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Wild Jack Genome

ABSTRACT: Genome assembly of Artocarpus hirsutus

PROVIDER: PRJEB55580 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR10114956_1.fastq.gz	Fastqsanger.gz
	ERR10114956_2.fastq.gz	Fastqsanger.gz

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Jack of all trades: Genome assembly of Wild Jack and comparative genomics of <i>Artocarpus</i>.

Project description:Artocarpus (Moraceae), known as breadfruits for their diverse nutritious fruits, is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a larger tree, Artocarpus hirsutus, also called "Wild Jack" or "Ayani", is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from the sacred groves of Coorg, India. To decipher demographic and evolutionary history, we compared our Wild Jack genome with previously published Jackfruit and Breadfruit genomes. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which had a major contribution to its larger genome size. Several genes from starch, sucrose metabolism, and plant hormone signal transduction pathways, in Artocarpus species had signatures of selection and gene family evolution. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild Jack.

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nhSphHirs1

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Research on genomic test utilizing next generation sequencer for solid tumors and development of the genome database

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The Nationwide Cancer Genome Screening Projects for Gastrointestinal Cancer in Japan, Efficient Identification of Actionable Cancer Genome Alterations in Advanced Non-Colorectal Gastrointestinal Cancer (SCRUM-Japan GI Screen 2015-01-Non-CRC)

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A complete reference genome for the soybean cv. Jack.

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The Nationwide Cancer Genome Screening Project for Gastrointestinal Cancer in Japan (SCRUM-Japan GI-SCREEN):Efficient Identification of Actionable Cancer Genome Alterations in Advanced Colorectal Cancer (GI-SCREEN 2013-01)

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nhSphHirs1 alternate haplotype

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Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades.

Project description:The complete genome of Aeromonas hydrophila ATCC 7966(T) was sequenced. Aeromonas, a ubiquitous waterborne bacterium, has been placed by the Environmental Protection Agency on the Contaminant Candidate List because of its potential to cause human disease. The 4.7-Mb genome of this emerging pathogen shows a physiologically adroit organism with broad metabolic capabilities and considerable virulence potential. A large array of virulence genes, including some identified in clinical isolates of Aeromonas spp. or Vibrio spp., may confer upon this organism the ability to infect a wide range of hosts. However, two recognized virulence markers, a type III secretion system and a lateral flagellum, that are reported in other A. hydrophila strains are not identified in the sequenced isolate, ATCC 7966(T). Given the ubiquity and free-living lifestyle of this organism, there is relatively little evidence of fluidity in terms of mobile elements in the genome of this particular strain. Notable aspects of the metabolic repertoire of A. hydrophila include dissimilatory sulfate reduction and resistance mechanisms (such as thiopurine reductase, arsenate reductase, and phosphonate degradation enzymes) against toxic compounds encountered in polluted waters. These enzymes may have bioremediative as well as industrial potential. Thus, the A. hydrophila genome sequence provides valuable insights into its ability to flourish in both aquatic and host environments.

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