehydrogenase Genes in Kareniacean Dinoflagellates

The ancestral kareniacean dinoflagellate has undergone tertiary endosymbiosis, in which the original plastid is replaced by a haptophyte endosymbiont. During this plastid replacement, the endosymbiont genes were most likely flowed into the host dinoflagellate genome (endosymbiotic gene transfer or EGT). Such EGT may have generated the redundancy of functionally homologous genes in the host genome—one has resided in the host genome prior to the haptophyte endosymbiosis, while the other transferred from the endosymbiont genome. However, it remains to be well understood how evolutionarily distinct but functionally homologous genes were dealt in the dinoflagellate genomes bearing haptophyte‐derived plastids. To model the gene evolution after EGT in plastid replacement, we here compared the characteristics of the two evolutionally distinct genes encoding plastid‐type glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) in Karenia brevis and K. mikimotoi bearing haptophyte‐derived tertiary plastids: “gapC1h” acquired from the haptophyte endosymbiont and “gapC1p” inherited from the ancestral dinoflagellate. Our experiments consistently and clearly demonstrated that, in the two species examined, the principal plastid‐type GAPDH is encoded by gapC1h rather than gapC1p. We here propose an evolutionary scheme resolving the EGT‐derived redundancy of genes involved in plastid function and maintenance in the nuclear genomes of dinoflagellates that have undergone plastid replacements. Although K. brevis and K. mikimotoi are closely related to each other, the statuses of the two evolutionarily distinct gapC1 genes in the two Karenia species correspond to different steps in the proposed scheme.     

MORPHOLOGY,EVOLUTION, AND TAXONOMIC SIGNIFICANCE OF THE INFLORESCENCE IN CORDYLANTHUS (SCROPHULARIACEAE)

The genus Cordyhmthus has considerable diversity in its inflorescences while the other genera of tribe Rhinantheae (Scrophulariaceae) uniformly have racemes or spikes. Four distinct inflorescence types are recognized and their homologies and evolutionary history are postulated. Thus it is suggested that the basic florescence type, the elongated spike (Type I), has undergone evolutionary reduction to a few-flowered spike and ultimately to a single-flowered florescence (Type II). Further evolution involving processes of compaction and clustering of the single-flowered florescences has resulted in glomerulate clusters (Type III) and spiciform clusters (Type IV). Knowledge of inflorescence homologies and distribution of the four inflorescence types in the genus has been of considerable aid in formulating a new infrageneric classification. Using evidence primarily from inflorescence, floral, and seed morphology, as well as from geographical distribution and ecology, a classification is proposed establishing three subgenera, namely subg. Dicranostegia, subg. Hemistegia, and subg. Cordylanthus, the last with three sections, sect. Cordylanthus, sect. Anisocheila, and sect. Ramosi.     

Recent structural variations in the Medicago chloroplast genomes and their horizontal transfer into nuclear chromosomes

Medicago is a genus of legumes (Fabaceae) that resemble common clovers with pinnately trifoliate leaves and spirally coiled seed pods, and Medicago sativa is a famous forage crop throughout the world. In this study, we systematically assembled the complete plastid genomes of 18 Medicago species, representing 35 Medicago accessions, whose genome size ranged from ~119 to 125 kb, and identified one novel inverted repeat (IR) in two accessions of Medicago soleirolii (PI537242 and PI537243), albeit of no IRs in the most accessions. We built a phylogenetic tree based on common protein-coding sequences of 55 Medicago accessions in 38 species, which were placed into five clades with a divergence since 9.37 million years ago. Global alignment revealed independent genome evolution events, including eight inversions in nine species and four intron losses (ILs) in 10 species, among which four inversions and two ILs have not been reported previously. Within 109–111 unique genes, ndhA, rpl2, and ycf3 were under positive selection in 54 Medicago accessions. Finally, by aligning chloroplast genes against the nuclear genome assembly of M. sativa cultivar “Zhongmu No.1”, we found that a large number of chloroplast gene fragments were horizontally transferred to nuclear chromosomes in alfalfa, especially on the chr3:47518422–48722257 coordinates of chromosome 3. Our comprehensive exploration of Medicago chloroplast genomes provided insights for the understanding of Medicago diversity and their genomic evolution events.     

Subgenome analysis of two southern hemisphere allotriploid species in Sphagnum (Sphagnaceae)

Sphagnum ×australe s.l. and S. ×falcatulum s.l. are both cryptic species complexes of gametophytically allodiploid and allotriploid cytotypes, with the allodiploid cytotype being one parent of the respective allotriploid cytotype. Phylogenetic analyses of S. ×australe s.l. and S. ×falcatulum s.l. were undertaken using sequences from two plastid loci and cloned sequences from three nuclear loci. Subgenomes from three subgenera were detected in allotriploid S. ×australe. The haploid parent of allotriploid S. ×australe was S. fimbriatum (subg. Acutifolia). One of the two subgenomes contributed by allodiploid S. australe was associated with S. strictum (subg. Rigida); the parental species associated with the other subgenome could not be identified, either at the species level or in terms of subgenus association. It may represent an early diverging lineage of subg. Sphagnum or a previously undetected subgenus. Allotriploid S. ×falcatulum has subgenomes from two subgenera. This study confirms prior findings that S. cuspidatum (subg. Cuspidata) was the haploid parent of allotriploid S. ×falcatulum. One of the two subgenomes contributed by allodiploid S. ×falcatulum was associated with subg. Cuspidata (species unidentified) and the second was associated with subg. Subsecunda (species unidentified). Recurrent allopolyploidy appears to have been associated with the complex evolutionary processes (inter-subgeneric hybridization, interploidal hybridization, double allopolyploidy) which resulted in each of these two allotriploids. The highest level of divergence detected among the subgenomes in each of these Sphagnum allotriploids is comparable to the average genetic divergence reported for angiosperm allopolyploids.