Here, we report the isolation, identification, whole-genome sequencing, and annotation of four Bacillus species from internal stem tissue of the insulin plant Costus igneus, grown in Puerto Rico. The plant is of medicinal importance, as extracts from its leaves have been shown to lower blood sugar levels of hyperglycemic rats.
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6113) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.
Sex-specific ecology has management implications, but rapid sex-chromosome turnover in fishes hinders sex-marker development for monomorphic species. We used annotated genomes and reduced-representation sequencing data for two Australian percichthyids, Macquarie perch Macquaria australasica and golden perch M. ambigua, and whole genome resequencing for 50 Macquarie perch of each sex, to identify sex-linked loci and develop an affordable sexing assay. In silico pool-seq tests of 1,492,004 Macquarie perch SNPs revealed that a 275-kb scaffold was enriched for gametologous loci. Within this scaffold, 22 loci were sex-linked in a predominantly XY system, with females being homozygous for the X-linked allele at all 22, and males having the Y-linked allele at >7. Seven XY-gametologous loci (all males, but no females, are heterozygous or homozygous for the male-specific allele) were within a 146-bp region. A PCR-RFLP sexing assay targeting one Y-linked SNP, tested in 66 known-sex Macquarie perch and two of each sex of three confamilial species, plus amplicon sequencing of 400 bp encompassing the 146-bp region, revealed that the few sex-linked positions differ between species and between Macquarie perch populations. This indicates sex-chromosome lability in Percichthyidae, supported by nonhomologous scaffolds containing sex-linked loci for Macquarie- and golden perches. The present resources facilitate genomic research in Percichthyidae, including formulation of hypotheses about candidate genes of interest such as transcription factor SOX1b that occurs in the 275-kb scaffold ~38 kb downstream of the 146-bp region containing seven XY-gametologous loci. Sex-linked markers will be useful for determining genetic sex in some populations and studying sex chromosome turnover.
To date, Ganoderma boninense is known to be the causal agent of basal stem rot (BSR) disease in oil palm (Elaeis guineensis). This disease causes rotting in the roots, basal and upper stem of oil palm. Infection causes progressive destruction of the basal tissues at the oil palm trunk and internal dry rotting, particularly at the intersection between the bole and trunk. Molecular responses of oil palm during infection are not well study although this information is crucial to strategize effective measures to control or eliminate BSR. Here we report three sets of transcriptome data from samples of near-rot section of basal stem tissue of oil palm tree infected with G. boninense (IPIT), healthy section of basal stem tissue of the same G. boninense infected palm (IPHT) and the healthy section of basal stem tissue of the healthy palm (HPHT). The raw reads were deposited into NCBI database and can be accessed via BioProject accession number PRJNA530030.
Wood rot fungi form one of the main classes of phytopathogenic fungus. The group includes many species, but has remained poorly studied. Many species belonging to the Ganoderma genus are well known for causing decay in a wide range of tree species around the world. Ganoderma boninense, causal agent of oil palm basal stem rot, is responsible for considerable yield losses in Southeast Asian oil palm plantations. In a large-scale sampling operation, 357 sporophores were collected from oil palm plantations spread over peninsular Malaysia and Sumatra and genotyped using 11 SSR markers. The genotyping of these samples made it possible to investigate the population structure and demographic history of G. boninense across the oldest known area of interaction between oil palm and G. boninense. Results show that G. boninense possesses a high degree of genetic diversity and no detectable genetic structure at the scale of Sumatra and peninsular Malaysia. The fact that few duplicate genotypes were found in several studies including this one supports the hypothesis of spore dispersal in the spread of G. boninense. Meanwhile, spatial autocorrelation analysis shows that G. boninense is able to disperse across both short and long distances. These results bring new insight into mechanisms by which G. boninense spreads in oil palm plantations. Finally, the use of approximate Bayesian computation (ABC) modelling indicates that G. boninense has undergone a demographic expansion in the past, probably before the oil palm was introduced into Southeast Asia.
The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.
Cutaneous T-cell lymphomas (CTCLs) are a group of T-cell lymphomas with low incidence. Due to their indolent characteristics, treatment strategies have not yet been established for advanced CTCLs. In this study, relative incidence of CTCLs in Asia was estimated and the therapeutic outcomes presented based on various treatments currently used in clinics for advanced CTCLs. As part of a prospective registry study of peripheral T-cell lymphoma (PTCL) conducted across Asia, including Korea, China, Taiwan, Singapore, Malaysia, and Indonesia, subgroup analysis was performed for patients with CTCLs. Among 486 patients with PTCL, 37 with CTCL (7.6%) were identified between April 2016 and February 2019. Primary cutaneous ALK-negative anaplastic large cell lymphoma (ALCL, 35.1%) was the most common subtype. With a median follow-up period of 32.1 months, median progression-free survival (PFS) was 53.5 months (95% CI 0.0-122.5), and overall survival was not reached. 14 patients (48.2%) underwent subsequent treatment after the first relapse, but the response rate was 20% with a PFS of 2.2 months (95% CI 0.3-4.0). Six patients received autologous stem cell transplantation (auto-SCT). However, auto-SCT did not result in better outcomes. Additional studies are needed on standard care treatment of advanced or refractory and relapsed CTCLs.
Diversifying selection between populations that inhabit different environments can promote lineage divergence within species and ultimately drive speciation. The mitochondrial genome (mitogenome) encodes essential proteins of the oxidative phosphorylation (OXPHOS) system and can be a strong target for climate-driven selection (i.e., associated with inhabiting different climates). We investigated whether Pleistocene climate changes drove mitochondrial selection and evolution within Australian birds. First, using phylogeographic analyses of the mitochondrial ND2 gene for 17 songbird species, we identified mitochondrial clades (mitolineages). Second, using distance-based redundancy analyses, we tested whether climate predicts variation in intraspecific genetic divergence beyond that explained by geographic distances and geographic position. Third, we analysed 41 complete mitogenome sequences representing each mitolineage of 17 species using codon models in a phylogenetic framework and a biochemical approach to identify signals of selection on OXPHOS protein-coding genes and test for parallel selection in mitolineages of different species existing in similar climates. Of 17 species examined, 13 had multiple mitolineages (range: 2-6). Climate was a significant predictor of mitochondrial variation in eight species. At least two amino acid replacements in OXPHOS complex I could have evolved under positive selection in specific mitolineages of two species. Protein homology modelling showed one of these to be in the loop region of the ND6 protein channel and the other in the functionally critical helix HL region of ND5. These findings call for direct tests of the functional and evolutionary significance of mitochondrial protein candidates for climate-associated selection.
We report here the first high-quality draft genome sequence of Pasteurella multocida sequence type 128, which was isolated from the infected finger bone of an adult female who was bitten by a domestic dog. The draft genome will be a valuable addition to the scarce genomic resources available for P. multocida.
Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm.
Acetamide (CH3CONH2) is the largest molecule containing an amide bond that has been detected in an interstellar medium; it is considered to be a precursor for complex organic molecules (COM). We utilized the advantages of a para-hydrogen (p-H2) quantum-solid matrix host to perform efficient reactions of hydrogen atoms with CH3CONH2. The H-abstraction reaction from the methyl group of CH3CONH2 to produce the 2-amino-2-oxoethyl radical, ˙CH2CONH2, was observed as the sole reaction channel in solid p-H2 at 3.3 K, consistent with theoretical predictions that this reaction has the smallest barrier among all possible channels. Our results show that the amide bond of acetamide is unaffected by hydrogen exposure, but the hydrogen abstraction activates this molecule to react with other species on its methyl site to extend its size or to include other functional groups as a first step to form COM under prebiotic or abiotic conditions. This previously neglected path should be considered in the astrochemical modeling. The photolysis of ˙CH2CONH2 at wavelengths 380-450 nm produces ketene; this step might provide a plausible mechanism to explain the anti-correlated abundance of ketene and acetamide in some astronomical observations.
Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.
The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.
The mitochondrial genome of the rock pool prawn (Palaemon serenus), is sequenced, making it the third for genera of the family Palaemonidae and the first for the genus Palaemon. The mitogenome is 15,967 base pairs in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The P. serenus mitogenome has an AT bias of 58.97% and a base composition of 29.79% for T, 24.14% for C, 29.18% for A, and 16.89% for G. The mitogenome gene order of P. serenus is identical to Exopalaemon carinicauda.
The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.
The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.
The clawed lobster Nephrops norvegicus is an important commercial species in European waters. We have sequenced the complete mitochondrial genome of the species from a partial genome scan using Next-Gen sequencing. The N. norvegicus has a mitogenome of 16,132 base pairs (71.22% A+ T content) comprising 13 protein-coding genes, 2 ribosomal subunit genes, 21 transfer RNAs, and a putative 1259 bp non-coding AT-rich region. This mitogenome is the second fully characterized for the family Nephropidae and the first for the genus Nephrops. The mitogenome gene order is identical to the Maine lobster, Homarus americanus with the exception of the possible loss of the trnI gene.
The invasive freshwater crayfish Orconectes limosus mitogenome was recovered by genome skimming. The mitogenome is 16,223 base pairs in length consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The O. limosus mitogenome has an AT bias of 71.37% and base composition of 39.8% for T, 10.3% for C, 31.5% for A, and 18.4% for G. The mitogene order is identical to two other genera of northern hemisphere crayfish that have been sequenced for this organelle.
The mitogenome of the Australian freshwater blackfish, Gadopsis marmoratus was recovered coverage by genome skimming using the MiSeq sequencer (GenBank Accession Number: NC_024436). The blackfish mitogenome has 16,407 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the 5th mitogenome sequence to be reported for the family Percichthyidae.
The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compared with other Triops species. Triops australiensis has a mitochondrial genome of 15,125 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The T. australiensis mitogenome is composed of 36.4% A, 16.1% C, 12.3% G and 35.1% T. The mitogenome gene order conforms to the primitive arrangement for Branchiopod crustaceans, which is also conserved within the Pancrustacean.