A draft genome assembly of “Cas” (Psidium friedrichsthalianum (O. Berg) Nied.): an indigenous crop of Costa Rica untapped

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.

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Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

The Plant Journal ◽

10.1111/j.1365-313x.2012.05017.x ◽

2012 ◽

Vol 71 (6) ◽

pp. 895-906 ◽

Cited By ~ 99

Author(s):

Luming Yang ◽

Dal-Hoe Koo ◽

Yuhong Li ◽

Xuejiao Zhang ◽

Feishi Luan ◽

...

Keyword(s):

Genetic Mapping ◽

Genome Assembly ◽

Draft Genome ◽

High Density ◽

Chromosome Rearrangements ◽

Draft Genome Assembly

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First draft genome of loach (Orenectus shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish

10.21203/rs.3.rs-192229/v1 ◽

2021 ◽

Author(s):

Zhijin Liu ◽

Xuekun Qian ◽

Ziming Wang ◽

Huamei Wen ◽

Ling Han ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Eye Development ◽

Draft Genome ◽

Evolutionary Process ◽

Integrated Approach ◽

Sequencing Data ◽

Retina Development ◽

Draft Genome Assembly ◽

Surface Dwelling

Abstract BcakgroundLoaches of the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth. The genus Oreonectes with 18 currently recognized species contains representatives for all three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable resource for research into the evolution of cavefishes.ResultsHere we assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. Based on in total 50.9 Gb of sequencing data, our genome assembly from Canu and Pilon spans approximately 515.64 Mb (estimated coverage of 100 ×), containing 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. We also performed genome re-sequencing of three additional cave-dwelling Oreonectes fishes. Twenty-nine pseudogenes annotated using DAVID showed significant enrichment for the GO terms of “eye development” and “retina development in camera-type eye”. It is presumed that these pseudogenes might lead to eye degeneration of semi/complete cave-dwelling Oreonectes species. Furthermore, Mc1r (melanocortin-1 receptor) is a pseudogenization by a deletion in O. daqikongensis, likely blocking biosynthesis of melanin and leading to the albino phenotype.ConclusionsWe here report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. Pseudogenization of genes related to body color and eye development may be responsible for loss of pigmentation and vision deterioration in cave-dwelling species. This genome assembly will contribute to the study of the evolution and adaptation of fishes within Oreonectes and beyond (Cobitidea).

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Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

10.1101/2021.11.11.468259 ◽

2021 ◽

Author(s):

Roger Huerlimann ◽

Jeff A Cowley ◽

Nicholas M Wade ◽

Yinan Wang ◽

Naga Kasinadhuni ◽

...

Keyword(s):

Genome Assembly ◽

Draft Genome ◽

Penaeus Monodon ◽

Penaeid Shrimp ◽

Protein Coding ◽

Black Tiger Shrimp ◽

Draft Genome Assembly ◽

Repeat Content ◽

Tiger Shrimp ◽

Endogenous Viral Elements

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements (EVEs) have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such EVEs and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ~4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of conjoined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.

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Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

Genome Biology and Evolution ◽

10.1093/gbe/evaa016 ◽

2020 ◽

Vol 12 (2) ◽

pp. 3917-3925

Author(s):

Greer A Dolby ◽

Matheo Morales ◽

Timothy H Webster ◽

Dale F DeNardo ◽

Melissa A Wilson ◽

...

Keyword(s):

Genome Assembly ◽

Mojave Desert ◽

De Novo ◽

Stop Codon ◽

Draft Genome ◽

Gene Families ◽

Sea Turtle ◽

Desert Tortoise ◽

Draft Genome Assembly ◽

Gene Expansion

Abstract Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.

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Draft Genome Sequence of Bacillus marisflavi CK-NBRI-03, Isolated from Agricultural Soil

Microbiology Resource Announcements ◽

10.1128/mra.00044-20 ◽

2020 ◽

Vol 9 (7) ◽

Author(s):

Mayank Gupta ◽

Puneet Singh Chauhan ◽

Sudhir K. Sopory ◽

Sneh L. Singla-Pareek ◽

Nidhi Adlakha ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Agricultural Soil ◽

Draft Genome ◽

Uttar Pradesh ◽

Draft Genome Sequence ◽

Positive Bacterium ◽

Gram Positive ◽

Content Type ◽

Draft Genome Assembly

Here, we report the 4.34-Mb draft genome assembly of Bacillus marisflavi CK-NBRI-03 (or P3), a Gram-positive bacterium, with an average G+C content of 48.66%. P3 was isolated from agricultural soil from the Badaun (midwestern plain zone) region of Uttar Pradesh, India.

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Draft Genome Sequence ofBacillus subtilisIa1a, a New Strain for Poly-γ-Glutamic Acid and Exopolysaccharide Production

Genome Announcements ◽

10.1128/genomea.01361-16 ◽

2016 ◽

Vol 4 (6) ◽

Author(s):

Mohammad H. A. Ibrahim ◽

Brady F. Cress ◽

Robert J. Linhardt ◽

Mattheos A. G. Koffas ◽

Richard A. Gross

Keyword(s):

Bacillus Subtilis ◽

Glutamic Acid ◽

Genome Sequence ◽

Genome Assembly ◽

Draft Genome ◽

Carbon Sources ◽

Draft Genome Sequence ◽

High Quality ◽

Exopolysaccharide Production ◽

Draft Genome Assembly

We report here the 4.092-Mb high-quality draft genome assembly of a newly isolated poly-γ-glutamic acid–producing strain,Bacillus subtilisIa1a. The genome sequence is considered a critical tool to facilitate the engineering of improved production strains. Exopolysaccharides and many industrially important enzymes can be produced by this new strain utilizing different carbon sources.

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A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis

Genome Biology and Evolution ◽

10.1093/gbe/evaa112 ◽

2020 ◽

Vol 12 (7) ◽

pp. 1074-1079 ◽

Cited By ~ 1

Author(s):

Ruihao Shu ◽

Jihong Zhang ◽

Qian Meng ◽

Huan Zhang ◽

Guiling Zhou ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Draft Genome ◽

Gene Clusters ◽

Tibet Plateau ◽

Protein Coding ◽

Draft Genome Assembly ◽

Ophiocordyceps Sinensis ◽

Homologous Protein ◽

Genome Features

Abstract Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or “DongChongXiaCao,” is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genome assembly of O. sinensis. The assembly of 23 contigs was ∼110.8 Mb with a N50 length of 18.2 Mb. We used RNA-seq and homologous protein sequences to identify 8,916 protein-coding genes in the IOZ07 assembly. Moreover, 63 secondary metabolite gene clusters were identified in the improved assembly. The improved assembly and genome features described in this study will further inform the evolutionary study and resource utilization of Chinese cordyceps.

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