Assessment of Microsatellite Markers (SSRs) For Genetic Diversity in Asparagus Officinalis L. And Allied Species

The present study was hypothesized to evaluate a set of SSRs for the assessment of genetic variations in Asparagus officinalis L. and their allied species. Nine genic SSR markers were especially developed for Asparagus genome and employed for DNA profiling studies of Asparagus species. These SSRs markers have revealed the allelic polymorphism ranging from 1.0 to 2.0. Allele frequency was found highest for psbD-trnL (1.0), petB (1.0) and AG7 (1.0), while it was lowest for ZHD1 (0.1). Polymorphism Information content (PIC) was highest for TC7 (0.9) while it was lowest (0.0) for psbD-trnL, petB and AG7 respectively. The genetic similarity coefficients were found to range from 0.42 to 1.0. The UPGMA clustering algorithm based on SSRs data have clustered Asparagus species into 4 groups (I, II, III & IV) indicating Asparagus officinalis (L.) cultivars and allied species in the first clade, while Asparagus officinalis (L.) ‘Gersengum’, Asparagus densiflorus (Kunth) Jessop, and Asparagus racemosus willd. were clustered in separate clades respectively. The present study has endorsed the origin status of Asparagus officinalis and their allied species. A. officinalis cultivars and other allied Asparagus species are clustered in separate clades, and it was revealed that they have monophyletic origin. It was established that SSRs markers could be informative markers for the differentiation of Asparagus officinalis cultivars, and their allied Asparagus species. Bangladesh J. Bot. 50(3): 595-602, 2021 (September)

Genetic diversity and phylogenetic analysis in Asian and European Asparagus subgenus species

Garden asparagus (Asparagus officinalis L.) is a diploid (2n = 2x = 20), perennial and dioecious species belonging to Asparagus subgenus and worldwide cultivated as a vegetable crop. A narrow genetic base has been pointed out for the current cultivars. Crop wild related species (CWR) could be a valuable genetic resource in this crop but they have been underused up to now. To investigate the phylogenetic relationships between CWR asparagus species from different origin and A. officinalis L., 12 EST-SSR markers were used to assess the genetic variability of 20 accessions. These accessions belong to 10 Asparagus spp. from Asparagus subgenus including wild and naturalized A. officinalis L. (2x, 4x, 8x, 10x) and CWR species with European (A. tenuifolius Lam. (2x), A. pseudoscaber Grec. (6x), A. macrorrhizus Pedrol & al. (12x), A. prostratus Dumort (4x), A. brachyphyllus Turcz. (6x), A. maritimus (L.) Mill. (6x)) and Asian distribution (A. verticillatus L. (2x), A. persicus Baker (2x), A. breslerianus Schult. & Schult. (8x)). A. albus L. (2x) from the Protasparagus subgenus was used as outgroup. As a result, a total of 248 alleles were obtained and specific alleles of accessions were detected among them. After cluster analysis the accessions did not group by their geographical origin. All wild polyploid accessions with European and Asian distributions were grouped together with A. officinalis L. Hence, that cluster could be considered as the ‘officinalis group’ suggesting a monophyletic origin. The diploid accessions of A. verticillatus L. and A. persicus Baker clustered together and were the most genetically distant respect to ‘officinalis group’. The results obtained in this study may provide useful information to design new crosses among accessions aimed to develop new asparagus germplasm or pre-breeding populations.

Systematics and Multi-Gene Phylogeny of the Subfamily Nothoholostichinae (Ciliophora, Hypotrichia), With Integrative Description of a New Marine Species Nothoholosticha luporinii n. sp.

Morphogenesis of ciliated protists attracts a lot of attention, because their huge morphological diversity is related to formation of ciliary structures during cell division. In the present work, the morphology and morphogenesis as well as the phylogenetic position of a new, marine hypotrich ciliate, Nothoholosticha luporinii n. sp., were investigated. The new species is characterized by having a combination of the following features: a bicorona whose anterior row contains four frontal cirri and posterior row includes only two cirri, a single buccal cirrus, midventral complex composed of about 30 cirral pairs, one pretransverse cirrus, 3–6 transverse cirri, one left and one right marginal cirral row; three bipolar dorsal kineties; contractile vacuole located in about 2/3 of the body length, two types of cortical granules, and many macronuclear nodules scattered throughout the cytoplasm. The morphogenesis of N. luporinii follows the ontogenetic mode of Pseudokeronopsis, a well-known and closely related genus except that the macronucleus fuses into a single mass in the middle fission stage. Phylogenetic analyses based on the rDNA operon classify Nothoholosticha in the family Pseudokeronopsidae and support the distinctness of the new taxon as well as the monophyletic origin of the subfamily Nothoholostichinae.

Spidroin profiling of cribellate spiders provides insight into the evolution of spider prey capture strategies

Orb-weaving spiders have two main methods of prey capture: cribellate spiders use dry, sticky capture threads, and ecribellate spiders use viscid glue droplets. Predation behaviour is a major evolutionary driving force, and it is important on spider phylogeny whether the cribellate and ecribellate spiders each evolved the orb architecture independently or both strategies were derived from an ancient orb web. These hypotheses have been discussed based on behavioural and morphological characteristics, with little discussion on this subject from the perspective of molecular materials of orb web, since there is little information about cribellate spider-associated spidroin genes. Here, we present in detail a spidroin catalogue of six uloborid species of cribellate orb-weaving spiders, including cribellate and pseudoflagelliform spidroins, with transcriptome assembly complemented with long read sequencing, where silk composition is confirmed by proteomics. Comparative analysis across families (Araneidae and Uloboridae) shows that the gene architecture, repetitive domains, and amino acid frequencies of the orb web constituting silk proteins are similar among orb-weaving spiders regardless of the prey capture strategy. Notably, the fact that there is a difference only in the prey capture thread proteins strongly supports the monophyletic origin of the orb web.

Genomic Organization and Generation of Genetic Variability in the RHS (Retrotransposon Hot Spot) Protein Multigene Family in Trypanosoma cruzi

Retrotransposon Hot Spot (RHS) is the most abundant gene family in Trypanosoma cruzi, with unknown function in this parasite. The aim of this work was to shed light on the organization and expression of RHS in T. cruzi. The diversity of the RHS protein family in T. cruzi was demonstrated by phylogenetic and recombination analyses. Transcribed sequences carrying the RHS domain were classified into ten distinct groups of monophyletic origin. We identified numerous recombination events among the RHS and traced the origins of the donors and target sequences. The transcribed RHS genes have a mosaic structure that may contain fragments of different RHS inserted in the target sequence. About 30% of RHS sequences are located in the subtelomere, a region very susceptible to recombination. The evolution of the RHS family has been marked by many events, including gene duplication by unequal mitotic crossing-over, homologous, as well as ectopic recombination, and gene conversion. The expression of RHS was analyzed by immunofluorescence and immunoblotting using anti-RHS antibodies. RHS proteins are evenly distributed in the nuclear region of T. cruzi replicative forms (amastigote and epimastigote), suggesting that they could be involved in the control of the chromatin structure and gene expression, as has been proposed for T. brucei.

Monophyletic Origin and Divergent Evolution of Animal Telomerase RNA

Telomerase RNA (TR) is a noncoding RNA essential for the function of telomerase ribonucleoprotein. TRs from vertebrates, fungi, ciliates, and plants exhibit extreme diversity in size, sequence, secondary structure, and biogenesis pathway. However, the evolutionary pathways leading to such unusual diversity among eukaryotic kingdoms remain elusive. Within the metazoan kingdom, the study of TR has been limited to vertebrates and echinoderms. To understand the origin and evolution of TR across the animal kingdom, we employed a phylogeny-guided, structure-based bioinformatics approach to identify 82 novel TRs from eight previously unexplored metazoan phyla, including the basal-branching sponges. Synthetic TRs from two representative species, a hemichordate and a mollusk, reconstitute active telomerase in vitro with their corresponding telomerase reverse transcriptase components, confirming that they are authentic TRs. Comparative analysis shows that three functional domains, template-pseudoknot (T-PK), CR4/5, and box H/ACA, are conserved between vertebrate and the basal metazoan lineages, indicating a monophyletic origin of the animal TRs with a snoRNA-related biogenesis mechanism. Nonetheless, TRs along separate animal lineages evolved with divergent structural elements in the T-PK and CR4/5 domains. For example, TRs from echinoderms and protostomes lack the canonical CR4/5 and have independently evolved functionally equivalent domains with different secondary structures. In the T-PK domain, a P1.1 stem common in most metazoan clades defines the template boundary, which is replaced by a P1-defined boundary in vertebrates. This study provides unprecedented insight into the divergent evolution of detailed TR secondary structures across broad metazoan lineages, revealing ancestral and later-diversified elements.

Morphological and Molecular Identification of Three Genera of the Family Heptageniidae (Ephemeroptera) from Ava Sheen Branch/ Greater Zab Tributary, North of Iraq

The aquatic Heptageniidae family of Ava-sheen branch (Greater Zab Tributary) in Duhok Governorate/ Iraq was studied. Samples were collected using Surber stream sampler to study their diagnostic morphological characteristics and molecular phylogenetic profile using a nuclear gene 16s ribosomal RNA. The morphological and molecular identification supported that the three species, Epeorus longimanus, Heptagenia elegantula and Ephemerella cornutus belong to Heptageniidae family, while the molecular results also confirmed the monophyletic origin of these three genera.

Complete Genome Sequence of the Lumpy Skin Disease Virus Recovered from the First Outbreak in the Northern Caucasus Region of Russia in 2015

We report here the complete genome sequence of a lumpy skin disease virus (LSDV) isolate obtained in the Northern Caucasus region of Russia in 2015. The LSDV/Russia/Dagestan/2015 genome sequence grouped with field LSDV isolates found in Serbia and Greece, suggesting the monophyletic origin of LSDV isolates that recently affected countries in the Northern Hemisphere.