scholarly journals A high-resolution genome of an euryhaline and eurythermal rhinogoby (Rhinogobius similis Gill 1895)

Author(s):  
Yun Hu ◽  
Liang Lu ◽  
Tao Zhou ◽  
Kishor Kumar Sarker ◽  
Junman Huang ◽  
...  

Abstract Rhinogobius similis is distributed in East and Southeast Asia. It is an amphidromous species found mostly in freshwater and sometimes brackish waters. We have obtained a high-resolution assembly of the R. similis genome using nanopore sequencing, high throughput chromosome conformation capture (Hi-C) and transcriptomic data. The assembled genome was 890.10 Mb in size and 40.15% in GC content. Including 1,373 contigs with contig N50 is 1.54 Mb, and scaffold N50 is 41.51 Mb. All of the 1,373 contigs were anchored on 22 pairs of chromosomes. The BUSCO evaluation score was 93.02% indicating high quality of genome assembly. The repeat sequences accounted for 34.92% of the whole genome, with Retroelements (30.13%), DNA transposons (1.64%), simple repeats (2.34%) and etc. A total of 31,089 protein-coding genes were predicted in the genome and functionally annotated using Maker, of those genes, 26,893 (86.50%) were found in InterProScan5. There were 1,910 gene families expanded in R. similis, 1,171 gene families contracted and 170 gene families rapidly evolving. We have compared one rapidly change gene family (PF05970) commonly found in four species (Boleophthalmus pectinirostris, Neogobius melanostomus, Periophthalmus magnuspinnatus and R. similis), which was found probably related to the lifespan of those species. During 400 Ka-10 Ka, the period of the Guxiang Ice Age, the population of R. similis decreased drastically, and then increased gradually following the last interglacial period. A high-resolution genome of R. similis should be useful to study taxonomy, biogeography, comparative genomics and adaptive evolution of the most speciose freshwater goby genus, Rhinogobius.

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Xyrus X. Maurer-Alcalá ◽  
Rob Knight ◽  
Laura A. Katz

ABSTRACTSeparate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences. Most studies of germline genome architecture in ciliates have focused on the model ciliatesOxytricha trifallax,Paramecium tetraurelia, andTetrahymena thermophila, for which the complete germline genome sequences are known. Outside of these model taxa, only a few dozen germline loci have been characterized from a limited number of cultivable species, which is likely due to difficulties in obtaining sufficient quantities of “purified” germline DNA in these taxa. Combining single-cell transcriptomics and genomics, we have overcome these limitations and provide the first insights into the structure of the germline genome of the ciliateChilodonella uncinata, a member of the understudied classPhyllopharyngea. Our analyses reveal the following: (i) large gene families contain a disproportionate number of genes from scrambled germline loci; (ii) germline-soma boundaries in the germline genome are demarcated by substantial shifts in GC content; (iii) single-cell omics techniques provide large-scale quality germline genome data with limited effort, at least for ciliates with extensively fragmented somatic genomes. Our approach provides an efficient means to understand better the evolution of genome rearrangements between germline and soma in ciliates.IMPORTANCEOur understanding of the distinctions between germline and somatic genomes in ciliates has largely relied on studies of a few model genera (e.g.,Oxytricha,Paramecium,Tetrahymena). We have used single-cell omics to explore germline-soma distinctions in the ciliateChilodonella uncinata, which likely diverged from the better-studied ciliates ~700 million years ago. The analyses presented here indicate that developmentally regulated genome rearrangements between germline and soma are demarcated by rapid transitions in local GC composition and lead to diversification of protein families. The approaches used here provide the basis for future work aimed at discerning the evolutionary impacts of germline-soma distinctions among diverse ciliates.


2018 ◽  
Author(s):  
Rajasri Ray ◽  
T V Ramachandra ◽  
Avik Ray

The climatic shifts in the Quaternary Period acted as an important driving force for evolution of the world's biodiversity. In this study, responses to the ice age of a rare and endangered tree of Indian Western Ghats, Syzygium travancoricum, was investigated through a combination of molecular data and ecological niche modeling.Results indicate the moderate (nrDNA) to high (cpDNA) population structure, presence of private alleles, and absence of phylogeographic structure. Spatial distribution of diversity does not signifi- cantly support southern colonisation, nor the Palghat Gap as a geographical barrier based on the genetic structure. Combined insights from Ecological Niche Modelling and population history de- picts a probable colonisation of the Western Ghats in the late Miocene or later followed by a split into separate southern and northern populations from the middle to late Pleistocene. The prevalence of favourable conditions in the post-Last interglacial period stimulated rapid population expansion and a very recent decline. The absence of phylogeographic structure and overall climatic stability from Last Interglacial do not offer support to an existence of refugia in the Western Ghats. We con- clude by discussing appropriate conservation measures for this rare and endangered tree based on our findings.


GigaScience ◽  
2019 ◽  
Vol 8 (8) ◽  
Author(s):  
Lu Wang ◽  
Jinwei Wu ◽  
Xiaomei Liu ◽  
Dandan Di ◽  
Yuhong Liang ◽  
...  

Abstract Background The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered colobine species endemic to China, which has several distinct traits including a unique social structure. Although a genome assembly for R. roxellana is available, it is incomplete and fragmented because it was constructed using short-read sequencing technology. Thus, important information such as genome structural variation and repeat sequences may be absent. Findings To obtain a high-quality chromosomal assembly for R. roxellana qinlingensis, we used 5 methods: Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, BioNano optical maps, 10X Genomics link-reads, and high-throughput chromosome conformation capture. The assembled genome was ∼3.04 Gb, with a contig N50 of 5.72 Mb and a scaffold N50 of 144.56 Mb. This represented a 100-fold improvement over the previously published genome. In the new genome, 22,497 protein-coding genes were predicted, of which 22,053 were functionally annotated. Gene family analysis showed that 993 and 2,745 gene families were expanded and contracted, respectively. The reconstructed phylogeny recovered a close relationship between R. rollexana and Macaca mulatta, and these 2 species diverged ∼13.4 million years ago. Conclusion We constructed a high-quality genome assembly of the Qinling golden snub-nosed monkey; it had superior continuity and accuracy, which might be useful for future genetic studies in this species and as a new standard reference genome for colobine primates. In addition, the updated genome assembly might improve our understanding of this species and could assist conservation efforts.


1988 ◽  
Vol 10 ◽  
pp. 199-200 ◽  
Author(s):  
J.M. Barnola ◽  
C. Genthon ◽  
D. Raynaud ◽  
J. Jouzel ◽  
Ye.S. Korotkevich ◽  
...  

This is a summary of the main CO2 results obtained from the Vostok core which have been presented in two papers recently published (Barnola and others 1987; Genthon and others 1987). Previous results of ice-core analysis have already provided valuable information on atmospheric CO2 variations associated with anthropogenic activities (Neftel and others 1985, Raynaud and Barnola 1985[a], Pearman and others 1986) and with climatic variations back to about 40 ka ago (Delmas and others 1980, Neftel and others 1982, Raynaud and Barnola 1985[b]). The Antarctic Vostok ice core provides a unique opportunity for extending the ice record of atmospheric CO2 variations over the last glacial–interglacial cycle back to the end of the penultimate ice age, about 160 ka ago. CO2 measurements were made at 66 different depth levels on the air enclosed in the 2083 m long core taken at Vostok Station. The air was extracted by crushing the ice, under vacuum, in a cold-room, and analysed by gas chromatography (Barnola and others 1983). The selected sampling corresponds to a time resolution between two neighbouring levels which range approximately from 2000 to 4500 years. The ages quoted in this abstract are based on the Vostok ice chronology given by Lorius and others (1985) and take into account the fact that the air is trapped in the firn well after snow deposition (between about 2500 and 4300 years after precipitation in the case of Vostok). The CO2 variations observed are compared directly with the changes in Antarctic temperature as depicted by the stable-isotope record of the Vostok ice (Jouzel and others 1988, this volume). Furthermore, a CO2-orbital forcing-climate interaction is suggested by spectral analysis of the CO2 and temperature profiles, which both show a concentration of variance around orbital frequencies. The temperature profile is clearly dominated by a 40 ka period (which can be related to the obliquity frequency) (Jouzel and others 1988, this volume), whereas the CO2 record exhibits a well-defined 21 ka peak (which can be related to the precession frequencies) and only a weak and doubtful 40 ka peak. To check the relative influence of CO2 and orbital forcings on the temperature at Vostok, we modelled the temperature signal deduced from the stable-isotope record of the ice as a response to CO2, Northern Hemisphere ice volume and local insolation forcings. The results indicate that more than 90% of the temperature variance can be explained by these three kinds of forcing and that the contribution of the CO2 radiative effect associated with an amplification factor (which should reflect the long-term feed-back mechanisms) lies between 27 and 85% of the explained variance. This approach stresses the important role that CO2 may generally have played in determining the Earth’s climate during the late Pleistocene. The most obvious feature of the Vostok CO2 record lies in its high correlation (r2 = 0.79) with the climatic record. The results obtained show high CO2 concentrations during warm periods (mean CO2 values of 263 ppm volume for the Holocene and 272 ppm volume for the last interglacial period) and low concentrations (between about 240 and 190 ppm volume) over glacial periods. Within the last glaciation, the CO2 concentrations are higher during the first part (mean CO2 value of 230 ppm volume between about 110–65 ka B.P.) than during the second part (203 ppm volume between 65–15 ka B.P.); the second part also indicates that climatic conditions were colder. Our results point to some limitation on the possible mechanisms driving the atmospheric CO2 variations and, in particular, the influence of some oceanic areas or of changes in sea-level (see, for example, Broecker and Peng 1986). The weak 41 ka cycle (this cycle seems to be a characteristic of the spectra of the proxy data for high latitudes) in our CO2 record suggests that high latitudes may not have a major influence on CO2 variations. Furthermore, the phase relationship between CO2 and the temperature variations indicates that at the beginning of the two deglaciations around 145ka B.P. and 15ka B.P., taking into account the time resolution of our profile, the CO2 increases roughly in phase with the Vostok temperature. As surface-temperature changes around Antarctica are expected to lead to changes in sea-level (see, for instance, CLIMAP Project Members 1984), our results suggest that the CO2 increase cannot lag the increase in sea-level and thus that this parameter cannot initiate the CO2 variation recorded at the beginning of those two deglaciations. Nevertheless, this does not rule out influence of variations in sea-level on atmospheric CO2 for other periods of interest, in particular during the last interglacial–glacial transition, where the CO2 lags the Vostok temperature.


1979 ◽  
Vol 34 (1) ◽  
pp. 43-49 ◽  
Author(s):  
C. Villarroel ◽  
K. Graf

Abstract. The town of La Paz is situated between the Bolivian Highland (Altiplano) and the Central Mountain Range. These two landscape units were mostly formed during the Tertiary. But at their intermediate bordering zone, geomorphological forms have 'later been reshaped. At the end of the Pliocene, a peneplain was formed (the Altiplano of today) and got covered by volcanic ashes. Since the fossilization of mammals (Posnanskytherium) in the late Pliocene, a tektonical uplift of about 3300 ft. has taken place, and huge moraines built up covering the whole city area of today. The enormous La Paz Valley was eroded above all during the last interglacial period. During the last ice age, the glaciers reached the present upper city border only and melted away very rapidly 9800 years ago at the latest.


Author(s):  
Xinghua Lin ◽  
Yang Huang ◽  
Dongneng Jiang ◽  
Huapu Chen ◽  
Siping Deng ◽  
...  

Abstract Silver sillago, Sillago sihama is a member of the family Sillaginidae and found in all Chinese inshore waters. It is an emerging commercial marine aquaculture species in China. In this study, high-quality chromosome-level reference genome of S. sihama was first constructed using PacBio Sequel sequencing and high-throughput chromosome conformation capture (Hi-C) technique. A total of 66.16 Gb clean reads were generated by PacBio sequencing platforms. The genome-scale was 521.63 Mb with 556 contigs, and 13.54 Mb of contig N50 length. Additionally, Hi-C scaffolding of the genome resulted in 24 chromosomes containing 96.93% of the total assembled sequences. A total of 23,959 protein-coding genes were predicted in the genome, and 96.51% of the genes were functionally annotated in public databases. A total of 71.86 Mb repetitive elements were detected, accounting for 13.78% of the genome. The phylogenetic relationships of silver sillago with other teleosts showed that silver sillago was separated from the common ancestor of S. sinica about 7.92 million years ago. Comparative genomic analysis of silver sillago with other teleosts showed that 45 unique and 100 expansion gene families were identified in silver sillago. In this study, the genomic resources provide valuable reference genomes for functional genomics research of silver sillago.


2020 ◽  
Vol 13 (5) ◽  
pp. 2337-2354
Author(s):  
Tristan Vadsaria ◽  
Laurent Li ◽  
Gilles Ramstein ◽  
Jean-Claude Dutay

Abstract. Recently, major progress has been made in the simulation of the ocean dynamics of the Mediterranean using atmospheric and oceanic models with high spatial resolution. High resolution is essential to accurately capture the synoptic variability required to initiate intermediate- and deep-water formation, the engine of the Mediterranean thermohaline circulation (MTC). In paleoclimate studies, one major problem with the simulation of regional climate changes is that boundary conditions are not available from observations or data reconstruction to drive high-resolution regional models. One consistent way to advance paleoclimate modelling is to use a comprehensive global-to-regional approach. However, this approach needs long-term integration to reach equilibrium (hundreds of years), implying enormous computational resources. To tackle this issue, a sequential architecture of a global–regional modelling platform has been developed for the first time and is described in detail in this paper. First of all, the platform is validated for the historical period. It is then used to investigate the climate and in particular, the oceanic circulation, during the Early Holocene. This period was characterised by a large reorganisation of the MTC that strongly affected oxygen supply to the intermediate and deep waters, which ultimately led to an anoxic crisis (called sapropel). Beyond the case study shown here, this platform may be applied to a large number of paleoclimate contexts from the Quaternary to the Pliocene, as long as regional tectonics remain mostly unchanged. For example, the climate responses of the Mediterranean basin during the last interglacial period (LIG), the Last Glacial Maximum (LGM) and the Late Pliocene all present interesting scientific challenges which may be addressed using this numerical platform.


2020 ◽  
Vol 40 (4) ◽  
pp. 390-400 ◽  
Author(s):  
Werner P Veldsman ◽  
Yaqin Wang ◽  
Jiaojiao Niu ◽  
J Antonio Baeza ◽  
Ka Hou Chu

Abstract We present a full description and analysis of the complete mitochondrial genome of a Pacific Ocean specimen of the coconut crab Birgus latro (Linnaeus, 1767), the largest extant terrestrial arthropod in the world. Our de novo-assembled mitogenome has a massive 16,161 times organelle read coverage, a length of 16,411 bp, contains 22 tDNAs (20 unique), 13 protein-coding genes, two rDNAs, and a putative control region of length 1,381 bp. The control region contains three microsatellites and two pairs of inverted repeats. Contrary to the mitochondrial sentinel gene concept, two-dimensional nucleotide analysis reveals higher GC-content in cox gene families than in nadh gene families. Moreover, cox gene families are more conserved than nadh gene families among the species of Coenobitidae selected for comparison. Secondary structure prediction of the 22 tDNAs shows major deviations from the cloverleaf pattern, which points to a relatively high rate of mutation in these genes. We also present a repertoire of mitochondrial variation between our male Okinawan coconut crab and an Indian Ocean specimen that consists of one insertion, one deletion, 135 SNPs, three MNPs and nine complex polymorphisms. We provide confirmatory evidence that the superfamily Paguroidea, to which the coconut crab belongs, is polyphyletic, that all the protein-coding genes of B. latro are under purifying selection, and that a Pacific versus Indian Ocean coconut crab population divergence occurred during the Pleistocene.


GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Fanming Meng ◽  
Zhuoying Liu ◽  
Han Han ◽  
Dmitrijs Finkelbergs ◽  
Yangshuai Jiang ◽  
...  

Abstract Background Blowflies (Diptera: Calliphoridae) are the most commonly found entomological evidence in forensic investigations. Distinguished from other blowflies, Aldrichina grahami has some unique biological characteristics and is a species of forensic importance. Its development rate, pattern, and life cycle can provide valuable information for the estimation of the minimum postmortem interval. Findings Herein we provide a chromosome-level genome assembly of A. grahami that was generated by Pacific BioSciences sequencing platform and chromosome conformation capture (Hi-C) technology. A total of 50.15 Gb clean reads of the A. grahami genome were generated. FALCON and Wtdbg were used to construct the genome of A. grahami, resulting in an assembly of 600 Mb and 1,604 contigs with an N50 size of 1.93 Mb. We predicted 12,823 protein-coding genes, 99.8% of which was functionally annotated on the basis of the de novo genome (SRA: PRJNA513084) and transcriptome (SRA: SRX5207346) of A. grahami. According to the co-analysis with 11 other insect species, clustering and phylogenetic reconstruction of gene families were performed. Using Hi-C sequencing, a chromosome-level assembly of 6 chromosomes was generated with scaffold N50 of 104.7 Mb. Of these scaffolds, 96.4% were anchored to the total A. grahami genome contig bases. Conclusions The present study provides a robust genome reference for A. grahami that supplements vital genetic information for nonhuman forensic genomics and facilitates the future research of A. grahami and other necrophagous blowfly species used in forensic medicine.


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