scholarly journals The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

2019 ◽  
Author(s):  
Mosè Manni ◽  
Felipe A. Simao ◽  
Hugh M. Robertson ◽  
Marco A. Gabaglio ◽  
Robert M. Waterhouse ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gene Families ◽  
Sister Group ◽  
Sensu Stricto ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Animal Group ◽  
Origin And Evolution ◽  
Genomic Analyses ◽  
Metabolism Gene

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

scholarly journals The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations

2019 ◽  
Vol 12 (1) ◽  
pp. 3534-3549
Author(s):  
Mosè Manni ◽  
Felipe A Simao ◽  
Hugh M Robertson ◽  
Marco A Gabaglio ◽  
Robert M Waterhouse ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gene Families ◽  
Sister Group ◽  
Sensu Stricto ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Animal Group ◽  
Origin And Evolution ◽  
Genomic Analyses ◽  
Metabolism Gene

Abstract The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

scholarly journals Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Rose Waldron ◽  
Jamie McGowan ◽  
Natasha Gordon ◽  
Charley McCarthy ◽  
E. Bruce Mitchell ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Prediction ◽  
Draft Genome ◽  
Dermatophagoides Pteronyssinus ◽  
Mite Species ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Genomic Analyses ◽  
Dust Mite ◽  
Functional Analyses

ABSTRACT Dermatophagoides pteronyssinus is the European dust mite and a major source of human allergens. Here, we present the first draft genome sequence of the mite, as well as the ab initio gene prediction and functional analyses that will facilitate comparative genomic analyses with other mite species.

scholarly journals The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Lisong Hu ◽  
Zhongping Xu ◽  
Maojun Wang ◽  
Rui Fan ◽  
Daojun Yuan ◽  
...  
Keyword(s):  
Reference Genome ◽  
Gene Families ◽  
Black Pepper ◽  
Piper Nigrum ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Phylogenomic Analysis ◽  
Genomic Analyses ◽  
Species Specific ◽  
Insight Into

Abstract Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

scholarly journals Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome

2021 ◽  
Author(s):  
Andre Luiz de Oliveira ◽  
Jessica Mitchell ◽  
Peter Girguis ◽  
Monika Bright
Keyword(s):  
Immune System ◽  
Draft Genome ◽  
Gene Families ◽  
Gene Repertoire ◽  
Riftia Pachyptila ◽  
Intracellular Digestion ◽  
Obligate Symbiont ◽  
Highly Expressed Genes ◽  
Complete Mitogenome ◽  
Genome Information

The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulphur metabolism, detoxification, anti-oxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establishes that the trophosome is a multi-functional organ marked by intracellular digestion of endosymbionts, storage of excretory products and haematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbour highly expressed genes involved with cell cycle, programmed cell death, and immunity indicating a high cell turnover and defence mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whilst simultaneously provides new insights into the development, whole organism functions and evolution in the giant tubeworm.

scholarly journals The genome of the camphor tree and the genetic and climatic relevance of the top-geoherbalism in this medicinal plant

2021 ◽  
Author(s):  
Rihong Jiang ◽  
Xianlian Chen ◽  
Xuezhu Liao ◽  
Dan Peng ◽  
Xiaoxu Han ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Three Dimensional ◽  
Sister Group ◽  
Cold Season ◽  
Comparative Genomic ◽  
Climate Data ◽  
Volatile Oils ◽  
Expression Of Genes ◽  
Genomic Analyses ◽  
Camphor Tree

Camphor tree (Cinnamomum camphora (L.) J. Presl), a species in the magnoliid family Lauraceae, is known for its rich volatile oils and is used as a medical cardiotonic and as a scent in many perfumed hygiene products. Here, we present a high-quality chromosome-scale genome of C. camphora with a scaffold N50 of 64.34 Mb and an assembled genome size of 755.41 Mb. Phylogenetic inference revealed that the magnoliids are a sister group to the clade of eudicots and monocots. Comparative genomic analyses identified two rounds of ancient whole-genome duplication (WGD). Tandem duplicated genes exhibited a higher evolutionary rate, a more recent evolutionary history and a more clustered distribution on chromosomes, contributing to the production of secondary metabolites, especially monoterpenes and sesquiterpenes, which are the principal essential oil components. Three-dimensional analyses of the volatile metabolites, gene expression and climate data of samples with the same genotype grown in different locations showed that low temperature and low precipitation during the cold season modulate the expression of genes in the terpenoid biosynthesis pathways, especially TPS genes, which facilitates the accumulation of volatile compounds. Our study lays a theoretical foundation for policy-making regarding the agroforestry applications of camphor tree.

scholarly journals Phylogenomic and Molecular Demarcation of the Core Members of the PolyphyleticPasteurellaceaeGeneraActinobacillus,Haemophilus, andPasteurella

2015 ◽  
Vol 2015 ◽  
pp. 1-15 ◽  
Author(s):  
Sohail Naushad ◽  
Mobolaji Adeolu ◽  
Nisha Goel ◽  
Bijendra Khadka ◽  
Aqeel Al-Dahwi ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Sensu Stricto ◽  
The Other ◽  
Comparative Genomic ◽  
Molecular Signatures ◽  
The Core ◽  
Conserved Signature Indels ◽  
Genomic Analyses ◽  
Large Clusters

The generaActinobacillus, Haemophilus,andPasteurellaexhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters ofActinobacillus, Haemophilus,andPasteurellaspecies which represent the “sensu stricto” members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared bysensu strictomembers ofActinobacillus, Haemophilus,andPasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing generaAggregatibacterandMannheimia, respectively. It is now possible to demarcate the generaActinobacillus sensu stricto, Haemophilus sensu stricto,andPasteurella sensu strictoon the basis of discrete molecular signatures. The other members of the generaActinobacillus, Haemophilus,andPasteurellathat do not fall within the “sensu stricto” clades and do not contain these molecular signatures should be reclassified as other genera. The CSIs identified here also provide useful diagnostic targets for the identification of current and novel members of the indicated genera.

scholarly journals Phylogenetic diversification of sirtuin genes with a description of a new family member

2020 ◽  
Author(s):  
Juan C. Opazo ◽  
Kattina Zavala ◽  
Michael W. Vandewege ◽  
Federico G. Hoffmann
Keyword(s):  
Gene Family ◽  
Family Member ◽  
Gene Families ◽  
Last Common Ancestor ◽  
Gene Repertoire ◽  
Origin And Evolution ◽  
New Family ◽  
Wide Range ◽  
Evolutionary Context ◽  
History Of

AbstractStudying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural work, as the correct interpretation of their results needs to be done in a robust evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our goal is to take advantage of the genomic data available in public databases to advance our understanding of how sirtuin genes are related to each other, and to characterize the gene repertoire in species representative of all the main groups of vertebrates. Our results show a well-resolved phylogeny that represents a significant improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin family member (SIRT3-like) that was apparently lost in amniotes, but retained in all other groups of jawed vertebrates. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.

scholarly journals The genome of the plague-resistant great gerbil reveals species-specific duplication of an MHCII gene

2018 ◽  
Author(s):  
Pernille Nilsson ◽  
Monica H. Solbakken ◽  
Boris V. Schmid ◽  
Russell J. S. Orr ◽  
Ruichen Lv ◽  
...  
Keyword(s):  
Adaptive Immune Response ◽  
Gene Families ◽  
Comparative Genomic ◽  
Immune Gene ◽  
Gene Repertoire ◽  
Great Gerbil ◽  
Genomic Landscape ◽  
A Genome ◽  
Natural Hosts ◽  
Species Specific

AbstractThe great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious diseases and is defined as a key reservoir species for plague (Yersinia pestis). Studies from the wild have shown that the great gerbil is largely resistant to plague but the genetic basis for resistance is yet to be determined. Here, we present a highly contiguous annotated genome assembly of great gerbil, covering over 96 % of the estimated 2.47 Gb genome. Comparative genomic analyses focusing on the immune gene repertoire, reveal shared gene losses within TLR gene families (i.e. TLR8, TLR10 and all members of TLR11-subfamily) for the Gerbillinae lineage, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes. The great gerbil genome provides new insights into the genomic landscape that confers immunological resistance towards plague. The high affinity for Yersinia epitopes could be key in our understanding of the high resistance in great gerbils, putatively conferring a faster initiation of the adaptive immune response leading to survival of the infection. Our study demonstrates the power of studying zoonosis in natural hosts through the generation of a genome resource for further comparative and experimental work on plague survival and evolution of host-pathogen interactions.

scholarly journals At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica

2021 ◽  
Vol 11 ◽  
Author(s):  
François Renoz ◽  
Vincent Foray ◽  
Jérôme Ambroise ◽  
Patrice Baa-Puyoulet ◽  
Bertrand Bearzatto ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Comparative Genomic ◽  
Intermediate Hosts ◽  
Bacterial Symbiosis ◽  
Early Stages ◽  
Genomic Analyses ◽  
Significant Enrichment ◽  
New Hosts ◽  
Serratia Symbiotica ◽  
Metabolism Gene

Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial associates of insects that are at the gateway to a host-dependent lifestyle.

scholarly journals Genome sequence of the Chinese white wax scale insect Ericerus pela: the first draft genome for the Coccidae family of scale insects

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Pu Yang ◽  
Shuhui Yu ◽  
Junjun Hao ◽  
Wei Liu ◽  
Zunling Zhao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gene Families ◽  
Sister Group ◽  
Scale Insect ◽  
Fatty Acyl ◽  
Scale Insects ◽  
Sequence Length ◽  
Evolutionary Analysis ◽  
Chinese White

AbstractBackgroundThe Chinese white wax scale insect, Ericerus pela, is best known for producing wax, which has been widely used in candle production, casting, Chinese medicine, and wax printing products for thousands of years. The secretion of wax, and other unusual features of scale insects, is thought to be an adaptation to their change from an ancestral ground-dwelling lifestyle to a sedentary lifestyle on the higher parts of plants. As well as helping to improve its economic value, studies of E. pela might also help to explain the adaptation of scale insects. However, no genomic data are currently available for E. pela.FindingsTo assemble the E. pela genome, 303.92 Gb of data were generated using Illumina and Pacific Biosciences sequencing, producing 277.22 Gb of clean data for assembly. The assembled genome size was 0.66 Gb, with 1,979 scaffolds and a scaffold N50 of 735 kb. The guanine + cytosine content was 33.80%. A total of 12,022 protein-coding genes were predicted, with a mean coding sequence length of 1,370 bp. Twenty-six fatty acyl-CoA reductase genes and 35 acyltransferase genes were identified. Evolutionary analysis revealed that E. pela and aphids formed a sister group and split ∼241.1 million years ago. There were 214 expanded gene families and 2,219 contracted gene families in E. pela.ConclusionWe present the first genome sequence from the Coccidae family. These results will help to increase our understanding of the evolution of unique features in scale insects, and provide important genetic information for further research.

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