Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA

Background and AimsWith the advance of high-throughput sequencing, reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information, particularly from coding regions. As the off-target reads from such sequencing are expected to be similar to genome skimming (GS), we assessed the quality of repeat characterization in plant genomes using these data.MethodsRepeat composition obtained from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. In addition, a FISH probe was designed based on the most abundant satellite found in the TCS dataset of Rhynchospora cephalotes. Finally, repeat-based phylogenies of the five Rhynchospora species were constructed based on the GS and TCS datasets and the topologies were compared with a gene-alignment-based phylogenetic tree.Key ResultsAll the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01 % in the GS data. Rank correlations between GS and TCS repeat abundances were moderately high (r = 0.58–0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66–0.92). Repeat data obtained by TCS were also reliable in developing a cytogenetic probe of a new variant of the holocentromeric satellite Tyba. Repeat-based phylogenies from TCS data were congruent with those obtained from GS data and the gene-alignment tree.ConclusionsOur results show that off-target TCS reads can be recycled to identify repeats for cyto- and phylogenomic investigations. Given the growing availability of TCS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.     

The best of two worlds: ecology and evolution of ambophilous plants

Ambophily, the mixed mode of wind and insect pollination is still poorly understood, even though it has been known to science for over 130 years. While its presence has been repeatedly inferred, experimental data remain regrettably rare. No specific suite of morphological or ecological characteristics has yet been identified for ambophilous plants and their ecology and evolution remain uncertain. In this review we summarise and evaluate our current understanding of ambophily, primarily based on experimental studies. A total of 128 ambophilous species – including several agriculturally important crops – have been reported from most major habitat types worldwide, but this probably represents only a small subset of ambophilous species. Ambophilous species have evolved both from wind- and insect-pollinated ancestors, with insect-pollinated ancestors mostly representing pollination by small, generalist flower visitors. We compiled floral and reproductive traits for known ambophilous species and compared our results to traits of species pollinated either by wind or by small generalist insects only. Floral traits were found to be heterogeneous and strongly overlap especially with those of species pollinated by small generalist insects, which are also the prominent pollinator group for ambophilous plants. A few ambophilous species are only pollinated by specialised bees or beetles in addition to pollination by wind. The heterogeneity of floral traits and high similarity to generalist small insect-pollinated species lead us to conclude that ambophily is not a separate pollination syndrome but includes species belonging to different insect- as well as wind-pollination syndromes. Ambophily therefore should be regarded as a pollination mode. We found that a number of ecological factors promoted the evolution of ambophily, including avoidance of pollen limitation and self-pollination, spatial flower interference and population density. However, the individual ecological factors favouring the transition to ambophily vary among species depending on species distribution, habitat, population structure and reproductive system. Finally, a number of experimental studies in combination with observations of floral traits of living and fossil species and dated phylogenies may indicate evolutionary stability. In some clades ambophily has likely prevailed for millions of years, for example in the castanoid clade of the Fagaceae.     

Holocentric plant meiosis: first sisters,then homologues

Meiosis is a crucial process of sexual reproduction by forming haploid gametes from diploid precursor cells. It involves 2 subsequent divisions (meiosis I and meiosis II) after one initial round of DNA replication. Homologous monocentric chromosomes are separated during the first and sister chromatids during the second meiotic division. The faithful segregation of monocentric chromosomes is realized by mono-orientation of fused sister kinetochores at metaphase I and by bi-orientation of sister kinetochores at metaphase II. Conventionally this depends on a 2-step loss of cohesion, along chromosome arms during meiosis I and at sister centromeres during meiosis II.     

A fascinating island: 2n = 4

Abstract

Among Angiosperms, only six species are known to possess the lowest identified chromosome number, i.e. 2n = 4. These plants are the monocotyledons Zingeria biebersteiniana, Colpodium versicolor, Ornithogalum tenuifolium and Rhynchospora tenuis, and the dicotyledons Haplopappus gracilis and Brachyscome dichromosomatica. The low chromosome number may be cytogenetically derived from a different ancestral basic number, characteristic of each genus, by different processes, including tandem fusion or unequal reciprocal translocations with loss of centric fragments. All these plants possess low nuclear 4C DNA contents, ranging from 1.56 pg (R. tenuis) to 8.20 pg (H. gracilis), and they generally display a similar chromosome size and a similar position of the nucleolus organising region (NOR), that is often located in the terminal or subterminal region of the small chromosome pair. All these characteristics could be a consequence of common adaptative mechanisms. Peculiar characteristics within these karyotypes are the holocentric chromosomes of R. tenuis and the presence of B chromosomes in B. dichromosomatica. Plants with a very low chromosome number may be considered to constitute a fascinating “island of interest”; moreover, they represent simple systems helpful for the examination of the structural organisation and evolution of Angiosperm chromosomes.     

Comparative floral biology of Rhynchospora ciliata (Vahl) Kukenth and R. pubera (Vahl) Boeckeler (Cyperaceae): the role of white involucral bracts in attracting pollinating insects

Although Cyperaceae are considered anemophilous, some species exhibit features that are attractive to pollinators, such as the white UV‐reflecting involucral bracts of Rhynchospora ciliata. But how effective are these conspicuous adaptations? To address this question, we tested the hypothesis that species such as R. ciliata are visited by greater numbers of pollinating insects than similar species with green involucral bracts, such as R. pubera. We compared the floral biology of both species and the number of visits to sympatric populations of each species, associating them with the availability of pollen and the pollination system. We verified that species with white involucral bracts are preferred, because there were more visits to R. ciliata in the first 2 h the flowers were open. The peak visitation in R. pubera was 2 h after the flowers opened, when the pollen of R. ciliata was exhausted. Although the involucral bracts of R. pubera are green, the spikelet scales and anthers are white and reflect ultraviolet light. Overall, flowers of R. pubera exhibit fewer white or reflective surfaces and are probably less conspicuous to a bee than those of R. ciliata. It is possible that R. pubera is a second option for visitors after the first 2 h of anthesis. The two different peaks in visitation minimize interspecific competition for pollinators, suggesting that R. ciliata and R. pubera together could attract more generalist pollinators and, instead of competing, facilitate the pollination of both species. Although R. pubera is autogamous and self‐compatible, both wind and insects are important to its reproductive success.     

Comparison of the performance of horizontal and vertical flow constructed wetland planted with Rhynchospora corymbosa

Treatment performance of horizontal flow (HF) and vertical flow (VF) constructed wetland planted with Rhynchospora corymbosa were compared. The average porosity of the CW beds were 0.55, hydraulic retention time (HRT) of 3?days, hydraulic loading rate (HLR) and Organic Loading rate were 0.058?m/day and 3.96 (g·BOD/m²·day), respectively with a volumetric flow rate of 0.14 m³/day. The pollutant concentration of graywater before and after its introduction to the CWs was measured using standard sampling and analyses methods. The mean removal efficiencies (RE) for HF and VF CWs were BOD, 35% and 35.4%; COD, 61.9% and 56.7%; TN, 87% and 92%; TP, 95% and 65%; TSS, 86% and 59.6%; pH, 8.8% and 12.8%, respectively. The graywater was highly contaminated in terms of nutrient and organic load. The mean values of the parameters tested for different CWs were significantly different (P?≤?0.05). This comparative study favored HF over VF Constructed wetland with HF found to be a viable alternative for graywater treatment for organics, nutrients and suspended solids removal. The result provided insight into the performance of CWs planted with R. corymbosa.     

Mitotic Microtubule Development and Histone H3 Phosphorylation in the Holocentric Chromosomes of Rhynchospora Tenuis (Cyperaceae)

In the present work we report the phosphorylation pattern of histone H3 and the development of microtubular structures using immunostaining techniques, in mitosis of Rhynchospora tenuis (2n = 4), a Cyperaceae with holocentric chromosomes. The main features of the holocentric chromosomes of R. tenuis coincide with those of other species namely: the absence of primary constriction in prometaphase and metaphase, and the parallel separation of sister chromatids at anaphase. Additionaly, we observed a highly conserved chromosome positioning at anaphase and early telophase sister nuclei. Four microtubule arrangements were distinguished during the root tip cell cycle. Interphase cells showed a cortical microtubule arrangement that progressively forms the characteristic pre-prophase band. At prometaphase the microtubules were homogeneously distributed around the nuclear envelope. Metaphase cells displayed the spindle arrangement with kinetochore microtubules attached throughout the entire chromosome extension. At anaphase kinetochoric microtubules become progressively shorter, whereas bundles of interzonal microtubules became increasingly broader and denser. At late telophase the microtubules were observed equatorially extended beyond the sister nuclei and reaching the cell wall. Immunolabelling with an antibody against phosphorylated histone H3 revealed the four chromosomes labelled throughout their entire extension at metaphase and anaphase. Apparently, the holocentric chromosomes of R. tenuis function as an extended centromeric region both in terms of cohesion and H3 phosphorylation.