scholarly journals A Reference Genome for the Nectar-robbing Black-throated Flowerpiercer (Diglossa brunneiventris)

2021 ◽  
Author(s):  
Anna E Hiller ◽  
Robb T Brumfield ◽  
Brant C Faircloth
Keyword(s):  
Natural History ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Genetic Basis ◽  
Reference Genome ◽  
Nectar Robbing ◽  
Wild Female ◽  
Diverse Species ◽  
A Genome ◽  
Long Read

Abstract Black-throated Flowerpiercers (Diglossa brunneiventris) are one species representing a phenotypically specialized group of tanagers (Thraupidae) that have hooked bills which allow them to feed by stealing nectar from the base of flowers. Members of the genus are widely distributed in montane regions from Mexico to northern Argentina, and previous studies of Diglossa have focused on their systematics, phylogenetics, and interesting natural history. Despite numerous studies of species within the genus, no genome assembly exists to represent these nectivorous tanagers. We described the assembly of a genome sequence representing a museum-vouchered, wild, female Diglossa brunneiventris collected in Peru. By combining Pacific Biosciences Sequel long-read technology with 10X linked-read and reference-based scaffolding, we produced a 1.08 Gbp pseudochromosomal assembly including 600 scaffolds with a scaffold N50 of 67.3 Mbp, a scaffold L50 of 6, and a BUSCO completeness score of 95%. This new assembly improves representation of the diverse species that comprise the tanagers, improves on scaffold lengths and contiguity when compared to existing genomic resources for tanagers, and provides another avenue of research into the genetic basis of adaptations common to a nectivorous lifestyle among vertebrates.

scholarly journals The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769

2021 ◽  
Vol 6 ◽  
pp. 118
Author(s):  
Kerstin Howe ◽  
Melinda Dwinell ◽  
Mary Shimoyama ◽  
Craig Corton ◽  
Emma Betteridge ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sex Chromosomes ◽  
Genome Assembly ◽  
Rattus Norvegicus ◽  
Reference Genome ◽  
Norway Rat ◽  
Individual Male ◽  
A Genome

We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.

scholarly journals Genome sequence resource of Phomopsis longicolla strain YC2-1, a fungal pathogen causing Phomopsis stem blight in soybean

2021 ◽  
Author(s):  
Xiaolin Zhao ◽  
Zhichao Zhang ◽  
Sujiao Zheng ◽  
Wenwu Ye ◽  
Xiaobo Zheng ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Stem Canker ◽  
Quality Data ◽  
Phomopsis Longicolla ◽  
Protein Coding ◽  
Stem Blight ◽  
A Genome ◽  
Long Read ◽  
Genomic Resource ◽  
Blight Disease

Diaporthe-Phomopsis disease complex causes considerable yield losses in soybean production worldwide. As one of the major pathogens, Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is not only the primary agent of Phomopsis seed decay, but also one of the agents of Phomopsis pod and stem blight, and Phomopsis stem canker. We performed both PacBio long read sequencing and Illumina short read sequencing, and obtained a genome assembly for the P. longicolla strain YC2-1, which was isolated from soybean stem with Phomopsis stem blight disease. The 63.1 Mb genome assembly contains 87 scaffolds, with a minimum, maximum, and N50 scaffold length of 20 kb, 4.6 Mb, and 1.5 Mb respectively, and a total of 17,407 protein-coding genes. The high-quality data expand the genomic resource of P. longicolla species and will provide a solid foundation for a better understanding of their genetic diversity and pathogenic mechanisms.

scholarly journals The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 258
Author(s):  
Konrad Lohse ◽  
Alexander Mackintosh ◽  
Roger Vila ◽  
◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Protein Coding ◽  
Individual Male ◽  
Protein Coding Genes ◽  
A Genome ◽  
Inachis Io

We present a genome assembly from an individual male Aglais io (also known as Inachis io and Nymphalis io) (the European peacock; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority (99.91%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 11,420 protein coding genes.

scholarly journals Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveals expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions

2021 ◽  
pp. gr.275325.121
Author(s):  
Rodrigo P. Baptista ◽  
Yiran Li ◽  
Adam Sateriale ◽  
Karen L. Brooks ◽  
Alan Tracey ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Diarrheal Disease ◽  
Gene Copy ◽  
Future Research ◽  
Single Nucleotide Variants ◽  
Cryptosporidium Hominis ◽  
Entire Chromosome ◽  
Long Read ◽  
Subtelomeric Regions

Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community has only had access to a good, but incomplete, Cryptosporidium parvum IOWA reference genome sequence. Incomplete reference sequences hamper annotation, experimental design and interpretation. We have generated a new C. parvum IOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species C. parvum, Cryptosporidium hominis and Cryptosporidium tyzzeri. We made 1,926 C. parvum annotation updates based on experimental evidence. They include new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete Dnmt2 methylase ortholog. Comparative annotation between C. parvum, C. hominis and C. tyzzeri revealed that most "missing" orthologs are found suggesting that the biological differences between the species must result from gene copy number variation, differences in gene regulation and single nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers all 16 chromosome ends, 13 of which are contiguously assembled. The three remaining chromosome ends are provisionally placed. These ends represent duplication of entire chromosome ends including subtelomeric regions revealing a new level of genome plasticity that will both inform and impact future research.

scholarly journals The genome sequence of the common malachite beetle, Malachius bipustulatus (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 322
Author(s):  
Liam Crowley ◽  
◽  
◽  
◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Individual Female ◽  
A Genome ◽  
The Common

We present a genome assembly from an individual female Malachius bipustulatus (the common malachite beetle; Arthropoda; Insecta; Coleoptera; Melyridae). The genome sequence is 544 megabases in span. The majority (99.70%) of the assembly is scaffolded into 10 chromosomal pseudomolecules, with the X sex chromosome assembled.

scholarly journals The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758

2021 ◽  
Vol 6 ◽  
pp. 112
Author(s):  
Dan Mead ◽  
Rob Ogden ◽  
Anna Meredith ◽  
Gabriela Peniche ◽  
Michelle Smith ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sex Chromosomes ◽  
Genome Assembly ◽  
Golden Eagle ◽  
Aquila Chrysaetos ◽  
Individual Female ◽  
A Genome

We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.

scholarly journals The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788

2020 ◽  
Vol 5 ◽  
pp. 27
Author(s):  
Dan Mead ◽  
Kathryn Fingland ◽  
Rachel Cripps ◽  
Roberto Portela Miguez ◽  
Michelle Smith ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sex Chromosomes ◽  
Genome Assembly ◽  
Sciurus Carolinensis ◽  
Grey Squirrel ◽  
Individual Male ◽  
A Genome

We present a genome assembly from an individual male Sciurus carolinensis (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals The genome sequence of the sycamore, Acronicta aceris (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 326
Author(s):  
Douglas Boyes ◽  
Liam Crowley ◽  
Peter W.H. Holland ◽  
◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Individual Female ◽  
A Genome ◽  
Lepidoptera Noctuidae

We present a genome assembly from an individual female Acronicta aceris (the sycamore; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Genome Structure ◽  
Plant Genome ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

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