The Experts below are selected from a list of 1392 Experts worldwide ranked by ideXlab platform
Jan M. Strugnell - One of the best experts on this subject based on the ideXlab platform.
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De novo transcriptome assembly and functional annotation of the southern rock lobster (Jasus edwardsii)
Marine Genomics, 2018Co-Authors: Carla A. Souza, Nicholas P. Murphy, Jan M. StrugnellAbstract:Abstract Southern rock lobsters (Jasus edwardsii) are a valuable commodity and comprise important fishery resources in Australia and New Zealand. Population genomic methods (e.g. reduced representation sequencing) have been used to investigate patterns of dispersal and recruitment and the role of local adaptation within rock lobster species. However, application of these methods is constrained by the lack of pre-existing reference genome or transcriptome for Jasus and/or closely related species. In this study, we build a reference transcriptome assembly of 187,981 transcripts for Jasus edwardsii based on RNA sequencing data of four tissues (eyestalk, green gland, hepatopancreas and supraesophageal ganglion). This work will provide a significant resource to aid in investigation of the molecular basis of biological and evolutionary processes relevant to the fishing industry of spiny lobster and related taxonomic groups.
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efficiency of ddrad target enriched sequencing across spiny rock lobster species palinuridae Jasus
Scientific Reports, 2017Co-Authors: Carla A. Souza, Nicholas P. Murphy, Jan M. Strugnell, Cecilia Villacortarath, Laura N Woodings, Irina Ilyushkina, Cristian E Hernandez, Bridget S Green, James J BellAbstract:Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus. We designed probes based on ddRADseq libraries of two lobster species (Jasus edwardsii and Sagmariasus verreauxi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.
Jennifer R Ovenden - One of the best experts on this subject based on the ideXlab platform.
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distribution of Jasus spp decapoda palinuridae phyllosomas in southern waters implications for larval recruitment
Marine Ecology Progress Series, 2000Co-Authors: John D Booth, Jennifer R OvendenAbstract:We sampled the distribution of mid- and late-stage (= advanced) Jasus group 'lalandii' rock lobster phyllosomas at 28 approximately equidistant stations across similar to 16 000 km of ocean between the west coast of Africa and the west coast of New Zealand to determine whether the larvae were mostly associated with the patchy allopatric distribution of the adults or were widespread. The Jasus phyllosomas (n = 210) occurred in greatest abundance in the general vicinity of adults. Nucleotide-sequencing and restriction-fragment length polymorphism (RFLP) techniques were used to identify 93 of these larvae from 18 stations to species level. Most of the larvae caught were J. lalandii and J, edwardsii, and a few were probably J. paulensis. Most of these larvae were taken near (within a few hundred kilometres) their respective adult habitat off southern Africa, Australia and New Zealand, and Amsterdam Island. The exceptions were small numbers of J. lalandii larvae in the southwest Indian Ocean as far east as Amsterdam Island, adjacent to the J. paulensis habitat, and J. edwardsii larvae across the south Tasman Sea. A single larva off southwest Africa could not be identified to any known Jasus species and may indicate the presence in the genus of an as yet undiscovered species or subspecies. No J. caveorum, J. frontalis, or J. verreauxi (and probably no J. tristani) were found. Our results suggest that Jasus spp. larvae which subsequently recruit to benthic populations use behavioural strategies and/or physical mechanisms to avoid being carried too far away from their parental ground. However, a proportion of larvae, small yet possibly not insignificant, occurs great distances from where adults of the species are known. These larvae are unlikely to recruit to benthic populations, but their occurrence invites further consideration of how Jasus spp. maintain allopatric populations.
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mitochondrial dna variation and phylogenetic relationships of Jasus spp decapoda palinuridae
Journal of Zoology, 1992Co-Authors: D J Brasher, Jennifer R Ovenden, R W G WhiteAbstract:The seven species of rock lobster in the genus Jasus have a fragmented circumpolar distribution, inhabiting continental or island waters of the Southern Ocean. Gene flow between nominal species is possible as the planktonic larval stages of Jasus are widely dispersed in major oceanic gyres. Restriction endonuclease analysis of mitochondrial DNA (mtDNA) from five species (J. verreauxi, J. novaehollandiae, J. edwardsii, J. lalandii and J. tristani) was used to assess taxa previously defined only by morphological criteria. Intraspecific mtDNA nucleotide sequence diversity was generally high (0.33-0.99%). An absence of episodic population bottlenecks and extinctions, attributable to a teleplanic (far wandering) and prolonged pelagic stage, may be a significant factor contributing to this variation. New Zealand (J. edwardsii) and Australian (J. novaehollandiae) populations appear to be conspecific and should be referred to as J. edwardsii; however, a significant difference in the magnitude of mean sequence diversities between these populations may indicate restrictions to gene flow across the Tasman Sea. The genome of J. verreauxi is highly distinct from the genomes of the other species (nucleotide sequence diversity: 14.92-16.67%), supporting the existence of 'verreauxi' and 'lalandii' groups within Jasus. High sequence diversities separating J. edwardsii, J, lalandii and J. tristani (4.41-7.36%) indicates long-term reproductive isolation. Hypotheses for the evolution of 'lalandii' group Jasus, which suggest a relatively recent divergence of J. lalandii and J. tristani, are not supported by phylogenetic reconstruction. Instead, it gives systematic validity to the grouping of J. lalandii with J. edwardsii as proposed by the existing taxonomy.
Carla A. Souza - One of the best experts on this subject based on the ideXlab platform.
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De novo transcriptome assembly and functional annotation of the southern rock lobster (Jasus edwardsii)
Marine Genomics, 2018Co-Authors: Carla A. Souza, Nicholas P. Murphy, Jan M. StrugnellAbstract:Abstract Southern rock lobsters (Jasus edwardsii) are a valuable commodity and comprise important fishery resources in Australia and New Zealand. Population genomic methods (e.g. reduced representation sequencing) have been used to investigate patterns of dispersal and recruitment and the role of local adaptation within rock lobster species. However, application of these methods is constrained by the lack of pre-existing reference genome or transcriptome for Jasus and/or closely related species. In this study, we build a reference transcriptome assembly of 187,981 transcripts for Jasus edwardsii based on RNA sequencing data of four tissues (eyestalk, green gland, hepatopancreas and supraesophageal ganglion). This work will provide a significant resource to aid in investigation of the molecular basis of biological and evolutionary processes relevant to the fishing industry of spiny lobster and related taxonomic groups.
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efficiency of ddrad target enriched sequencing across spiny rock lobster species palinuridae Jasus
Scientific Reports, 2017Co-Authors: Carla A. Souza, Nicholas P. Murphy, Jan M. Strugnell, Cecilia Villacortarath, Laura N Woodings, Irina Ilyushkina, Cristian E Hernandez, Bridget S Green, James J BellAbstract:Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus. We designed probes based on ddRADseq libraries of two lobster species (Jasus edwardsii and Sagmariasus verreauxi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.
Chris G. Carter - One of the best experts on this subject based on the ideXlab platform.
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FT-NIR spectra of three spiny lobster species, Sagmariasus verreauxi, Jasus edwardsii, and Panilurus ornatus.
2016Co-Authors: Cedric J. Simon, Thomas Rodemann, Chris G. CarterAbstract:FT-NIR spectra of three spiny lobster species, Sagmariasus verreauxi, Jasus edwardsii, and Panilurus ornatus.
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Relationship between abdominal muscle carbon content (AMN) and hepatopancreas dry matter content (HPDM), hepatopancreas total lipid content (HPTL), and haemolymph total protein (TP) for all three species, Sagmariasus verreauxi, Jasus edwardsii, and Panilurus ornatus.
2016Co-Authors: Cedric J. Simon, Thomas Rodemann, Chris G. CarterAbstract:Relationship between abdominal muscle carbon content (AMN) and hepatopancreas dry matter content (HPDM), hepatopancreas total lipid content (HPTL), and haemolymph total protein (TP) for all three species, Sagmariasus verreauxi, Jasus edwardsii, and Panilurus ornatus.
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Relationship between abdominal muscle nitrogen content (AMC) and hepatopancreas dry matter content (HPDM), hepatopancreas total lipid content (HPTL), and haemolymph total protein (TP) for all three species, Sagmariasus verreauxi, Jasus edwardsii, and Panilurus ornatus.
2016Co-Authors: Cedric J. Simon, Thomas Rodemann, Chris G. CarterAbstract:Relationship between abdominal muscle nitrogen content (AMC) and hepatopancreas dry matter content (HPDM), hepatopancreas total lipid content (HPTL), and haemolymph total protein (TP) for all three species, Sagmariasus verreauxi, Jasus edwardsii, and Panilurus ornatus.
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Relationship between abdominal muscle dry matter content (AMDM) and hepatopancreas dry matter content (HPDM), hepatopancreas total lipid content (HPTL), and haemolymph total protein (TP) for all three species, Sagmariasus verreauxi, Jasus edwardsii, and Panilurus ornatus.
2016Co-Authors: Cedric J. Simon, Thomas Rodemann, Chris G. CarterAbstract:Relationship between abdominal muscle dry matter content (AMDM) and hepatopancreas dry matter content (HPDM), hepatopancreas total lipid content (HPTL), and haemolymph total protein (TP) for all three species, Sagmariasus verreauxi, Jasus edwardsii, and Panilurus ornatus.
Nicholas P. Murphy - One of the best experts on this subject based on the ideXlab platform.
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De novo transcriptome assembly and functional annotation of the southern rock lobster (Jasus edwardsii)
Marine Genomics, 2018Co-Authors: Carla A. Souza, Nicholas P. Murphy, Jan M. StrugnellAbstract:Abstract Southern rock lobsters (Jasus edwardsii) are a valuable commodity and comprise important fishery resources in Australia and New Zealand. Population genomic methods (e.g. reduced representation sequencing) have been used to investigate patterns of dispersal and recruitment and the role of local adaptation within rock lobster species. However, application of these methods is constrained by the lack of pre-existing reference genome or transcriptome for Jasus and/or closely related species. In this study, we build a reference transcriptome assembly of 187,981 transcripts for Jasus edwardsii based on RNA sequencing data of four tissues (eyestalk, green gland, hepatopancreas and supraesophageal ganglion). This work will provide a significant resource to aid in investigation of the molecular basis of biological and evolutionary processes relevant to the fishing industry of spiny lobster and related taxonomic groups.
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efficiency of ddrad target enriched sequencing across spiny rock lobster species palinuridae Jasus
Scientific Reports, 2017Co-Authors: Carla A. Souza, Nicholas P. Murphy, Jan M. Strugnell, Cecilia Villacortarath, Laura N Woodings, Irina Ilyushkina, Cristian E Hernandez, Bridget S Green, James J BellAbstract:Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus. We designed probes based on ddRADseq libraries of two lobster species (Jasus edwardsii and Sagmariasus verreauxi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.
