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High-coverage sequencing and annotated assemblies of the budgerigar genome.

Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, Wray G, Rasolonjatovo I, Winer R, Knight JR, Koren S, Warren WC, Zhang G, Phillippy AM, Jarvis ED - Gigascience (2014)

Bottom Line: The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing.Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions.This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.

ABSTRACT

Background: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome.

Findings: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing.

Conclusions: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

No MeSH data available.


Related in: MedlinePlus

Number of nucleotide gaps assess relative assembly incompleteness. A) Shows the total number of gaps in genes and the surrounding 10,000 base pair regions upstream and downstream (collectively called gene territories). B) Shows the number of such gene territories with gaps. In both the panels, different species assemblies are colored differently, with the budgerigar assemblies shown in dark blue. The budgerigar assemblies with the “-mega” suffix are optical map enhanced versions of the Budgerigar_v6.3 and PBcR assemblies. The budgerigar assemblies have the highest numbers of gapless gene territories (right panel) and the fewest number of gaps of all assemblies except the recent chicken v4 assembly, which used a similar technology (left panel).
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Figure 2: Number of nucleotide gaps assess relative assembly incompleteness. A) Shows the total number of gaps in genes and the surrounding 10,000 base pair regions upstream and downstream (collectively called gene territories). B) Shows the number of such gene territories with gaps. In both the panels, different species assemblies are colored differently, with the budgerigar assemblies shown in dark blue. The budgerigar assemblies with the “-mega” suffix are optical map enhanced versions of the Budgerigar_v6.3 and PBcR assemblies. The budgerigar assemblies have the highest numbers of gapless gene territories (right panel) and the fewest number of gaps of all assemblies except the recent chicken v4 assembly, which used a similar technology (left panel).

Mentions: Our budgerigar genome assemblies were compared with the zebra finch, chicken, and falcon genomes [15-17]. The other assemblies from the Assemblathon 2 competition are available from GigaDB [18]. The zebra finch and chicken had similar contig and scaffold N50 values (38.5 kb and 10.4 Mb for zebra finch, and 279.8 kb and 90.2 Mb for chicken, respectively). In addition, since the Peregrine Falcon is the closest relative to parrots [19], we also compared the budgerigar genome assemblies to this bird. However, it was not possible to do an in depth comparison of these genomes to the recently sequenced Scarlet Macaw and Puerto Rican Parrot genomes [20,21], because both bird genomes had N50 scaffold sizes under 20,000 and N50 contig sizes under 7,000. A summary of assemblies, including the Scarlet Macaw and Puerto Rican Parrot, are shown in Table 2. Apart from the standard genome assembly quality statistics, we assessed the quality of the budgerigar assemblies along two other dimensions: (1) the coverage of highly conserved avian exons, and (2) the number of gaps 10 Kbp upstream and downstream of each gene (gene territories), and conversely, the number gene territories assembled without gaps. Of 3,288 highly conserved exons (>86% coverage across >87% of their length) we identified between chicken and zebra finch, 3,165 (96.25%) and 3,134 (95.31%) were covered with >86% identity across >87% of their length in the Budgerigar_v6.3 and PBcR assemblies respectively, pointing to good coverage of coding regions in these assemblies. The budgerigar assemblies had fewer gaps within the coding sequences and gene territories than all other avian genomes examined, except the newer unpublished Galgal4 chicken assembly that is similar to the budgerigar in that it is a hybrid that includes both short and long sequences (Sanger and 454 FLX+) (Figure 2). This suggests that our budgerigar assemblies have very well assembled genes and promoter regions.


High-coverage sequencing and annotated assemblies of the budgerigar genome.

Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, Wray G, Rasolonjatovo I, Winer R, Knight JR, Koren S, Warren WC, Zhang G, Phillippy AM, Jarvis ED - Gigascience (2014)

Number of nucleotide gaps assess relative assembly incompleteness. A) Shows the total number of gaps in genes and the surrounding 10,000 base pair regions upstream and downstream (collectively called gene territories). B) Shows the number of such gene territories with gaps. In both the panels, different species assemblies are colored differently, with the budgerigar assemblies shown in dark blue. The budgerigar assemblies with the “-mega” suffix are optical map enhanced versions of the Budgerigar_v6.3 and PBcR assemblies. The budgerigar assemblies have the highest numbers of gapless gene territories (right panel) and the fewest number of gaps of all assemblies except the recent chicken v4 assembly, which used a similar technology (left panel).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4109783&req=5

Figure 2: Number of nucleotide gaps assess relative assembly incompleteness. A) Shows the total number of gaps in genes and the surrounding 10,000 base pair regions upstream and downstream (collectively called gene territories). B) Shows the number of such gene territories with gaps. In both the panels, different species assemblies are colored differently, with the budgerigar assemblies shown in dark blue. The budgerigar assemblies with the “-mega” suffix are optical map enhanced versions of the Budgerigar_v6.3 and PBcR assemblies. The budgerigar assemblies have the highest numbers of gapless gene territories (right panel) and the fewest number of gaps of all assemblies except the recent chicken v4 assembly, which used a similar technology (left panel).
Mentions: Our budgerigar genome assemblies were compared with the zebra finch, chicken, and falcon genomes [15-17]. The other assemblies from the Assemblathon 2 competition are available from GigaDB [18]. The zebra finch and chicken had similar contig and scaffold N50 values (38.5 kb and 10.4 Mb for zebra finch, and 279.8 kb and 90.2 Mb for chicken, respectively). In addition, since the Peregrine Falcon is the closest relative to parrots [19], we also compared the budgerigar genome assemblies to this bird. However, it was not possible to do an in depth comparison of these genomes to the recently sequenced Scarlet Macaw and Puerto Rican Parrot genomes [20,21], because both bird genomes had N50 scaffold sizes under 20,000 and N50 contig sizes under 7,000. A summary of assemblies, including the Scarlet Macaw and Puerto Rican Parrot, are shown in Table 2. Apart from the standard genome assembly quality statistics, we assessed the quality of the budgerigar assemblies along two other dimensions: (1) the coverage of highly conserved avian exons, and (2) the number of gaps 10 Kbp upstream and downstream of each gene (gene territories), and conversely, the number gene territories assembled without gaps. Of 3,288 highly conserved exons (>86% coverage across >87% of their length) we identified between chicken and zebra finch, 3,165 (96.25%) and 3,134 (95.31%) were covered with >86% identity across >87% of their length in the Budgerigar_v6.3 and PBcR assemblies respectively, pointing to good coverage of coding regions in these assemblies. The budgerigar assemblies had fewer gaps within the coding sequences and gene territories than all other avian genomes examined, except the newer unpublished Galgal4 chicken assembly that is similar to the budgerigar in that it is a hybrid that includes both short and long sequences (Sanger and 454 FLX+) (Figure 2). This suggests that our budgerigar assemblies have very well assembled genes and promoter regions.

Bottom Line: The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing.Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions.This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.

ABSTRACT

Background: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome.

Findings: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing.

Conclusions: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

No MeSH data available.


Related in: MedlinePlus