scholarly journals The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae) provides insight into host plant specialization

2020 ◽  
Author(s):  
Huai-Jun Xue ◽  
Yi-Wei Niu ◽  
Kari A. Segraves ◽  
Rui-E Nie ◽  
Ya-Jing Hao ◽  
...  
Keyword(s):  
Host Plant ◽  
Plant Cell Wall ◽  
Flea Beetle ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Ecological Speciation ◽  
High Quality ◽  
Secondary Chemistry ◽  
Host Plant Specialization ◽  
Insight Into

Abstract Background Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used as a model system in which to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this important group, here we present a high-quality draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome and the fourth chrysomelid genome reported thus far. Results The genome is 864.8 Mb and consists of 4,490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2,462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation. Conclusions The high-quality genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.

scholarly journals The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huai-Jun Xue ◽  
Yi-Wei Niu ◽  
Kari A. Segraves ◽  
Rui-E Nie ◽  
Ya-Jing Hao ◽  
...  
Keyword(s):  
Host Plant ◽  
Plant Cell Wall ◽  
Flea Beetle ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Gene Families ◽  
Ecological Speciation ◽  
Secondary Chemistry ◽  
Host Plant Specialization ◽  
Insight Into

Abstract Background Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far. Results The genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation. Conclusions The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.

scholarly journals The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)

2020 ◽  
Author(s):  
Huai-Jun Xue ◽  
Yi-Wei Niu ◽  
Kari A. Segraves ◽  
Rui-E Nie ◽  
Ya-Jing Hao ◽  
...  
Keyword(s):  
Host Plant ◽  
Plant Cell Wall ◽  
Flea Beetle ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Gene Families ◽  
Ecological Speciation ◽  
Secondary Chemistry ◽  
Host Plant Specialization ◽  
Insight Into

Abstract Background: Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome and the fifth chrysomelid genome reported thus far. Results: The genome is 864.8 Mb and consists of 4,490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2,462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation. Conclusions: The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.

scholarly journals Draft genome of the Reindeer (Rangifer tarandus)

2017 ◽  
Author(s):  
Zhipeng Li ◽  
Zeshan Lin ◽  
Lei Chen ◽  
Hengxing Ba ◽  
Yongzhi Yang ◽  
...  
Keyword(s):  
Rangifer Tarandus ◽  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Divergence Time ◽  
Capra Hircus ◽  
High Quality ◽  
Illumina Hiseq

AbstractBackgroundReindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovids’ milk. A high quality reference genome of this specie will assist efforts to elucidate these and other important features in the reindeer.FindingsWe obtained 723.2 Gb (Gigabase) of raw reads by an Illumina Hiseq 4000 platform, and a 2.64 Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21,555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1,339 snRNA and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus, and ancestors of Bos taurus and Capra hircus, is estimated to be 29.55 million years ago (Mya).ConclusionsOur results provide the first high-quality reference genome for the reindeer, and a valuable resource for studying evolution, domestication and other unusual characteristics of the reindeer.

scholarly journals The first high-quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa

2021 ◽  
Author(s):  
Liang Xu ◽  
Shengnan Li ◽  
Yanyun Yang ◽  
Yanping Xing ◽  
Zhongren Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Developmental Stages ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Edible Plant ◽  
High Quality ◽  
Protein Coding ◽  
Arctium Lappa ◽  
Coa Ligase ◽  
Highly Correlated

Arctium lappa has a long medicinal and edible history with great economic importance. We combined Illumina and PacBio sequences to generate the first high-quality chromosome-level draft genome of A. lappa. The assembled genome is approximately 1.79 Gb with a N50 contig size of 6.88 Mb. Approximately 1.70 Gb (95.4%) of the contig sequences were anchored onto 18 chromosomes using Hi-C data; the scaffold N50 was improved to be 91.64 Mb. Furthermore, we obtained 1.12 Gb (68.46%) of repetitive sequences and 32,771 protein-coding genes; 616 positively selected candidate genes were identified. Additionally, we compared the transcriptomes of A. lappa roots at three different developmental stages and identified 8,943 differentially expressed genes (DEGs) in these tissues. Among candidate genes related to lignan biosynthesis, the following were found to be highly correlated with the accumulation of arctiin: 4-coumarate-CoA ligase (4CL), dirigent protein (DIR), and hydroxycinnamoyl transferase (HCT). These data can be utilized to identify genes related to A. lappa quality or provide a basis for molecular identification and comparative genomics among related species.

scholarly journals High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids

2021 ◽  
Vol 12 ◽  
Author(s):  
Yongle Hu ◽  
Dongna Ma ◽  
Shuju Ning ◽  
Qi Ye ◽  
Xuanxuan Zhao ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Indole Alkaloids ◽  
Draft Genome ◽  
Herbal Medicines ◽  
Indole Alkaloid ◽  
Bhlh Transcription Factor ◽  
Sequencing Data ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes

Strobilanthes cusia (Nees) Kuntze is an important plant used to process the traditional Chinese herbal medicines “Qingdai” and “Nanbanlangen”. The key active ingredients are indole alkaloids (IAs) that exert antibacterial, antiviral, and antitumor pharmacological activities and serve as natural dyes. We assembled the S. cusia genome at the chromosome level through combined PacBio circular consensus sequencing (CCS) and Hi-C sequencing data. Hi-C data revealed a draft genome size of 913.74 Mb, with 904.18 Mb contigs anchored into 16 pseudo-chromosomes. Contig N50 and scaffold N50 were 35.59 and 68.44 Mb, respectively. Of the 32,974 predicted protein-coding genes, 96.52% were functionally annotated in public databases. We predicted 675.66 Mb repetitive sequences, 47.08% of sequences were long terminal repeat (LTR) retrotransposons. Moreover, 983 Strobilanthes-specific genes (SSGs) were identified for the first time, accounting for ~2.98% of all protein-coding genes. Further, 245 putative centromeric and 29 putative telomeric fragments were identified. The transcriptome analysis identified 2,975 differentially expressed genes (DEGs) enriched in phenylpropanoid, flavonoid, and triterpenoid biosynthesis. This systematic characterization of key enzyme-coding genes associated with the IA pathway and basic helix-loop-helix (bHLH) transcription factor family formed a network from the shikimate pathway to the indole alkaloid synthesis pathway in S. cusia. The high-quality S. cusia genome presented herein is an essential resource for the traditional Chinese medicine genomics studies and understanding the genetic underpinning of IA biosynthesis.

Host Plant Specialization Driven by Sexual Selection

2007 ◽  
Vol 169 (6) ◽  
pp. 830
Author(s):  
Tiago B. Quental ◽  
Manus M. Patten ◽  
Pierce
Keyword(s):  
Sexual Selection ◽  
Host Plant ◽  
Host Plant Specialization

scholarly journals High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae

2014 ◽  
Vol 9 (1) ◽  
Author(s):  
Oleg Mediannikov ◽  
Thi-Thien Nguyen ◽  
Lesley Bell-Sakyi ◽  
Roshan Padmanabhan ◽  
Pierre-Edouard Fournier ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
High Quality ◽  
The Family

scholarly journals A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

2021 ◽  
Author(s):  
Tomas N Generalovic ◽  
Shane A McCarthy ◽  
Ian A Warren ◽  
Jonathan M D Wood ◽  
James Torrance ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Animal Feed ◽  
Repetitive Sequences ◽  
Genomic Variation ◽  
Runs Of Homozygosity ◽  
High Quality ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Chromosome Conformation ◽  
Important Species

Abstract Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome five. Release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterisation of genes of interest and genetic modification of this economically important species.

scholarly journals Draft Genome Sequence of the Nitrogen-Fixing and Hormogonia-Inducing CyanobacteriumNostoc cycadaeStrain WK-1, Isolated from the Coralloid Roots ofCycas revoluta

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Yu Kanesaki ◽  
Masaki Hirose ◽  
Yuu Hirose ◽  
Takatomo Fujisawa ◽  
Yasukazu Nakamura ◽  
...  
Keyword(s):  
Host Plant ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nitrogen Fixing ◽  
Coralloid Roots ◽  
Cycas Revoluta

ABSTRACTWe report here the whole-genome sequence ofNostoc cycadaestrain WK-1, which was isolated from cyanobacterial colonies growing in the coralloid roots of the gymnospermCycas revoluta. It can provide valuable resources to study the mutualistic relationships and the syntrophic metabolisms between the cyanobacterial symbiont and the host plant,C. revoluta.

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