Sibling Trees Research Articles

Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation

Baobab (Adansonia digitata) is a long-lived tree endemic to Africa with economic, ecological, and cultural importance, yet its genomic features are underexplored. Here, we report a chromosome-level reference genome anchored to 42 chromosomes for A. digitata, alongside draft assemblies for a sibling tree, two trees from distinct locations in Africa, and A. za from Madagascar. The baobab genome is uniquely rich in DNA transposons, which make up 33%, while LTR retrotransposons account for 10%. A. digitata experienced whole genome multiplication (WGM) around 30 million years ago (MYA), followed by a second WGM event 3–11 MYA, likely linked to autotetraploidy. Resequencing of 25 trees identify three subpopulations, with gene flow across West Africa distinct from East Africa. Gene enrichment and fixation index (Fst) analyses show baobab retained multiple circadian, flowering, and light-responsive genes, which likely support longevity through the UV RESISTANCE LOCUS 8 (UVR8) pathway. In sum, we provide genomic resources and insights for baobab breeding and conservation.

Inverse Domination in X-Trees and Sibling Trees

A set $D$ of vertices in a graph $G$ is a dominating set if every vertex not in $D$ is adjacent to at least one vertex in $D$. The minimum cardinality of a dominating set in $G$ is called the domination number and is denoted by $\gamma(G)$. Let $D$ be a minimum dominating set of $G$. If $V-D$ contains a dominating set say $D^{'}$ of $G$, then $D^{'}$ is called an inverse dominating set with respect to $D$. The inverse domination number $\gamma^{'}(G)$ is the cardinality of a minimum inverse dominating set of $G$. A dominating set $D$ is called a connected dominating set or an independent dominating set of $G$ according as the induced subgraph $\langle D \rangle$ is connected or independent in $G$. The minimum of the cardinalities of the connected dominating sets of $G$ or the independent dominating sets of $G$ is called the connected domination number $\gamma_{c} (G)$ or the independent domination number $\gamma_{i} (G)$ respectively. In this paper, we determine the inverse domination numbers in X-Trees and Sibling Trees. We have also determined the independent domination numbers of both the trees and the connected domination number of Sibling Trees. A result on inverse domination number of some classes of Hypertrees is also included.

Total Face Irregularity Strength of Certain Graphs

The edge k-labeling ψ of G is defined by a mapping from EG to a set of integers 1,2,…,k, where the integer weight assigned to the vertex x∈VG is given as wψx=∑ψxy, such that the sum is taken over every vertex of y∈VG that is adjacent to x and the integer weights of adjacent vertices must be distinct for all vertices with x≠y. An irregular assignment of G using atmost k labels which is considered to be a minimum k is defined as irregularity strength of a graph G and can be denoted as sG. There are also further works on familiar irregular assignments, such as edge irregular labelings, vertex irregular total labelings, edge irregular total labelings, and face irregular entire k-labelings of plane graphs. A plane graph can be defined as a graph that is embedded in the plane in which no two lines will be intersected. In a plane graph the number of regions present are called faces and we denote it as F. The concept of total face irregularity strength is defined by the motivation of irregular networks and entire irregular face k-labeling. In our paper, we have obtained a minimum bound for the total face irregularity strength of two-connected plane graphs like cycle-of-ladder, C-necklace graph, P-necklace graph, sibling tree, and triangular graph.

Insights of smallholder farmers on the trade-offs of eucalyptus plantation

Eucalyptus is a popular evergreen perennial tree that grows quickly. Due to its diverse economic value and wide range of adaptations, the eucalyptus is commonly grown in tropical and subtropical regions. Eucalyptus is an economically important tree. However, the economic importance of eucalyptus ensued at the expense of undesirable ecological consequences. This qualitative study reports the advantages and disadvantages of eucalyptus woodlot establishment on the productivity of arable and grazing lands. In this study, nine knowledgeable farmers were involved in an in-depth individual interview and four focus group discussions were conducted. Farmers have frequently reported the negative impact of eucalyptus plantations on the productivity of the agricultural system. Eucalyptus serves as a refuge for crop pests and pathogens such as aphids and rust. Besides, the shade suppresses the development of the understory and adjacent crops, pastures, fodder, and other species of native trees and shrubs if they are planted together. Eucalyptus has increasingly replaced eco-friendly native trees and shrubs traditionally used as hedges, windbreaks, fodder, shelters for domestic and wild animals, and enhancers of soil fertility. Besides deteriorating soil fertility, structure, and moisture, it drains wetlands, springs, and streams and reduces the flow of rivers. Nevertheless, farmers acknowledged the importance of eucalyptus as a construction material, a source of fuelwood and charcoal, and income. To make the best use of eucalyptus woodlots without imposing adverse effects on agroecology, farmers have suggested that plantation sites should be marginally suitable for crop and livestock production. The expanded plantation needs to be contracted by removing a significant proportion of the established eucalyptus woodlots. Plantations of eucalyptus around watering points should be discouraged. Fast-growing, resilient, and eco-friendly tree species, such as those from Grevillea and Populus species, and sibling (leguminous) trees and shrubs delivering comparable products and services should be sought after to replace the significant proportion of the established eucalyptus woodlot.

Isometric Path Partition Problem on Tree Derived Architectures

An isometric path partition of a graph G is defined as a set of isometric paths that partition the vertex set of G. The problem of isometric path partition is to obtain a minimum isometric path partition of G. The isometric path partition number of a graph G, denoted by ip p (G) is the minimum cardinality of isometric path partition in G. In this paper, we compute the isometric path partition number of certain tree derived architectures like hypertrees, 1-rooted sibling trees, k-rooted sibling trees, l-complete binary trees, and l-sibling trees.

On the optimal layout of balanced complete multipartite graphs into grids and tree related structures

An interconnection network is a complex connection of a set of processors and communication links between different processors which is utilized to exchange data between processors in the parallel computing system. Graph embedding is a vital tool used to run parallel algorithms in computer networks in which placing different modules on the board is one of the main cost criteria. By finding the optimal layout, the placement problem in circuit designs which does not have any deterministic algorithms can be solved. The complete multipartite graph is a widely used network topology with a high degree of reliability due to its flexible choice of network size. Recently a study was made by computing the optimal layout of balanced complete multipartite graphs into host graphs taken from the Cartesian product of elements in the set {path, cycle}, but leaving the case of product of paths as an open problem. This paper aims to solve such an open problem and the key idea is to locate suitable optimal sets in balanced complete multipartite graphs with respect to maximizing the number of edges in the located sets. Besides, we compute the layout in the case of host graphs like k-rooted complete binary trees, k-rooted sibling trees and the Cartesian product of path P2 and complete binary trees.

Computing Eccentricity-Based Topological Indices of 2-Power Interconnection Networks

In a connected graph G with a vertex v, the eccentricity εv of v is the distance between v and a vertex farthest from v in the graph G. Among eccentricity-based topological indices, the eccentric connectivity index, the total eccentricity index, and the Zagreb index are of vital importance. The eccentric connectivity index of G is defined by ξG = ∑v∈VGdvεv, where dv is the degree of the vertex v and εv is the eccentricity of v in G. The topological structure of an interconnected network can be modeled by using graph explanation as a tool. This fact has been universally accepted and used by computer scientists and engineers. More than that, practically, it has been shown that graph theory is a very powerful tool for designing and analyzing the topological structure of interconnection networks. The topological properties of the interconnection network have been computed by Hayat and Imran (2014), Haynes et al. (2002), and Imran et al. (2015). In this paper, we compute the close results for eccentricity-based topological indices such as the eccentric connectivity index, the total eccentricity index, and the first, second, and third Zagreb eccentricity index of a hypertree, sibling tree, and X-tree for k-level by using the edge partition method.

Domination parameters in hypertrees and sibling trees

A locating-dominating set (LDS) of a graph G is a dominating set S of G such that for every two vertices u and v in V(G)∖S, N(u)∩S≠N(v)∩S. The locating-domination number γL(G) is the minimum cardinality of a LDS of G. Further if S is a total dominating set then S is called a locating-total dominating set. In this paper we determine the domination, total domination, locating-domination and locating-total domination numbers for hypertrees and sibling trees.

Node set optimization problem for complete Josephus cubes

The problem of finding an optimal node set in an interconnection network plays an important role in minimizing the layout of embedding the network into linear chassis. In this paper we find the nested optimal node sets for a complete Josephus cube, a recently proposed fault-tolerant node cluster architecture variant of the binary hypercube which has the same number of nodes as the hypercube but exhibits enhanced embedding, fault tolerance and communications performance than the hypercube and many of its variants. As a byproduct we obtain the minimum layout of embedding the complete Josephus cube into a path, 1-rooted complete binary tree, sibling tree and caterpillar.

A graph theoretical approach for node covering in tree based architectures and its application to bioinformatics

Investigation of DNA sequences is a paramount stage for apprehending biological structures and functions. The known methods for investigating DNA sequence alignments usually fail to produce an exact solution. Motivated by the problem of finding similarities in DNA and amino sequences, we study certain classes of phylogenetic trees and present an exact solution for the minimum node cover which can be used for genetic sequence comparisons. The smallest number of nodes removed to disconnect a graph $$G$$ is the smallest node cover. In this paper, we address the problem of finding a minimum node cover for certain tree-derived architectures, namely, Hyper trees, Slim trees, $$X$$ trees, $$l$$-sibling trees, and $$k$$-rooted sibling trees. Trees are advantageous in biology especially for bioinformatics, systematics, and phylogenetics. The smallest node cover set is the minimum number of nodes in a graph which monitors all the edges in the graph. Therefore, these sets are much useful in bioinformatics workflow management system. Moreover, our results can also be applied to identify genetic variants and to characterize common DNA variants.

Phloem Regeneration Is a Mechanism for Huanglongbing-Tolerance of "Bearss" Lemon and "LB8-9" Sugar Belle® Mandarin.

Huanglongbing (HLB) is an extremely destructive and lethal disease of citrus worldwide, presumably caused by phloem-limited bacteria, Candidatus Liberibacter asiaticus (CLas). The widespread invasiveness of the HLB pathogen and lack of natural HLB-resistant citrus cultivars have underscored the need for identifying tolerant citrus genotypes to support the current citrus industry’s survival and potentially to lead to future natural HLB resistance. In this study, transverse sections of leaf lamina and midribs were examined with light and epifluorescence microscopy to determine anatomical characteristics that underlie HLB-tolerant mechanisms operating among “Bearss” lemon, “LB8-9” Sugar Belle® mandarin, and its sibling trees compared with HLB-sensitive “Valencia” sweet orange. The common anatomical aberrations observed in all CLas-infected varieties are as follows: phloem necrosis, hypertrophic phloem parenchyma cells, phloem plugging with abundant callose depositions, phloem collapse with cell wall distortion and thickening, excessive starch accumulation, and sometimes even cambium degeneration. Anatomical distribution of starch accumulation even extended to tracheid elements. Although there were physical, morphological, and pathological similarities in the examined foliage, internal structural preservation in “Bearss” lemon and “LB8-9” Sugar Belle® mandarin was superior compared with HLB-sensitive “Valencia” sweet orange and siblings of “LB8-9” Sugar Belle® mandarin. Intriguingly, there was substantial phloem regeneration in the tolerant types that may compensate for the dysfunctional phloem, in comparison with the sensitive selections. The lower levels of phloem disruption, together with greater phloem regeneration, are two key elements that contribute to HLB tolerance in diverse citrus cultivars.

Inequality, familial aggregation, and risk prediction of caries in Siblings. A natiowide study of Danish adolescents

Introduction Sibling designs in assessing familial aggregation and risk prediction of dental caries have been largely unutilized. This large-scale investigation evaluated the robustness of parental socioeconomic position (SEP) as a cardinal determinant of caries experience by appraising it at the family level. Moreover, sibling-specific aggregation of caries within families and the discriminant ability of sibling caries in predicting co-sibling caries was ascertained. Methods A nationwide, register-based cross-sectional study was conducted on Danish adolescent siblings (n = 23,847 sibling pairs; index siblings/probands: all 15-year-olds in 2003; co-siblings: biological siblings born to the same mother within ± 3 years). Clinical (caries) data for each study subject were acquired from the national dental database (Sundhedsstyrelsens Centrale Odontologiske Register [SCOR]). Data on social variables, namely, parental SEP (parental education, income, and occupation), ethnicity, age/birth order, gender, and household type, were compiled from administrative registers at Statistics Denmark (e.g., the Danish population, education, labor market affiliation, and income and transfer payments registers). The social gradient in the magnitude of caries experience among the index- and co-siblings was estimated using negative binomial regression and generalized estimating equations taking into account family level clustering. Familial aggregation of caries was ascertained using probandwise concordance rates and adjusted pairwise odds ratios (PORs) from alternating logistic regressions. In order to determine the discriminant ability of proband caries and that of the other study covariates to effectively predict the absence or presence of caries in a sibling, a classification and regression tree (CART) analysis was undertaken. The predictive power of the CART models was evaluated using the area under the Receiver Operating Characteristic curve (AUROC) statistic. Results The prevalence of dental caries experience in the overall study population was 73.6% (index siblings 74.3%, co-siblings 72.9%). Conspicuous social patterning of caries was observed in both the index- and co-sibling populations even after adjustment for all study covariates. Significant sibling-specific familial aggregation of caries was observed, which varied in a stepwise graded fashion across the social hierarchy. Overall, 70.6% of sibling pairs were concordant in terms of their caries experience (caries 58.9%, caries-free 11.7%). Co-siblings of affected probands had 3.9 times (95% CI: 3.65–4.18) higher (adjusted) odds of having caries compared to those with caries-free siblings. This sibling similarity was further amplified in those with relative socioeconomic disadvantage (e.g., the adjusted PORs varied from 3.39 [95% CI: 3.04–3.77] in the highest to 5.47 [95% CI: 4.36–6.86] in the lowest parental education category). AUROCs from the CART models ranged from 0.7–0.82, indicating useful to excellent overall predictive power of the models. These models revealed sibling (proband) caries experience to be the single-most important risk predictor of caries in individuals (co-siblings), with the results indicating that caries could be expected in ≥ 84% of siblings of adolescents with 3 or more caries-affected tooth surfaces. Conclusions Graded clustering patterns of caries and socioeconomic disadvantage are encapsulated within families in Denmark, contributing to the engendering of health inequalities in society. With sibling caries being such a pertinent marker of increased caries risk, caries in a sibling should elicit preventive family-based approaches targeting co-siblings, particularly in socially disadvantaged households. Since caries shares common risk factors with other non-communicable diseases and conditions (such as diabetes and obesity), such policy constructs could reduce not only caries experience but also wider health inequalities in society.

Maximum incomplete recursive circulants in graph embeddings

An incomplete recursive circulant possesses virtually every advantage of a complete recursive circulant, including simple deadlock-free routing, a small diameter, a good support of parallel algorithms, and so on. It is natural to reconfigure a faulty recursive circulant into a maximum incomplete recursive circulant so as to lower potential performance degradation. For [Formula: see text], the maximum incomplete subgraph problem is to identify a subgraph [Formula: see text] of a graph [Formula: see text] on [Formula: see text] vertices having the maximum number of edges among all subgraphs on [Formula: see text] vertices and is NP-complete. In this paper we identify maximum incomplete recursive circulants and use them as a tool to compute the exact wirelength of embedding recursive circulants into special classes of trees, such as [Formula: see text]-rooted complete binary trees, [Formula: see text]-rooted sibling trees, binomial trees, certain caterpillars and path.

Embedding hypercubes and folded hypercubes onto Cartesian product of certain trees

The hypercube network is one of the most popular interconnection networks since it has simple structure and is easy to implement. The folded hypercube is an important variation of the hypercube. Interconnection networks play a major role in the performance of distributed memory multiprocessors and the one primary concern for choosing an appropriate interconnection network is the graph embedding ability. A graph embedding of a guest graph G into a host graph H is an injective map on the vertices such that each edge of G is mapped into a path of H. The wirelength of this embedding is defined to be the sum of the lengths of the paths corresponding to the edges of G. In this paper we embed hypercube and folded hypercube onto Cartesian product of trees such as 1-rooted complete binary tree and path, sibling tree and path to minimize the wirelength.

2-Power Domination in Certain Interconnection Networks

Abstract The k-power domination problem generalizes domination and power domination problems. The k-power domination problem is to determine a minimum size vertex set S ⊆ V(G) such that after setting X = N[S] and iteratively adding to X vertices x that have a neighbour v in X such that at most k neighbours of v are not yet in X till we get X = V(G). The least cardinality of such set is called the k-power domination number of G and is denoted by γp,k (G). In this paper, we restrict our discussion to k = 2, referred to as 2-power domination. We compute 2-power domination number for certain interconnection networks such as hypertree, sibling tree, X-tree, Christmas tree, mesh, honeycomb mesh, hexagonal mesh, cylinder, generalized Petersen graph and subdivision of graphs.

Embedding of hypercubes into sibling trees

The aim of this paper is to generalize the Congestion Lemma, which has been considered an efficient tool to compute the minimum wirelength (Manuel et al., 2009) and thereby obtain the minimum wirelength of embedding hypercubes into sibling trees.

Dissection of chilling requirement and bloom date QTLs in peach using a whole genome sequencing of sibling trees from an F2 mapping population

Chilling requirement (CR) for floral bud dormancy release is one of the major limiting factors for geographical adaptation of fruiting trees. Using a whole genome sequencing approach (Illumina platform), we explored polymorphism underlying phenotypic differences among individuals in a peach F2 cross segregating for chilling requirement and bloom date. Allelic configuration of individuals, which represented phenotypic extremes in the cross (300 vs. 1,100 chill hours) allowed reconstruction of low- and high-chill haplotypes within three most significant quantitative trait locus (QTL) intervals on the Prunus G1, G4, and G7. We detected single nucleotide polymorphic sites (SNPs), small deletions and insertions (DIPs), and large structural variants (SVs) associated with low-chill haplotypes and created a prioritized list of candidate genes based on functionally characterized homologs from Arabidopsis thaliana. Two dormancy associated genes PpeDAM5 and PpeDAM6 are the strongest candidate genes for the major QTL signal at the lower end of G1. Also, key functional genes involved in the Polycomb repressive mechanism, cell cycle progression, and hormone regulation were evident as strong candidate genes underlying QTL intervals in this peach cross.

Wirelength of hypercubes into certain trees

A lot of research has been devoted to finding efficient embedding of trees into hypercubes. On the other hand, in this paper, we consider the problem of embedding hypercubes into k-rooted complete binary trees, k-rooted sibling trees, binomial trees and certain classes of caterpillars to minimize the wirelength.

Prolonged Somatic Transposition in Citrus: The Autonomous Ac Transposable Element Remains Active in the Citrus Genome for Several Years

The maize transposable element Activator (Ac) has been shown to be active in a number of dicots, including arabidopsis [Arabidopsis thaliana (L.) Heynh.], tobacco (Nicotiana tabacum L.), tomato (Lycopersicon esculentum Mill.), potato (Solanum tuberosum L.), and aspen (Populus tremuloides Michx.). However, no information is available on somatic transposition in any plant during several years of growth and development. It is not known how transposition affects genetic variability among vegetative parts that have developed during a long period of growth. In order to explore the possibility of using somatic Ac transposition for gene tagging and mutagenesis in fruit trees, a derivative of the maize Ac transposable element was introduced into `Duncan' grapefruit (Citrus paradisi Macf.) by Agrobacterium tumefaciens (Smith & Towns.) Conn.-mediated stable transformation. Genetically identical 4-year-old sibling trees were established by grafting one of the transformants on Troyer citrange [Citrus sinensis (L.) Osbec. × Poncirus trifoliate (L.) Ras.] rootstocks. We demonstrated that the Ac element was active upon transformation in citrus (Citrus L.) trees and that transposition can create genetic variability among tree siblings and among leaves collected from different parts of the same tree. Ac was still active among propagated plants 4 years after transformation, clearly indicating that it is capable of maintaining itself in citrus trees for a long period of time. The observation of different integration patterns in different parts of the same tree and within tree siblings originating from the same transformant suggests that an Ac-based mutagenesis system could be very useful in creating somatic mutations in citrus trees.

Previous-year reproduction reduces photosynthetic capacity and slows lifetime growth in females of a neotropical tree.

Females of dioecious plant species typically invest more in reproduction than males because they produce seeds, fruits, and associated structures in addition to flowers. If females are unable to compensate by up-regulating rates of photosynthesis or by reproducing less frequently than males, their greater reproductive investment may result in reduced growth or higher mortality. Here we provide evidence of the cost of reproduction in Ocotea tenera (Lauraceae), a dioecious neotropical tree common in lower montane forests of Monteverde, Costa Rica. Over periods of 12-21 years, females grew more slowly than males in a natural population and in two experimental plots where we were able to control for genotype, age, habitat, and reproductive history. Simultaneous measurements of 10 matched pairs of sibling trees of the opposite sex but same age demonstrated that the photosynthetic capacities of females were 13% lower than those of males. Among females, photosynthetic capacity was negatively correlated with fruit production during the most recent reproductive season but not with lifetime fruit production. Sexual size dimorphism in adult O. tenera trees appears to be a nonadaptive consequence of trading off recent reproduction against maintenance of the photosynthetic apparatus, with long-term negative effects on growth.