scholarly journals Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 170 ◽  
Author(s):  
Marcelo R. J. Castro ◽  
Clément Goubert ◽  
Fernando A. Monteiro ◽  
Cristina Vieira ◽  
Claudia M. A. Carareto
Keyword(s):  
New Species ◽  
Genetic Variability ◽  
Transposable Elements ◽  
Species Complex ◽  
De Novo ◽  
Repetitive Sequences ◽  
Sudden Expansion ◽  
Additional Species ◽  
Original Genome ◽  
Evolutionary Trajectories

Transposable elements (TEs) are widely distributed repetitive sequences in the genomes across the tree of life, and represent an important source of genetic variability. Their distribution among genomes is specific to each lineage. A phenomenon associated with this feature is the sudden expansion of one or several TE families, called bursts of transposition. We previously proposed that bursts of the Mariner family (DNA transposons) contributed to the speciation of Rhodnius prolixus Stål, 1859. This hypothesis motivated us to study two additional species of the R. prolixus complex: Rhodnius montenegrensis da Rosa et al., 2012 and Rhodnius marabaensis Souza et al., 2016, together with a new, de novo annotation of the R. prolixus repeatome using unassembled short reads. Our analysis reveals that the total amount of TEs present in Rhodnius genomes (19% to 23.5%) is three to four times higher than that expected based on the original quantifications performed for the original genome description of R. prolixus. We confirm here that the repeatome of the three species is dominated by Class II elements of the superfamily Tc1-Mariner, as well as members of the LINE order (Class I). In addition to R. prolixus, we also identified a recent burst of transposition of the Mariner family in R. montenegrensis and R. marabaensis, suggesting that this phenomenon may not be exclusive to R. prolixus. Rather, we hypothesize that whilst the expansion of Mariner elements may have contributed to the diversification of the R. prolixus-R. robustus species complex, the distinct ecological characteristics of these new species did not drive the general evolutionary trajectories of these TEs.

scholarly journals The de novo genome of the “Spanish” slug Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

2020 ◽  
Author(s):  
Zeyuan Chen ◽  
Özgül Doğan ◽  
Nadège Guiglielmoni ◽  
Anne Guichard ◽  
Michael Schrödl
Keyword(s):  
Transposable Elements ◽  
Genome Assembly ◽  
De Novo ◽  
Repetitive Sequences ◽  
Land Snails ◽  
Whole Genome ◽  
Pest Species ◽  
High Quality ◽  
Genome Duplication Event ◽  
Arion Vulgaris

AbstractBackgroundThe “Spanish” slug, Arion vulgaris Moquin-Tandon, 1855, is considered to be among the 100 worst pest species in Europe. It is common and invasive to at least northern and eastern parts of Europe, probably benefitting from climate change and the modern human lifestyle. The origin and expansion of this species, the mechanisms behind its outstanding adaptive success and ability to outcompete other land slugs are worth to be explored on a genomic level. However, a high-quality chromosome-level genome is still lacking.FindingsThe final assembly of A. vulgaris was obtained by combining short reads, linked reads, Nanopore long reads, and Hi-C data. The genome assembly size is 1.54 Gb with a contig N50 length of 8.6 Mb. We found a recent expansion of transposable elements (TEs) which results in repetitive sequences accounting for more than 75% of the A. vulgaris genome, which is the highest among all known gastropod species. We identified 32,518 protein coding genes, and 2,763 species specific genes were functionally enriched in response to stimuli, nervous system and reproduction. With 1,237 single-copy orthologs from A. vulgaris and other related mollusks with whole-genome data available, we reconstructed the phylogenetic relationships of gastropods and estimated the divergence time of stylommatophoran land snails (Achatina) and Arion slugs at around 126 million years ago, and confirmed the whole genome duplication event shared by them.ConclusionsTo our knowledge, the A. vulgaris genome is the first land slug genome assembly published to date. The high-quality genomic data will provide valuable genetic resources for further phylogeographic studies of A. vulgaris origin and expansion, invasiveness, as well as molluscan aquatic-land transition and shell formation.

scholarly journals Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3590
Author(s):  
Pierre Capy
Keyword(s):  
Genetic Variability ◽  
Transposable Elements ◽  
Environmental Constraints ◽  
The Third ◽  
Evolutionary Trajectories ◽  
Pass Through ◽  
Horizontal Transfers ◽  
Population Fitness

During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.

Description of two new species of Neoplea Esaki & China (Hemiptera: Pleidae) from Colombia

Zootaxa ◽  
2020 ◽  
Vol 4860 (1) ◽  
pp. 55-66
Author(s):  
JERRY L. COOK ◽  
SILVIA P. MONDRAGÓN-F. ◽  
IRINA MORALES
Keyword(s):  
New Species ◽  
Species Complex ◽  
Additional Species ◽  
Number Of Species ◽  
Two New Species

Neoplea hyaloderma n. sp. and N. melanosoma n. sp. (Insecta: Hemiptera: Pleidae) are described from Colombia. This increases the number of species of pleids known from Colombia to four, all of which are in the genus Neoplea Esaki & China. A key to the species of Neoplea of Colombia is included. Neoplea melanosoma appears to be part of a species complex with N. maculosa (Berg) and N. tenuistyla Roback & Nieser, and herein is called the N. maculosa species complex. We also note that there is probably at least one additional species in this complex from Suriname that was previously identified as N. maculosa. Neoplea melanosoma n. sp. appears to most closely resemble N. maculosa from Argentina, Bolivia and Paraguay than the geographically closer N. tenuistyla. Neoplea hyaloderma n. sp. appears most closely related to N. lingula Roback & Nieser, which is also in Colombia. 

scholarly journals Centromere Repeats: Hidden Gems of the Genome

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 223 ◽  
Author(s):  
Gabrielle Hartley ◽  
Rachel O’Neill
Keyword(s):  
Transposable Elements ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Repetitive Sequences ◽  
Chromosomal Evolution ◽  
Satellite Dnas ◽  
Integral Role ◽  
Chromosomal Breakpoints ◽  
Karyotypic Variation ◽  
Species Specific

Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’.

scholarly journals Evolution of genome structure in the Drosophila simulans species complex

2020 ◽  
Author(s):  
Mahul Chakraborty ◽  
Ching-Ho Chang ◽  
Danielle E. Khost ◽  
Jeffrey Vedanayagam ◽  
Jeffrey R. Adrion ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Species Complex ◽  
Repetitive Sequences ◽  
Drosophila Simulans ◽  
Gene Duplications ◽  
Phenotypic Evolution ◽  
Complex Species ◽  
Structural Divergence

ABSTRACTThe rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 years ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster due to structural divergence—twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, while the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.

A new species of the genus Parapachymorpha Brunner von Wattenwyl, 1893 (Phasmida, Phasmatidae, Clitumninae) from Laos

Zootaxa ◽  
2020 ◽  
Vol 4732 (1) ◽  
pp. 196-200
Author(s):  
CHANG-MOON JANG ◽  
YANG˗SEOP BAE
Keyword(s):  
New Species ◽  
Body Surface ◽  
Type Species ◽  
Lateral View ◽  
Lower Margin ◽  
Additional Species ◽  
The World ◽  
A New Species ◽  
Egg Capsule

Parapachymorpha is one of eight genera within the tribe Medaurini of subfamily Clitumninae (Phasmatidae). It was established by Brunner von Wattenwyl (1893), with the type species Parapachymorpha nigra by subsequent designation of Kirby (1904), from Myanmar. Species of this genus are widely distributed in oriental tropics (Laos, China, Thailand, Myanmar, Vietnam and Cambodia), with only 11 known species in the world (Brock et al. 2018, Ho 2017). Species of the genus Parapachymorpha can be recognized by following characters (Brunner von Wattenwyl 1893;1907, Henmemann & Conle 2008, Ho 2017): 1) body robust in female and slender in male with long leg in relation to the length; 2) body surface of female granulose or spinose; 3) mesonotum of female more and less expanded posteriorly; 4) abdominal tergites lacking expanded prostero–lateral angles in both sexes; 5) laminal supraanalis undeveloped in female; 6) semi–tergite of male irregularly rectangular, with an additional finger­–like ventro–apical appendix on the lower margin and reduced or absent; 7) egg capsule oval to oblong and covered with a raised net–like structure in lateral view; 8) micropylar plate oval; 9) operculum concave or convex. In the present study, we describe additional species, Parapachymorpha minuta sp. nov. from Laos, with photographs of both sexes of adults and egg. 

A new species and further records of quill mites (Acari: Cheyletoidea: Syringophilidae) parasitic on birds (Aves) in England

Zootaxa ◽  
2009 ◽  
Vol 2133 (1) ◽  
pp. 49-54 ◽  
Author(s):  
BARRY NATTRESS ◽  
MACIEJ SKORACKI
Keyword(s):  
New Species ◽  
Length Ratio ◽  
Additional Species ◽  
Tawny Owl ◽  
Strix Aluco ◽  
Quill Mites ◽  
The Family ◽  
Transverse Branch ◽  
One New Species ◽  
A New Species

Four additional species of quill mites of the family Syringophilidae Lavoipierre have now been recorded in England. This includes one new species, Bubophilus aluconis sp. nov., which parasitizes the tawny owl Strix aluco (Strigiformes: Strigidae). It differs from other species of this genus, B. ascalaphus Philips et Norton, 1978 and B. asiobius Skoracki et Bochkov, 2002 by the number of chambers in transverse branch of the peritremes (2-3), the length ratio of setae vi and ve (1:1.6-2), and the lengths of the stylophore and aggenital setae ag1 (180 and 135-145, respectively).

scholarly journals Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0190385 ◽  
Author(s):  
Hernán Alvarado-Sizzo ◽  
Alejandro Casas ◽  
Fabiola Parra ◽  
Hilda Julieta Arreola-Nava ◽  
Teresa Terrazas ◽  
...  
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Species Complex ◽  
A New Species
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