共查询到20条相似文献，搜索用时 0 毫秒
1.
Qian Zhou Haoyang Gao Yong Zhang Guangyi Fan Hao Xu Jieming Zhai Wenteng Xu Zhangfan Chen He Zhang Shanshan Liu Yipeng Niu Wensheng Li Weiming Li Haoran Lin Songlin Chen 《Molecular ecology resources》2019,19(5):1322-1332
The giant grouper (Epinephelus lanceolatus) is the largest coral reef teleost, with a native range that spans temperate and tropical waters in the Pacific and the Indian Oceans. It is cultured artificially and used as a breeding species in aquaculture due to its rapid growth rate. Here we report a giant grouper genome assembled at the chromosome scale from sequences generated using Illumina and high‐throughput chromatin conformation capture (Hi‐C) technology. The assembly comprised 1.086 Gb, with 98.4% of the scaffold sequences anchored into 24 chromosomes. The contig and scaffold N50 values were 119.9 kb and 46.2 Mb, respectively. The assembly is of high integrity, including 96.4% universal single‐copy orthologues based on BUSCO analysis. Through chromosome‐scale evolution analysis, we identified alignments of six giant grouper chromosomes to three stickleback chromosomes and some of the genes located within the breakpoints of reshuffling events may related to development and growth. From the 24,718 protein‐coding genes, we found that several gene families related to innate immunity and glycan biosynthesis were significantly expanded in the giant grouper genome compared to other teleost genomes. In addition, we identified several genes related to the hormone signalling pathway and innate immunity that have experienced positive selection or accelerated evolution, implicating their roles in immune defence and fast growth of the species. The high‐quality genome assembly will provide a valuable genomic resource for further biological and evolutionary studies, and useful genomic tools for breeding of the giant grouper. 相似文献
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Aleksey V Zimin Alaina Shumate Ida Shinder Jakob Heinz Daniela Puiu Mihaela Pertea Steven L Salzberg 《Genetics》2022,220(2)
Until 2019, the human genome was available in only one fully annotated version, GRCh38, which was the result of 18 years of continuous improvement and revision. Despite dramatic improvements in sequencing technology, no other genome was available as an annotated reference until 2019, when the genome of an Ashkenazi individual, Ash1, was released. In this study, we describe the assembly and annotation of a second individual genome, from a Puerto Rican individual whose DNA was collected as part of the Human Pangenome project. The new genome, called PR1, is the first true reference genome created from an individual of African descent. Due to recent improvements in both sequencing and assembly technology, and particularly to the use of the recently completed CHM13 human genome as a guide to assembly, PR1 is more complete and more contiguous than either GRCh38 or Ash1. Annotation revealed 37,755 genes (of which 19,999 are protein coding), including 12 additional gene copies that are present in PR1 and missing from CHM13. Fifty-seven genes have fewer copies in PR1 than in CHM13, 9 map only partially, and 3 genes (all noncoding) from CHM13 are entirely missing from PR1. 相似文献
4.
Stefano Lonardi María Muoz‐Amatriaín Qihua Liang Shengqiang Shu Steve I. Wanamaker Sassoum Lo Jaakko Tanskanen Alan H. Schulman Tingting Zhu Ming‐Cheng Luo Hind Alhakami Rachid Ounit Abid Md. Hasan Jerome Verdier Philip A. Roberts Jansen R.P. Santos Arsenio Ndeve Jaroslav Doleel Jan Vrna Samuel A. Hokin Andrew D. Farmer Steven B. Cannon Timothy J. Close 《The Plant journal : for cell and molecular biology》2019,98(5):767-782
Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single‐molecule real‐time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination‐poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high‐recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS‐LRR and the SAUR‐like auxin superfamilies compared with other warm‐season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented. 相似文献
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Philipp E. Bayer Bhavna Hurgobin Agnieszka A. Golicz Chon‐Kit Kenneth Chan Yuxuan Yuan HueyTyng Lee Michael Renton Jinling Meng Ruiyuan Li Yan Long Jun Zou Ian Bancroft Boulos Chalhoub Graham J. King Jacqueline Batley David Edwards 《Plant biotechnology journal》2017,15(12):1602-1610
As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor‐bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor‐bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome. 相似文献
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超级杂交稻父本‘93-11＇的基因组序列测定的完成,为进行作物遗传改良和不同作物之间的比较基因组学研究提供了又一重要序列资源.但是,该基因组序列中还存在很多“缺口”,为使‘93-11＇的基因组序列更加精确,同时提供一些“缺口”填补策略和方法,本研究采用PCR扩增、回收克隆测序的方法对该基因组中一段长约160 kb、含有6个“缺口”的基因组序列进行了完善,并运用相关分子生物学和生物信息学软件进行了详细分析,结果表明：该6个“缺口”中,存在1个“缺口”估计错误,2个序列拼接错误;“缺口”主要位于非编码区,位于编码区的只有1个,其改变了对本处基因的注释,使此基因由原来的9个外显子增加为11个;填补“缺口”后,基因密度增加. 相似文献
9.
Vanessa Messmer Morgan S. Pratchett Andrew S. Hoey Andrew J. Tobin Darren J. Coker Steven J. Cooke Timothy D. Clark 《Global Change Biology》2017,23(6):2230-2240
Global warming is expected to reduce body sizes of ectothermic animals. Although the underlying mechanisms of size reductions remain poorly understood, effects appear stronger at latitudinal extremes (poles and tropics) and in aquatic rather than terrestrial systems. To shed light on this phenomenon, we examined the size dependence of critical thermal maxima (CTmax) and aerobic metabolism in a commercially important tropical reef fish, the leopard coral grouper (Plectropomus leopardus) following acclimation to current‐day (28.5 °C) vs. projected end‐of‐century (33 °C) summer temperatures for the northern Great Barrier Reef (GBR). CTmax declined from 38.3 to 37.5 °C with increasing body mass in adult fish (0.45–2.82 kg), indicating that larger individuals are more thermally sensitive than smaller conspecifics. This may be explained by a restricted capacity for large fish to increase mass‐specific maximum metabolic rate (MMR) at 33 °C compared with 28.5 °C. Indeed, temperature influenced the relationship between metabolism and body mass (0.02–2.38 kg), whereby the scaling exponent for MMR increased from 0.74 ± 0.02 at 28.5 °C to 0.79 ± 0.01 at 33 °C, and the corresponding exponents for standard metabolic rate (SMR) were 0.75 ± 0.04 and 0.80 ± 0.03. The increase in metabolic scaling exponents at higher temperatures suggests that energy budgets may be disproportionately impacted in larger fish and contribute to reduced maximum adult size. Such climate‐induced reductions in body size would have important ramifications for fisheries productivity, but are also likely to have knock‐on effects for trophodynamics and functioning of ecosystems. 相似文献
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Courtney P. Leisner John P. Hamilton Emily Crisovan Norma C. Manrique‐Carpintero Alexandre P. Marand Linsey Newton Gina M. Pham Jiming Jiang David S. Douches Shelley H. Jansky C. Robin Buell 《The Plant journal : for cell and molecular biology》2018,94(3):562-570
Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self‐compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825 767 562 bp in 8260 scaffolds with an N50 scaffold size of 713 602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49 124 high‐confidence gene models representing 37 740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158 367 Solanaceae genes and 1897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome‐enabled development of inbred diploid potatoes with the potential to accelerate potato breeding. 相似文献
11.
Samuel D. Payet Jake R. Lowe Bruce D. Mapstone Morgan S. Pratchett Tane H. Sinclair-Taylor Brett M. Taylor Peter A. Waldie Hugo B. Harrison 《Journal of fish biology》2020,97(4):1165-1176
Understanding the spatial and environmental variation in demographic processes of fisheries target species, such as coral grouper (Genus: Plectropomus), is important for establishing effective management and conservation strategies. Herein we compare the demography of Plectropomus leopardus and P. laevis between Australia's Great Barrier Reef Marine Park (GBRMP), which has been subject to sustained and extensive fishing pressure, and the oceanic atolls of Australia's Coral Sea Marine Park (CSMP), where there is very limited fishing for reef fishes. Coral grouper length-at-age data from contemporary and historical otolith collections across 9.4 degrees of latitude showed little difference in lifetime growth between GBRMP and CSMP regions. Plectropomus laevis populations in GBRMP reefs had significantly higher rates of total mortality than populations in the CSMP. Mean maximum lengths and mean maximum ages of P. laevis were also smaller in the GBRMP than in the CSMP, even when considering populations sampled within GBRMP no-take marine reserves (NTMRs). Plectropomus leopardus, individuals were on average smaller on fished reefs than NTMRs in the GBRMP, but all other aspects of demography were broadly similar between regions despite the negligible levels of fishing pressure in the CSMP. Similarities between regions in growth profiles and length-at-age comparisons of P. laevis and P. leopardus suggest that the environmental differences between the CSMP and the GBRMP may not have significant impacts on lifetime growth. Our results show that fishing may have influenced the demography of coral grouper on the GBR, particularly for the slower growing and longer lived species, P. laevis. 相似文献
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Yuwei Han Weixiong Zhang Botong Zhou Peng Zeng Zunzhe Tian Jing Cai 《Molecular ecology resources》2022,22(1):391-403
Welwitschia mirabilis, which is endemic to the Namib Desert, is the only living species within the family Welwitschiaceae. This species has an extremely long lifespan of up to 2,000 years and bears a single pair of opposite leaves that persist whilst alive. However, the underlying genetic mechanisms and evolution of the species remain poorly elucidated. Here, we report on a chromosome-level genome assembly for W. mirabilis, with a 6.30-Gb genome sequence and contig N50 of 27.50 Mb. In total, 39,019 protein-coding genes were predicted from the genome. Two brassinosteroid-related genes (BRI1 and CYCD3), key regulators of cell division and elongation, were strongly selected in W. mirabilis and may contribute to their long ever-growing leaves. Furthermore, 29 gene families in the mitogen-activated protein kinase signalling pathway showed significant expansion, which may contribute to the desert adaptations of the plant. Three positively selected genes (EHMT1, EIF4E, SOD2) may be involved in the mechanisms leading to long lifespan. Based on molecular clock dating and fossil calibrations, the divergence time of W. mirabilis and Gnetum montanum was estimated at ~123.5 million years ago. Reconstruction of population dynamics from genome data coincided well with the aridification of the Namib Desert. The genome sequence detailed in the current study provides insight into the evolution of W. mirabilis and should be an important resource for further study on gnetophyte and gymnosperm evolution. 相似文献
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Lijuan Zhang Song Li Junyu Luo Pei Du Linke Wu Yarong Li Xiangzhen Zhu Li Wang Shuai Zhang Jinjie Cui 《Molecular ecology resources》2020,20(1):292-307
The ladybird beetle Propylea japonica is an important natural enemy in agro‐ecological systems. Studies on the strong tolerance of P. japonica to high temperatures and insecticides, and its population and phenotype diversity have recently increased. However, abundant genome resources for obtaining insights into stress‐resistance mechanisms and genetic intra‐species diversity for P. japonica are lacking. Here, we constructed the P. japonica genome maps using Pacific Bioscience (PacBio) and Illumina sequencing technologies. The genome size was 850.90 Mb with a contig N50 of 813.13 kb. The Hi‐C sequence data were used to upgrade draft genome assemblies; 4,777 contigs were assembled to 10 chromosomes; and the final draft genome assembly was 803.93 Mb with a contig N50 of 813.98 kb and a scaffold N50 of 100.34 Mb. Approximately 495.38 Mb of repeated sequences was annotated. The 18,018 protein‐coding genes were predicted, of which 95.78% were functionally annotated, and 1,407 genes were species‐specific. The phylogenetic analysis showed that P. japonica diverged from the ancestor of Anoplophora glabripennis and Tribolium castaneum ~ 236.21 million years ago. We detected that some important gene families involved in detoxification of pesticides and tolerance to heat stress were expanded in P. japonica, especially cytochrome P450 and Hsp70 genes. Overall, the high‐quality draft genome sequence of P. japonica will provide invaluable resource for understanding the molecular mechanisms of stress resistance and will facilitate the research on population genetics, evolution and phylogeny of Coccinellidae. This genome will also provide new avenues for conserving the diversity of predator insects. 相似文献
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J. L. Johansen V. Messmer D. J. Coker A. S. Hoey M. S. Pratchett 《Global Change Biology》2014,20(4):1067-1074
Large‐bodied fish are critical for sustaining coral reef fisheries, but little is known about the vulnerability of these fish to global warming. This study examined the effects of elevated temperatures on the movement and activity patterns of the common coral trout Plectropomus leopardus (Serranidae), which is an important fishery species in tropical Australia and throughout the Indo West‐Pacific. Adult fish were collected from two locations on Australia's Great Barrier Reef (23°S and 14°S) and maintained at one of four temperatures (24, 27, 30, 33 °C). Following >4 weeks acclimation, the spontaneous swimming speeds and activity patterns of individuals were recorded over a period of 12 days. At 24–27 °C, spontaneous swimming speeds of common coral trout were 0.43–0.45 body lengths per second (bls?1), but dropped sharply to 0.29 bls?1 at 30 °C and 0.25 bls?1 at 33 °C. Concurrently, individuals spent 9.3–10.6% of their time resting motionless on the bottom at 24–27 °C, but this behaviour increased to 14.0% at 30 °C and 20.0% of the time at 33 °C (mean ± SE). The impact of temperature was greatest for smaller individuals (<45 cm TL), showing significant changes to swimming speeds across every temperature tested, while medium (45–55 cm TL) and large individuals (>55 cm TL) were first affected by 30 °C and 33 °C, respectively. Importantly, there was some indication that populations can adapt to elevated temperature if presented with adequate time, as the high‐latitude population decreased significantly in swimming speeds at both 30 °C and 33 °C, while the low‐latitude population only showed significant reductions at 33 °C. Given that movement and activity patterns of large mobile species are directly related to prey encounter rates, ability to capture prey and avoid predators, any reductions in activity patterns are likely to reduce overall foraging and energy intake, limit the energy available for growth and reproduction, and affect the fitness and survival of individuals and populations. 相似文献
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Filip Wierzbicki Florian Schwarz Odontsetseg Cannalonga Robert Kofler 《Molecular ecology resources》2022,22(1):102-121
In most animals, it is thought that the proliferation of a transposable element (TE) is stopped when the TE jumps into a piRNA cluster. Despite this central importance, little is known about the composition and the evolutionary dynamics of piRNA clusters. This is largely because piRNA clusters are notoriously difficult to assemble as they are frequently composed of highly repetitive DNA. With long reads, we may finally be able to obtain reliable assemblies of piRNA clusters. Unfortunately, it is unclear how to generate and identify the best assemblies, as many assembly strategies exist and standard quality metrics are ignorant of TEs. To address these problems, we introduce several novel quality metrics that assess: (a) the fraction of completely assembled piRNA clusters, (b) the quality of the assembled clusters and (c) whether an assembly captures the overall TE landscape of an organisms (i.e. the abundance, the number of SNPs and internal deletions of all TE families). The requirements for computing these metrics vary, ranging from annotations of piRNA clusters to consensus sequences of TEs and genomic sequencing data. Using these novel metrics, we evaluate the effect of assembly algorithm, polishing, read length, coverage, residual polymorphisms and finally identify strategies that yield reliable assemblies of piRNA clusters. Based on an optimized approach, we provide assemblies for the two Drosophila melanogaster strains Canton-S and Pi2. About 80% of known piRNA clusters were assembled in both strains. Finally, we demonstrate the generality of our approach by extending our metrics to humans and Arabidopsis thaliana. 相似文献
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超级杂交稻父本93-11的基因组序列测定的完成,为进行作物遗传改良和不同作物之间的比较基因组学研究提供了又一重要序列资源.但是,该基因组序列中还存在很多缺口\",为使93-11的基因组序列更加精确,同时提供一些缺口\"填补策略和方法,本研究采用PCR扩增、回收克隆测序的方法对该基因组中一段长约160kb、含有6个缺口\"的基因组序列进行了完善,并运用相关分子生物学和生物信息学软件进行了详细分析,结果表明:该6个缺口\"中,存在1个缺口\"估计错误,2个序列拼接错误;缺口\"主要位于非编码区,位于编码区的只有1个,其改变了对本处基因的注释,使此基因由原来的9个外显子增加为11个;填补缺口\"后,基因密度增加. 相似文献
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Tessa N. Hempson Nicholas A. J. Graham M. Aaron MacNeil David H. Williamson Geoffrey P. Jones Glenn R. Almany 《Ecology and evolution》2017,7(8):2626-2635
Diet specificity is likely to be the key predictor of a predator's vulnerability to changing habitat and prey conditions. Understanding the degree to which predatory coral reef fishes adjust or maintain prey choice, in response to declines in coral cover and changes in prey availability, is critical for predicting how they may respond to reef habitat degradation. Here, we use stable isotope analyses to characterize the trophic structure of predator–prey interactions on coral reefs of the Keppel Island Group on the southern Great Barrier Reef, Australia. These reefs, previously typified by exceptionally high coral cover, have recently lost much of their coral cover due to coral bleaching and frequent inundation by sediment‐laden, freshwater flood plumes associated with increased rainfall patterns. Long‐term monitoring of these reefs demonstrates that, as coral cover declined, there has been a decrease in prey biomass, and a shift in dominant prey species from pelagic plankton‐feeding damselfishes to territorial benthic algal‐feeding damselfishes, resulting in differences in the principal carbon pathways in the food web. Using isotopes, we tested whether this changing prey availability could be detected in the diet of a mesopredator (coral grouper, Plectropomus maculatus). The δ13C signature in grouper tissue in the Keppel Islands shifted from a more pelagic to a more benthic signal, demonstrating a change in carbon sources aligning with the change in prey availability due to habitat degradation. Grouper with a more benthic carbon signature were also feeding at a lower trophic level, indicating a shortening in food chains. Further, we found a decline in the coral grouper population accompanying a decrease in total available prey biomass. Thus, while the ability to adapt diets could ameliorate the short‐term impacts of habitat degradation on mesopredators, long‐term effects may negatively impact mesopredator populations and alter the trophic structure of coral reef food webs. 相似文献
19.
lvaro Rodríguez del Río Andr E. Minoche Nikolaus F. Zwickl Anja Friedrich Susan Liedtke Thomas Schmidt Heinz Himmelbauer Juliane C. Dohm 《The Plant journal : for cell and molecular biology》2019,99(6):1242-1253
We present draft genome assemblies of Beta patula, a critically endangered wild beet endemic to the Madeira archipelago, and of the closely related Beta vulgaris ssp. maritima (sea beet). Evidence‐based reference gene sets for B. patula and sea beet were generated, consisting of 25 127 and 27 662 genes, respectively. The genomes and gene sets of the two wild beets were compared with their cultivated sister taxon B. vulgaris ssp. vulgaris (sugar beet). Large syntenic regions were identified, and a display tool for automatic genome‐wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of B. patula to sea beet and sugar beet. A comparative analysis of the Rz2 locus, responsible for rhizomania resistance, suggested that the sequenced B. patula accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies, B. patula conservation management, and sugar beet breeding research. 相似文献
20.
Seunghyun Kang Jin‐Hyoung Kim Euna Jo Seung Jae Lee Jihye Jung Bo‐Mi Kim Jun Hyuck Lee Tae‐Jin Oh Seungshic Yum Jae‐Sung Rhee Hyun Park 《Molecular ecology resources》2020,20(2):520-530
The Tetraodontidae family are known to have relatively small and compact genomes compared to other vertebrates. The obscure puffer fish Takifugu obscurus is an anadromous species that migrates to freshwater from the sea for spawning. Thus the euryhaline characteristics of T. obscurus have been investigated to gain understanding of their survival ability, osmoregulation, and other homeostatic mechanisms in both freshwater and seawater. In this study, a high quality chromosome‐level reference genome for T. obscurus was constructed using long‐read Pacific Biosciences (PacBio) Sequel sequencing and a Hi‐C‐based chromatin contact map platform. The final genome assembly of T. obscurus is 381 Mb, with a contig N50 length of 3,296 kb and longest length of 10.7 Mb, from a total of 62 Gb of raw reads generated using single‐molecule real‐time sequencing technology from a PacBio Sequel platform. The PacBio data were further clustered into chromosome‐scale scaffolds using a Hi‐C approach, resulting in a 373 Mb genome assembly with a contig N50 length of 15.2 Mb and and longest length of 28 Mb. When we directly compared the 22 longest scaffolds of T. obscurus to the 22 chromosomes of the tiger puffer Takifugu rubripes, a clear one‐to‐one orthologous relationship was observed between the two species, supporting the chromosome‐level assembly of T. obscurus. This genome assembly can serve as a valuable genetic resource for exploring fugu‐specific compact genome characteristics, and will provide essential genomic information for understanding molecular adaptations to salinity fluctuations and the evolution of osmoregulatory mechanisms. 相似文献