scholarly journals Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Gangchun Xu ◽  
Chao Bian ◽  
Zhijuan Nie ◽  
Jia Li ◽  
Yuyu Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Genetic Resource ◽  
Economic Importance ◽  
Seasonal Migration ◽  
Migratory Fish ◽  
High Quality ◽  
Coilia Nasus ◽  
High Quality Genome ◽  
Important Fish ◽  
Chromosome Level

Abstract Background Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents). Results In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents. Conclusions We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.

scholarly journals Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shell

2021 ◽  
Author(s):  
Teng Weiming ◽  
Xie Xi ◽  
Hongtao Nie ◽  
Yamin Sun ◽  
Liu Xiangfeng ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Basis ◽  
Molecular Mechanisms ◽  
Heme Biosynthesis ◽  
High Quality ◽  
Protein Coding ◽  
Conserved Genes ◽  
Long Time ◽  
Muddy Sediments ◽  
Chromosome Level

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we reported a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50=2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the hemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

scholarly journals High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Qionghua Gao ◽  
Zijun Xiong ◽  
Rasmus Stenbak Larsen ◽  
Long Zhou ◽  
Jie Zhao ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Genome Rearrangement ◽  
Gene Annotation ◽  
Full Length ◽  
Comparative Genomic ◽  
High Quality ◽  
Monomorium Pharaonis ◽  
Transcript Isoforms ◽  
Chromosome Level

Abstract Background Ants with complex societies have fascinated scientists for centuries. Comparative genomic and transcriptomic analyses across ant species and castes have revealed important insights into the molecular mechanisms underlying ant caste differentiation. However, most current ant genomes and transcriptomes are highly fragmented and incomplete, which hinders our understanding of the molecular basis for complex ant societies. Findings By hybridizing Illumina, Pacific Biosciences, and Hi-C sequencing technologies, we de novo assembled a chromosome-level genome for Monomorium pharaonis, with a scaffold N50 of 27.2 Mb. Our new assembly provides better resolution for the discovery of genome rearrangement events at the chromosome level. Analysis of full-length isoform sequencing (ISO-seq) suggested that ∼15 Gb of ISO-seq data were sufficient to cover most expressed genes, but the number of transcript isoforms steadily increased with sequencing data coverage. Our high-depth ISO-seq data greatly improved the quality of gene annotation and enabled the accurate detection of alternative splicing isoforms in different castes of M. pharaonis. Comparative transcriptome analysis across castes based on the ISO-seq data revealed an unprecedented number of transcript isoforms, including many caste-specific isoforms. We also identified a number of conserved long non-coding RNAs that evolved specifically in ant lineages and several that were conserved across insect lineages. Conclusions We produced a high-quality chromosome-level genome for M. pharaonis, which significantly improved previous short-read assemblies. Together with full-length transcriptomes for all castes, we generated a highly accurate annotation for this ant species. These long-read sequencing results provide a useful resource for future functional studies on the genetic mechanisms underlying the evolution of social behaviors and organization in ants.

scholarly journals Complete Genome Sequence Resource for Xanthomonas fragariae Causing Crown Infection Pockets in Strawberry

2021 ◽  
Author(s):  
Feng Wei ◽  
Danjuan Wang ◽  
Sihao Fan ◽  
Jiancheng Shi ◽  
Xiaolin Cai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Host Adaptation ◽  
Pathological Process ◽  
High Quality ◽  
Leaf Spots ◽  
Xanthomonas Fragariae ◽  
Quarantine Pathogen ◽  
High Quality Genome

Xanthomonas fragariae (X. fragariae ) is a global quarantine pathogen, which typically inflicting angular leaf spots. In the present study, we report a new 4.11 Mb high-quality genome sequence of X. fragariae YL19. YL19 can make the strawberry plants have the typical angular leaf spot symptom and have crown infection pockets symptom in China. This new symptom has not been reported in other X. fragariae. Compared with typical X. fragariae strains, including PD885, NBC2815, PD5205, Fap21, and Fap29, the genome and plasmid in YL19 were smaller in size, which lacked 109 coding genes and has more CAZymes genes and secondary metabolism genes. The YL19 genome ought to clarify the molecular mechanisms of genome evolution, host adaptation, and pathological process of X. fragariae and the improvement of strawberry management strategies.

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 Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

2020 ◽  
Author(s):  
Saptarathi Deb ◽  
Suvratha J ◽  
Samathmika Ravi ◽  
Raksha Rao K ◽  
Saurabh Whadgar ◽  
...  
Keyword(s):  
Reference Genome ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Draft Genome ◽  
Local Environment ◽  
High Quality ◽  
Low Coverage ◽  
High Quality Genome ◽  
Chromosome Level

ABSTRACTIn the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly A. cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

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

scholarly journals High-Quality Genome Resource of the Pathogen of Diaporthe (Phomopsis) phragmitis Causing Kiwifruit Soft Rot

2020 ◽  
Author(s):  
Pu Liu ◽  
Wang Xiaojie ◽  
Dong Hongjie ◽  
Jianbin Lan ◽  
Kuan Liang ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Management Strategies ◽  
Soft Rot ◽  
Fruit Rot ◽  
Economic Plant ◽  
High Quality ◽  
Total Size ◽  
Genome Wide ◽  
Solid Foundation ◽  
High Quality Genome

Diaporthe spp. are critical plant pathogens that cause wood cankers, wilt, dieback, and fruit rot in a wide variety of economic plant hosts and are regarded as one of the most acute threats faced by kiwifruit industry worldwide. Diaporthe phragmitis strain NJD1 is a highly pathogenic isolate of soft rot of kiwifruit. Here, we present a high-quality genome-wide sequence of D. phragmitis NJD1 that was assembled into 28 contigs containing a total size of 58.33 Mb and N50 length of 3.55 Mb. These results lay a solid foundation for understanding host–pathogen interaction and improving disease management strategies.

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