scholarly journals Bicolor angelfish (Centropyge bicolor) provides the first chromosome-level genome of the Pomacanthidae family

Gigabyte ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Chunhua Li ◽  
Xianwei Yang ◽  
Libin Shao ◽  
Rui Zhang ◽  
Qun Liu ◽  
...  
Keyword(s):  
Chromosome Level

A Chromosome-Level Genome Assembly Identifies the Origin of Neo-Y Chromosome to the Unique X 1X 2Y System

2019 ◽  
Author(s):  
Yongshuang Xiao ◽  
Zhizhong Xiao ◽  
Daoyuan Ma ◽  
Chenxi Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Genome Assembly ◽  
Chromosome Level

scholarly journals The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nathalie Raharimalala ◽  
Stephane Rombauts ◽  
Andrew McCarthy ◽  
Andréa Garavito ◽  
Simon Orozco-Arias ◽  
...  
Keyword(s):  
Wild Species ◽  
Illegitimate Recombination ◽  
Recombination Mechanism ◽  
Comparative Analyses ◽  
Robusta Coffee ◽  
Caffeine Synthase ◽  
The World ◽  
Decaffeinated Coffee ◽  
Chromosome Level

AbstractCaffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

scholarly journals Chromosome-level genome assembly of a regenerable maize inbred line A188

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guifang Lin ◽  
Cheng He ◽  
Jun Zheng ◽  
Dal-Hoe Koo ◽  
Ha Le ◽  
...  
Keyword(s):  
Inbred Line ◽  
Genome Assembly ◽  
Gene Function ◽  
Maize Inbred Line ◽  
Carotenoid Cleavage Dioxygenase ◽  
Structural Variations ◽  
Embryonic Callus ◽  
Network Analyses ◽  
A Genome ◽  
Chromosome Level

Abstract Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

scholarly journals De novo chromosome-level assembly of Centella asiatica genome

Genomics ◽  
2021 ◽  
Author(s):  
Wirulda Pootakham ◽  
Chaiwat Naktang ◽  
Wasitthee Kongkachana ◽  
Chutima Sonthirod ◽  
Thippawan Yoocha ◽  
...  
Keyword(s):  
De Novo ◽  
Centella Asiatica ◽  
Chromosome Level

scholarly journals Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amit Rai ◽  
Hideki Hirakawa ◽  
Ryo Nakabayashi ◽  
Shinji Kikuchi ◽  
Koki Hayashi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Experimental Validation ◽  
Genome Duplication ◽  
Indole Alkaloids ◽  
Whole Genome ◽  
Comparative Genome Analysis ◽  
Plant Genomes ◽  
Genome Triplication ◽  
Chromosome Level

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

scholarly journals Chromosome‐level genome assembly of the bean bug Riptortus pedestris

2021 ◽  
Author(s):  
Hai‐Jian Huang ◽  
Yu‐Xuan Ye ◽  
Zhuang‐Xin Ye ◽  
Xiao‐Tian Yan ◽  
Xin Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Riptortus Pedestris ◽  
Bean Bug ◽  
Chromosome Level

scholarly journals Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome

2020 ◽  
Vol 12 (11) ◽  
pp. 1953-1960
Author(s):  
Andrey A Yurchenko ◽  
Hans Recknagel ◽  
Kathryn R Elmer
Keyword(s):  
Linkage Map ◽  
Single Copy ◽  
Phenotypic Traits ◽  
Sequencing Data ◽  
High Coverage ◽  
Squamate Reptiles ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common ◽  
Chromosome Level

Abstract Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

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