Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)?

BACKGROUND: Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation. RESULTS: The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels. CONCLUSIONS: This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.

The complete chloroplast genome sequence of Phlomoides kirghisorum Adylov, Kamelin & Makhmedov 1987 (Lamiaceae), an endemic species of Fergana Valley.

Phlomoides kirghisorum Adylov, Kamelin & Makhmedov 1987 is one of the poorly studied narrow endemics of Fergana Valley, one of Central Asia's most densely human-populated regions. In this study, we sequenced, assembled, and characterized the complete plastome of P. kirghisorum by using high-throughput Illumina reads. The complete chloroplast genome consisted of 151,324 bp, including a large single-copy (LSC) region (82,775 bp), a small single-copy (SSC) region (17,357 bp), and two inverted repeat regions (25,596 bp each). In the chloroplast genome of P. kirghisorum, 133 genes were detected, comprising 88 protein-encoding genes, eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. The phylogenetic analysis indicated that the genetic relationship between P. kirghisorum and P. alpina was very close. This study provides basic information to explore the molecular evolution of the Phlomoides genus and the Lamiaceae family.

The complete chloroplast genome of Eremurus zoae Vved. (Asphodelaceae), an endemic species of Kyrgyz Republic.

Eremurus zoae Vved. 1971 is a perennial herbaceous plant in the family Asphodelaceae and an endemic species of the Kyrgyz Republic; however, its complete chloroplast genome sequence has not been reported. Here, we investigated the complete chloroplast (cp) genome of E. zoae using next-generation sequencing. The cp genome was 153,744 bp long, with a large single copy (84,020 bp), a small single copy (16,766 bp), and a pair of inverted repeats (26,479 bp). The genome encodes 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that the genus Eremurus forms a monophyletic group and E. zoae is closely related to E. chinensis. This study provides a molecular foundation for future phylogenetic studies of Eremurus.

The complete chloroplast genome sequence of Ligularia stenocephala (Maxim.) Matsum. & Koidz. (Asteraceae: Senecioneae).

Ligularia stenocephala (Maxim.) Matsum. & Koidz is a widely known edible plant species in Korea. It contains various useful antioxidant compounds and has been developed as a horticultural cultivar blooming showy inflorescence. We report the complete plastid genome (plastome) of Ligularia stenocephala, a collection from Korea. The plastome of L. stenocephala is 151,158 base pairs (bp) long and includes a pair of inverted repeat (IR) regions (24,830 bp each) that are separated by a large single copy (LSC) region (83,265 bp) and a small single copy (SSC) region (18,233 bp). The phylogenetic tree shows that L. stenocephala is closely related to L. fischeri with strong bootstrap support.

Species conservation profile and amended distribution of Cousinia knorringiae (Asteraceae), a narrow endemic of the Western Tian-Shan.

BACKGROUND: Cousinia knorringiae Bornm. (Asteraceae) belongs to C. sect. Subappendiculatae Tscherneva, a group of the species-rich and taxonomically difficult genus Cousinia Cass. This species is narrowly distributed in the Western Tian-Shan and has been known as endemic to Kyrgyzstan. It inhabits bare rocks and screes at elevations of 1200-1500 m above sea level. This species is of conservation interest because of its small population size and limited distribution. NEW INFORMATION: Cousinia knorringiae is reported for the first time from eastern Uzbekistan on the basis of specimens collected on Ungur-Tepa Mt., a south-western outlier of the Bozbu-Too Mts. (Western Tian-Shan). The conservation status of the species is assessed as Endangered (EN), based on criterion D (estimated population size 200-250 mature individuals), according to the IUCN Red List Categories and Criteria (version 3.1). A new distribution map and a line drawing for C. knorringiae are provided and its type locality is clarified. The new knowledge suggests that the species is endemic to the East Fergana botanical hotspot, which includes a transborder territory shared between Kyrgyzstan and Uzbekistan and should, therefore, be subjected to international conservation measures. The southern extension of Ungur-Tepa Mt. harbours important plant species, which cannot be found elsewhere in Uzbekistan and may, therefore, be proposed for legal protection.

The complete chloroplast genome sequences of the Iris loczyi kanitz (Iridaceae).

Iris loczyi is a perennial rhizomatous herb distributed in Central Asia. We examined genomic architecture of the complete chloroplast genome in I. loczyi by assembling the Illumina MiSeq reads using de novo strategy. The chloroplast genome is 150,940 bp in length harboring 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. It exhibits typical quadripartite structure comprising LSC (80,907 bp), SSC (17,853 bp), and a pair of IRs (26,090 bp). Phylogenetic analysis of 20 chloroplast genomes from Asparagales revealed that Iridaceae is a monophyletic group and the I. loczyi is clustered together with the congener, I. sanguinea.

A preliminary phylogeny of the 'didymocarpoid Gesneriaceae' based on three molecular data sets: Incongruence with available tribal classifications.

The 'didymocarpoid Gesneriaceae' (traditional subfam. Cyrtandroideae excluding Epithemateae) are the largest group of Old World Gesneriaceae, comprising 85 genera and 1800 species. We attempt to resolve their hitherto poorly understood generic relationships using three molecular markers on 145 species, of which 128 belong to didymocarpoid Gesneriaceae. Our analyses demonstrate that consistent topological relationships can be retrieved from data sets with missing data using subsamples and different combinations of gene sequences. We show that all available classifications in Old World Gesneriaceae are artificial and do not reflect natural relationships. At the base of the didymocarpoids are grades of clades comprising isolated genera and small groups from Asia and Europe. These are followed by a clade comprising the African and Madagascan genera. The remaining clades represent the advanced Asiatic and Malesian genera. They include a major group with mostly twisted capsules. The much larger group of remaining genera comprises exclusively genera with straight capsules and the huge genus Cyrtandra with indehiscent fruits. Several genera such as Briggsia, Henckelia, and Chirita are not monophyletic; Chirita is even distributed throughout five clades. This degree of incongruence between molecular phylogenies, traditional classifications, and generic delimitations indicates the problems with classifications based on, sometimes a single, morphological characters.

Chromosomal stasis in diploids contrasts with genome restructuring in auto- and allopolyploid taxa of Hepatica (Ranunculaceae).

Polyploidization and chromosomal rearrangements are recognized as major forces in plant evolution. Their role is investigated in the disjunctly distributed northern hemisphere Hepatica (Ranunculaceae). Chromosome numbers, karyotype morphology, banding patterns, 5S and 35S rDNA localization in all known species were investigated and interpreted in a phylogenetic context established from nuclear internal transcribed spacer (ITS) and plastid matK sequences. All species had a chromosome base number of x = 7. The karyotype was symmetric and showed little variation among diploids with one locus each of 5S and 35S rDNA, except for interpopulational variation concerning 35S rDNA loci number and localization in H. asiatica. Tetraploids exhibited chromosomal changes, including asymmetry and/or loss of rDNA loci. Nuclear and plastid sequences resulted in incongruent topologies because of the positions of some tetraploid taxa. The diversification of Hepatica occurred not earlier than the Pliocene. Genome restructuring, especially involving 35S rDNA, within a few million yr or less characterizes evolution of both auto- and allopolyploids and of the diploid species H. asiatica, which is the presumptive ancestor of two other diploid species.

Phylogeny of holoparasitic Orobanche (Orobanchaceae) inferred from nuclear ITS sequences.

Orobanche is the largest genus among the holoparasitic members of Orobanchaceae. We present the first molecular phylogenetic analysis (using nuclear ITS sequences) that includes members of all sections of Orobanche, Gymnocaulis, Myzorrhiza, Trionychon, and Orobanche. Orobanche is not monophyletic, but falls into two lineages: (1) the Orobanche group comprises Orobanche sect. Orobanche and the small Near Asian genus Diphelypaea and is characterized by a chromosome base number of x=19 and (2) the Phelipanche group contains Orobanche sects. Gymnocaulis, Myzorrhiza, and Trionychon and possesses a chromosome base number of x=12. The relationships between these two groups and to other genera such as Boschniakia or Cistanche remain unresolved. Within the Orobanche group, Orobanche macrolepis and Orobanche anatolica (including Orobanche colorata) constitute two phylogenetically distinct lineages. Intrasectional structurings proposed by some authors for O. sect. Orobanche are not confirmed by the molecular data. In most cases, intraspecific sequence divergence between accessions, if present, is negligible and not correlated with morphological or ecological traits. In a few cases, however, there is evidence for the presence of cryptic taxa.

Chromosome termini of the monocot plant Othocallis siberica are maintained by telomerase, which specifically synthesises vertebrate-type telomere sequences.

Lack of Arabidopsis-type T3AG3 telomere sequences has recently been reported for the majority of investigated taxa of the monocot order Asparagales. In order to investigate this phenomenon in more detail, we conducted extensive cytogenetic and molecular analyses of the telomeres in Othocallis siberica, a member of this order. Terminal restriction fragment analysis together with Bal31 exonuclease assay showed that chromosome termini in O. siberica are formed by long stretches (more than 10 kbp) of vertebrate-type T2AG3 repeats. In addition, telomerase activity specifically synthesising (T2AG3)n sequence was detected in O. siberica protein extracts by telomerase repeat amplification protocol (TRAP). Fluorescence in situ hybridisation (FISH) revealed the presence of the vertebrate-type T2AG3 telomere sequences at all chromosome termini and at a few additional regions of O. siberica chromosomes, whereas Arabidopsis-type T3AG3 DNA and peptide nucleic acid (PNA) probes did not hybridise to chromosomes of Othocallis, except for polymorphic blocks in chromosomes 2 (interstitial) and 4 (terminal). These interstitial/terminal regions are apparently composed of large blocks of (T2AG3)n and (T3AG3)n DNA and represent a unique example of interspersion of two types of telomeric repeats within one genome. This may be a reflection of the recent evolutionary switch from Arabidopsis- to vertebrate-type telomeric repeats in this plant group.