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July 7, 2019

An investigation of Y chromosome incorporations in 400 species of Drosophila and related genera.

Y chromosomes are widely believed to evolve from a normal autosome through a process of massive gene loss (with preservation of some male genes), shaped by sex-antagonistic selection and complemented by occasional gains of male-related genes. The net result of these processes is a male-specialized chromosome. This might be expected to be an irreversible process, but it was found in 2005 that the Drosophila pseudoobscura Y chromosome was incorporated into an autosome. Y chromosome incorporations have important consequences: a formerly male-restricted chromosome reverts to autosomal inheritance, and the species may shift from an XY/XX to X0/XX sex-chromosome system. In order to assess the frequency and causes of this phenomenon we searched for Y chromosome incorporations in 400 species from Drosophila and related genera. We found one additional large scale event of Y chromosome incorporation, affecting the whole montium subgroup (40 species in our sample); overall 13% of the sampled species (52/400) have Y incorporations. While previous data indicated that after the Y incorporation the ancestral Y disappeared as a free chromosome, the much larger data set analyzed here indicates that a copy of the Y survived as a free chromosome both in montium and pseudoobscura species, and that the current Y of the pseudoobscura lineage results from a fusion between this free Y and the neoY. The 400 species sample also showed that the previously suggested causal connection between X-autosome fusions and Y incorporations is, at best, weak: the new case of Y incorporation (montium) does not have X-autosome fusion, whereas nine independent cases of X-autosome fusions were not followed by Y incorporations. Y incorporation is an underappreciated mechanism affecting Y chromosome evolution; our results show that at least in Drosophila it plays a relevant role and highlight the need of similar studies in other groups.

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July 7, 2019

Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Background: The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase with important roles in animals. Although GSK3 genes have been studied for more than 30years, plant GSK genes have been studied only since the last decade. Previous research has confirmed that plant GSK genes are involved in diverse processes, including floral development, brassinosteroid signaling, and responses to abiotic stresses. Result: In this study, 20, 15 (including 5 different transcripts) and 10 GSK genes were identified in G. hirsutum, G. raimondii and G. arboreum, respectively. A total of 65 genes from Arabidopsis, rice, and cotton were classified into 4 clades. High similarities were found in GSK3 protein sequences, conserved motifs, and gene structures, as well as good concordance in gene pairwise comparisons (G. hirsutum vs. G. arboreum, G. hirsutum vs. G. raimondii, and G. arboreum vs. G. raimondii) were observed. Whole genome duplication (WGD) within At and Dt sub-genomes has been central to the expansion of the GSK gene family. Furthermore, GhSK genes showed diverse expression patterns in various tissues. Additionally, the expression profiles of GhSKs under different stress treatments demonstrated that many are stress-responsive genes. However, none were induced by brassinolide treatment. Finally, nine co-expression sub- networks were observed for GhSKs and the functional annotations of these genes suggested that some GhSKs might be involved in cotton fiber development. Conclusion: In this present work, we identified 45 GSK genes from three cotton species, which were divided into four clades. The gene features, muti-alignment, conversed motifs, and syntenic blocks indicate that they have been highly conserved during evolution. Whole genome duplication was determined to be the dominant factor for GSK gene family expansion. The analysis of co-expressed sub-networks and tissue-specific expression profiles suggested functions of GhSKs during fiber development. Moreover, their different responses to various abiotic stresses indicated great functional diversity amongst the GhSKs. Briefly, data presented herein may serve as the basis for future functional studies of GhSKs.

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July 7, 2019

Single-phase PacBio de novo assembly of the genome of the chytrid fungus Batrachochytrium dendrobatidis, a pathogen of Amphibia.

Here, we present an updated genome assembly of the diploid chytrid fungus Batrachochytrium dendrobatidis strain RTP6. This strain is part of the global panzootic lineage (BdGPL) and was isolated in Dunedin, New Zealand. The assembly was generated using PacBio long-read and Illumina short-read data, allowing for the accurate phasing of heterozygosities.

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July 7, 2019

Complete genome sequence of WM99c, an antibiotic-resistant Acinetobacter baumannii global clone 2 (GC2) strain representing an Australian GC2 lineage.

The extensively antibiotic-resistant Acinetobacter baumannii isolate WM99c recovered in Sydney, Australia, in 1999 is an early representative of a distinct lineage of global clone 2 (GC2) seen on the east coast of Australia. We present the complete 4.121-Mbp genome sequence (chromosome plus 2 plasmids), generated via long-read sequencing (PacBio).

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July 7, 2019

Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies.

Clostridium formicoaceticum, a Gram-negative mixotrophic homoacetogen, produces acetic acid as the sole metabolic product from various carbon sources, including fructose, glycerol, formate, and CO2. Its genome of 4.59-Mbp contains a highly conserved Wood-Ljungdahl pathway gene cluster with the same layout as that in other mixotrophic acetogens, including Clostridium aceticum, Clostridium carboxidivorans, and Clostridium ljungdahlii. For energy conservation, C. formicoaceticum does not have all the genes required for the synthesis of cytochrome or quinone used for generating proton gradient in H+-dependent acetogens such as Moorella thermoacetica; instead, it has the Rnf system and a Na+-translocating ATPase similar to the one in Acetobacterium woodii. Its growth in both heterotrophic and autotrophic media were dependent on the sodium concentration. C. formicoaceticum has genes encoding acetaldehyde dehydrogenases, alcohol dehydrogenases, and aldehyde oxidoreductases, which could convert acetyl-CoA and acetate to ethanol and butyrate to butanol under excessive reducing equivalent conditions. Copyright © 2018 Elsevier Inc. All rights reserved.

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July 7, 2019

Overview of the germline and expressed repertoires of the TRB genes in Sus scrofa.

The a/ß T cell receptor (TR) is a complex heterodimer that recognizes antigenic peptides and binds to major histocompatibility complex (MH) molecules. Both a and ß chains are encoded by different genes localized on two distinct chromosomal loci: TRA and TRB. The present study employed the recent release of the swine genome assembly to define the genomic organization of the TRB locus. According to the sequencing data, the pig TRB locus spans approximately 400 kb of genomic DNA and consists of 38 TRBV genes belonging to 24 subgroups located upstream of three in tandem TRBD-J-C clusters, which are followed by a TRBV gene in an inverted transcriptional orientation. Comparative analysis confirms that the general organization of the TRB locus is similar among mammalian species, but the number of germline TRBV genes varies greatly even between species belonging to the same order, determining the diversity and specificity of the immune response. However, sequence analysis of the TRB locus also suggests the presence of blocks of conserved homology in the genomic region across mammals. Furthermore, by analysing a public cDNA collection, we identified the usage pattern of the TRBV, TRBD, and TRBJ genes in the adult pig TRB repertoire, and we noted that the expressed TRBV repertoire seems to be broader and more diverse than the germline repertoire, in line with the presence of a high level of TRBV gene polymorphisms. Because the nucleotide differences seems to be principally concentrated in the CDR2 region, it is reasonable to presume that most T cell ß-chain diversity can be related to polymorphisms in pig MH molecules. Domestic pigs represent a valuable animal model as they are even more anatomically, genetically and physiologically similar to humans than are mice. Therefore, present knowledge on the genomic organization of the pig TRB locus allows the collection of increased information on the basic aspects of the porcine immune system and contributes to filling the gaps left by rodent models.

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July 7, 2019

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.

The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism. Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.

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July 7, 2019

Signatures of selection and environmental adaptation across the goat genome post-domestication.

Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds.Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments.These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.

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July 7, 2019

Methanogenic and bacterial endosymbionts of free-living anaerobic ciliates

Trimyema compressum thrives in anoxic freshwater environments in which it preys on bacteria and grows with fermentative metabolisms. Like many anaerobic protozoa, instead of mitochondria, T. compressum possess hydrogenosomes, which are hydrogen-producing, energy-generating organelles characteristic of anaerobic protozoa and fungi. The cytoplasm of T. compressum harbours hydrogenotrophic methanogens that consume the hydrogen produced by hydrogenosome, which confers an energetic advantage to the host ciliate. Symbiotic associations between methanogenic archaea and Trimyema ciliates are thought to be established independently and/or repeatedly in their evolutional history. In addition to methanogenic symbionts, T. compressum houses bacterial symbiont TC1 whose function is unknown in its cytoplasm. Recently, we analysed whole-genome sequence of TC1 symbiont to investigate its physiological function in the tripartite symbiosis and found that fatty acid synthesis fab operon of TC1 symbiont lacked typical transcriptional repressor, which is normally coded on the upstream of the fab operon. The sequence data suggested that TC1 symbiont contributes to host Trimyema by the synthesis of fatty acid or its derivative. In this review, we summarize the early works and recent progress of the studies on Trimyema ciliates, including a stably cultivable model protozoa T. compressum, and discuss about symbiotic associations in oxygen-scarce environments.

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July 7, 2019

Complete genome sequence of Sulfitobacter sp. strain D7, a virulent bacterium isolated from an Emiliania huxleyi algal bloom in the North Atlantic.

A Rhodobacterales bacterium, Sulfitobacter sp. strain D7, was isolated from an Emiliania huxleyi bloom in the North Atlantic and has been shown to act as a pathogen and induce cell death of E. huxleyi during lab coculturing. We report here its complete genome sequence comprising one chromosome and five low-copy-number plasmids.

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July 7, 2019

Pilot satellitome analysis of the model plant, Physcomitrellapatens, revealed a transcribed and high-copy IGS related tandem repeat.

Satellite DNA (satDNA) constitutes a substantial part of eukaryotic genomes. In the last decade, it has been shown that satDNA is not an inert part of the genome and its function extends beyond the nuclear membrane. However, the number of model plant species suitable for studying the novel horizons of satDNA functionality is low. Here, we explored the satellitome of the model “basal” plant, Physcomitrellapatens (Hedwig, 1801) Bruch & Schimper, 1849 (moss), which has a number of advantages for deep functional and evolutionary research. Using a newly developed pyTanFinder pipeline (https://github.com/Kirovez/pyTanFinder) coupled with fluorescence in situ hybridization (FISH), we identified five high copy number tandem repeats (TRs) occupying a long DNA array in the moss genome. The nuclear organization study revealed that two TRs had distinct locations in the moss genome, concentrating in the heterochromatin and knob-rDNA like chromatin bodies. Further genomic, epigenetic and transcriptomic analysis showed that one TR, named PpNATR76, was located in the intergenic spacer (IGS) region and transcribed into long non-coding RNAs (lncRNAs). Several specific features of PpNATR76 lncRNAs make them very similar with the recently discovered human lncRNAs, raising a number of questions for future studies. This work provides new resources for functional studies of satellitome in plants using the model organism P.patens, and describes a list of tandem repeats for further analysis.

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July 7, 2019

Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35.

The efficient depolymerization and utilization of lignin are one of the most important goals for the renewable use of lignocelluloses. The degradation and complete mineralization of lignin by bacteria represent a key step for carbon recycling in land ecosystems as well. However, many aspects of this process remain unclear, for example, the complex network of metabolic pathways involved in the degradation of lignin and the catabolic pathway of intermediate aromatic metabolites. To address these subjects, we characterized the deconstruction and mineralization of lignin with milled wood lignin (MWL, the most representative molecule of lignin in its native state) and alkali lignin (AL), and elucidated metabolic pathways of their intermediate metabolites by a bacterium named Comamonas serinivorans SP-35.The degradation rate of MWL reached 30.9%, and its particle size range was decreased from 6 to 30 µm to 2-4 µm-when cultured with C. serinivorans SP35 over 7 days. FTIR analysis showed that the C-C and C-O-C bonds between the phenyl propane structures of lignin were oxidized and cleaved and the side chain structure was modified. More than twenty intermediate aromatic metabolites were identified in the MWL and AL cultures based on GC-MS analysis. Through genome sequencing and annotation, and from GC-MS analysis, 93 genes encoding 33 enzymes and 5 regulatory factors that may be involved in lignin degradation were identified and more than nine metabolic pathways of lignin and its intermediates were predicted. Of particular note is that the metabolic pathway to form the powerful antioxidant 3,4-dihydroxyphenylglycol is described for the first time in bacteria.Elucidation of the ß-aryl ether cleavage pathway in the strain SP-35 indicates that the ß-aryl ether catabolic system is not only present in the family of Sphingomonadaceae, but also other species of bacteria kingdom. These newly elucidated catabolic pathways of lignin in strain SP-35 and the enzymes responsible for them provide exciting biotechnological opportunities for lignin valorization in future.

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July 7, 2019

iMGEins: detecting novel mobile genetic elements inserted in individual genomes.

Recent advances in sequencing technology have allowed us to investigate personal genomes to find structural variations, which have been studied extensively to identify their association with the physiology of diseases such as cancer. In particular, mobile genetic elements (MGEs) are one of the major constituents of the human genomes, and cause genome instability by insertion, mutation, and rearrangement.We have developed a new program, iMGEins, to identify such novel MGEs by using sequencing reads of individual genomes, and to explore the breakpoints with the supporting reads and MGEs detected. iMGEins is the first MGE detection program that integrates three algorithmic components: discordant read-pair mapping, split-read mapping, and insertion sequence assembly. Our evaluation results showed its outstanding performance in detecting novel MGEs from simulated genomes, as well as real personal genomes. In detail, the average recall and precision rates of iMGEins are 96.67 and 100%, respectively, which are the highest among the programs compared. In the testing with real human genomes of the NA12878 sample, iMGEins shows the highest accuracy in detecting MGEs within 20?bp proximity of the breakpoints annotated.In order to study the dynamics of MGEs in individual genomes, iMGEins was developed to accurately detect breakpoints and report inserted MGEs. Compared with other programs, iMGEins has valuable features of identifying novel MGEs and assembling the MGEs inserted.

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