<i>De novo</i> genome assembly of the white-spotted flower chafer (<i>Protaetia brevitarsis</i>)

Wang, Kui; Li, Pengpeng; Gao, Yongyang; Liu, Chunqin; Wang, Qinglei; Yin, Jing; Zhang, Jie; Li, Geng; Shu, Changlong

doi:10.1093/gigascience/giz019

Cited by 37 publications

(33 citation statements)

References 47 publications

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“…We used r8s (Sanderson, 2003) to estimate the divergent times among species with divergence times of two nodes, i.e. Tribolium castaneum and Anoplophora glabripennis (Wang et al, 2019), Trichoplusia ni and S. litura (Wan et al, 2019) as calibrations. The Computational Analysis of gene Family Evolution (CAFE) version 3.1 (Bie et al, 2006) was used to analyze gene family expansion and contraction.…”

Section: Methodsmentioning

confidence: 99%

The oriental fruit moth genome provides insights into evolutionary adaptation of tortricid pests

Song

Cao

Yue

et al. 2020

Preprint

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Moths of the family Tortricidae (Insecta: Lepidoptera) usually distribute in temperate and tropical high upland regions. The oriental fruit moth (OFM) Grapholita molesta is a globally important pest of stone and pome fruit from this family. In this study, we assembled a chromosome-level genome for the OFM and conducted a comparative genomic analysis with other lepidopterans. This genome was assembled to 28 chromosomes with a size of 517.71 Mb, an N50 of 19.5 Mb, and a BUSCO completeness of 97.1%. In total, 19968 protein-coding genes were predicted, among which 15269 were functionally annotated. We manually annotated ten gene families for 13 representative genomes from the Lepidopteran. In general, two tortricid moths have a moderate number of detoxification and receptor genes and the lowest number of HSP genes, congruent with their polyphagous dietary and pattern of distribution. However, the OFM has the highest number of P450, IRs and ORs among all species. Compared to the other tortricid species of the codling moth Cydia pomonella, the OFM has more genes in all gene families. Our results indicate that the high number of some detoxification and receptor genes may be related to the strong adaptation of OFM as a global pest. The high-quality genome of OFM provides an invaluable resource for understanding the ecology, genetics, and evolution of tortricid moths.

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Section: Methodsmentioning

confidence: 99%

The oriental fruit moth genome provides insights into evolutionary adaptation of tortricid pests

Song

Cao

Yue

et al. 2020

Preprint

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“…Pairwise BLASTP (v. 2.6.0, e-value 0.00001) searches were done between proteins of Marronus and O. borbonicus and best reciprocal hits were extracted to estimate the median protein sequence identity between orthologous gene pairs. For further comparative genomic analyses, we obtained protein sequences for Nicrophorus vespilloides and Aethina tumida from the i5k website (https://i5k.nal.usda.gov/, accessed July, 12th 2019) 45 , Anoplophora glabripennis , Dendroctonus ponderosae , Tribolium castaneum from Ensembl Metazoa (release 44), Protaetia brevitarsis , Pyrocoelia pectoralis , Hycleus cichorii and Hycleus phaleratus from GigaDB [46][47][48] , Onthophagus taurus from the U.S. Department of Agriculture website (https://data.nal.usda.gov, accessed July, 12th 2019), Agrilus planipennis and Leptinotarsa decemlineata 49 from the ftp server of the Human Genome Sequencing Center of the Baylor College of Medicine (ftp://ftp.hgsc.bcm.tmc.edu/I5K-pilot/, accessed July, 12th 2019), and Hypothenemus hampei from the website of the NYU Center for Health Informatics and Bioinformatics (https://genome.med.nyu.edu/) 50 . In cases of multiple isoforms per gene, the sequence corresponding to the longest protein was taken for further analysis.…”

Section: Gene Annotation and Comparative Genomic Analysismentioning

confidence: 99%

Museum phylogenomics of extinctOryctesbeetles from the Mascarene Islands

Latorre

Herrmann

Paulsen³

et al. 2020

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The evolution of island systems is characterized by processes that result in extreme morphological diversity, high endemism and high extinction rates. These dynamics can make phylogenetic reconstruction difficult, i.e. the extinct flightless Dodo from Mauritius was assigned to the family of doves only through DNA analysis of subfossils. Many insect species on islands have gone extinct through habitat loss, and face similar challenges to decipher their evolutionary history, however historical specimens have not yet been harnessed for phylogenomic reconstructions. Here, we employed historical museum specimens from the Mascarene Islands to generate the first whole-genome based phylogeny of three presumably extinct species of the rhinoceros beetle genus Oryctes . We compared their genomes with those of an extant Oryctes species from the island of Réunion, as well as a flightless Réunion-based species previously placed into the supposedly unrelated genus Marronus . We found that Marronus borbonicus belongs instead to the genus Oryctes and that the two Réunion-based species ( O. borbonicus and M. borbonicus ) are not sister taxa, suggesting two independent colonizations. The divergence time between them (<3Myr) overlaps with the volcanic formation of Réunion, likely indicating that M. borbonicus became flightless in situ . Our study showcases the power of genomes from insect museum specimens to address evolutionary questions in light of increasing extinction rates.

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“…Consequently, the genome for A. viridicyanea will add to our genomic resources for a monophagous member of the Chrysomelidae. Furthermore, this assembly will also expand our knowledge of beetles in general as we currently have only 21 published beetle genome assemblies [22,[24][25][26][27][28][29][30][31][32][33] (Table S1) which is a comparably small number for a diverse insect group with nearly 400,000 described species [34][35][36]. Finally, the high-quality genome assembled here will provide an important resource for further studies on host plant adaptation and functionally a liated genes.…”

Section: Introductionmentioning

confidence: 97%

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

Xue

Niu

Segraves

et al. 2020

Preprint

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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.

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De novo genome assembly of the white-spotted flower chafer (Protaetia brevitarsis)

Cited by 37 publications

References 47 publications

The oriental fruit moth genome provides insights into evolutionary adaptation of tortricid pests

The oriental fruit moth genome provides insights into evolutionary adaptation of tortricid pests

Museum phylogenomics of extinctOryctesbeetles from the Mascarene Islands

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

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