scholarly journals A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

2020 ◽  
Author(s):  
Tanaporn Uengwetwanit ◽  
Wirulda Pootakham ◽  
Intawat Nookaew ◽  
Chutima Sonthirod ◽  
Pacharaporn Angthong ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Penaeus Monodon ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Breeding Programs ◽  
Crustacean Species ◽  
Black Tiger Shrimp ◽  
Tiger Shrimp ◽  
High Quality Genome ◽  
Chromosome Level

AbstractThe black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

scholarly journals Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

2020 ◽  
Author(s):  
Jarrod Lee Guppy ◽  
David B. Jones ◽  
Shannon R. Kjeldsen ◽  
Agnes Le Port ◽  
Mehar S. Khatkar ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Read Depth ◽  
Call Rate ◽  
High Quality ◽  
Breeding Programs ◽  
Reduced Representation ◽  
Black Tiger Shrimp ◽  
Tiger Shrimp ◽  
Target Capture ◽  
Genome Wide

Abstract Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp ( Penaeus monodon ) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 660 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertake genomic selection at less than $15 AUD per sample.

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

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.

scholarly journals A chromosome‐level assembly of the black tiger shrimp ( Penaeus monodon ) genome facilitates the identification of growth‐associated genes

2021 ◽  
Author(s):  
Tanaporn Uengwetwanit ◽  
Wirulda Pootakham ◽  
Intawat Nookaew ◽  
Chutima Sonthirod ◽  
Pacharaporn Angthong ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Black Tiger Shrimp ◽  
Tiger Shrimp ◽  
Chromosome Level

scholarly journals A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Minghui Kang ◽  
Rao Fu ◽  
Pingyu Zhang ◽  
Shangling Lou ◽  
Xuchen Yang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Malignant Tumors ◽  
Functional Divergence ◽  
Camptotheca Acuminata ◽  
Evolutionary Origin ◽  
High Quality ◽  
Genetic Changes ◽  
Positive Evolution ◽  
High Quality Genome ◽  
Chromosome Level

AbstractCamptothecin and its derivatives are widely used for treating malignant tumors. Previous studies revealed only a limited number of candidate genes for camptothecin biosynthesis in Camptotheca acuminata, and it is still poorly understood how its biosynthesis of camptothecin has evolved. Here, we report a high-quality, chromosome-level C. acuminata genome assembly. We find that C. acuminata experiences an independent whole-genome duplication and numerous genes derive from it are related to camptothecin biosynthesis. Comparing with Catharanthus roseus, the loganic acid O-methyltransferase (LAMT) in C. acuminata fails to convert loganic acid into loganin. Instead, two secologanic acid synthases (SLASs) convert loganic acid to secologanic acid. The functional divergence of the LAMT gene and positive evolution of two SLAS genes, therefore, both contribute greatly to the camptothecin biosynthesis in C. acuminata. Our results emphasize the importance of high-quality genome assembly in identifying genetic changes in the evolutionary origin of a secondary metabolite.

High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan

2021 ◽  
Author(s):  
Hui Zhang ◽  
Yuexing Wang ◽  
Ce Deng ◽  
Sheng Zhao ◽  
Peng Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Quality ◽  
Rice Hybrid ◽  
High Quality Genome

Acute toxicity, accumulation and sublethal effects of four neonicotinoids on juvenile Black Tiger Shrimp (Penaeus monodon)

Chemosphere ◽  
2021 ◽  
Vol 275 ◽  
pp. 129918
Author(s):  
Peter Butcherine ◽  
Brendan P. Kelaher ◽  
Matthew D. Taylor ◽  
Corinne Lawson ◽  
Kirsten Benkendorff
Keyword(s):  
Acute Toxicity ◽  
Sublethal Effects ◽  
Penaeus Monodon ◽  
Black Tiger Shrimp ◽  
Tiger Shrimp
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