Abstract
The genome of faba bean was first published in 2023. To promote future molecular breeding studies, we improved the quality of the faba genome based on high-density genetic maps and the Illumina and Pacbio RNA-seq datasets. Two high-density genetic maps were used to conduct the scaffold ordering and orientation of faba bean, culminating in an increased length (i.e., 14.28 Mbp) of chromosomes and a decrease in the number of scaffolds by 45. In gene model mining and optimisation, the PacBio and Illumina RNA-seq datasets from 37 samples allowed for the identification and correction 121,606 transcripts, and the data facilitated a prediction of 15,640 alternative splicing events, 2,148 lncRNAs, and 1,752 fusion transcripts, thus allowing for a clearer understanding of the gene structures underlying the faba genome. Moreover, a total of 38,850 new genes including 56,188 transcripts were identified compared with the reference genome. Finally, the genetic data of the reference genome was integrated and a comprehensive and complete faba bean transcriptome sequence of 103,267 transcripts derived from 54,753 uni-genes was formed.
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Claims 10
Claim · model-written summary
Scaffold ordering with two high-density genetic maps increased faba bean chromosome length to 14.28 Mbp
- Taxon
- faba bean
Vicia fabat0 - Outcome
- lengthe1
- Direction
- increasede1
- Value
- 14.28 Mbpe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e1“Two high-density genetic maps were used to conduct the scaffold ordering and orientation of faba bean, culminating in an increased length (i.e., 14.28 Mbp) of chromosomes and a decrease in the number of scaffolds by 45”
Claim · model-written summary
Scaffold ordering decreased the number of faba bean scaffolds by 45
- Taxon
- faba beanVicia fabat0
- Outcome
- number of scaffoldse1
- Direction
- decreasee1
- Value
- 45e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e1“Two high-density genetic maps were used to conduct the scaffold ordering and orientation of faba bean, culminating in an increased length (i.e., 14.28 Mbp) of chromosomes and a decrease in the number of scaffolds by 45”
Claim · model-written summary
PacBio and Illumina RNA-seq datasets from 37 samples allowed identification and correction of 121,606 transcripts
- Taxon
- faba beanVicia fabat0
- Outcome
- identification and correctione2
- Value
- 121,606 transcriptse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e2“the PacBio and Illumina RNA-seq datasets from 37 samples allowed for the identification and correction 121,606 transcripts”
Claim · model-written summary
RNA-seq data predicted 15,640 alternative splicing events in faba bean
- Taxon
- faba beanVicia fabat0
- Outcome
- alternative splicing eventse3
- Value
- 15,640e3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e3“the data facilitated a prediction of 15,640 alternative splicing events, 2,148 lncRNAs, and 1,752 fusion transcripts”
Claim · model-written summary
RNA-seq data predicted 2,148 lncRNAs in faba bean
- Taxon
- faba beanVicia fabat0
- Outcome
- lncRNAse3
- Value
- 2,148e3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e3“the data facilitated a prediction of 15,640 alternative splicing events, 2,148 lncRNAs, and 1,752 fusion transcripts”
Claim · model-written summary
RNA-seq data predicted 1,752 fusion transcripts in faba bean
- Taxon
- faba beanVicia fabat0
- Outcome
- fusion transcriptse3
- Value
- 1,752e3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e3“the data facilitated a prediction of 15,640 alternative splicing events, 2,148 lncRNAs, and 1,752 fusion transcripts”
Claim · model-written summary
Compared with the reference genome, 38,850 new faba bean genes were identified
- Taxon
- faba beanVicia fabat0
- Outcome
- new genese4
- Value
- 38,850e4
- Comparator
- reference genomee4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e4“Moreover, a total of 38,850 new genes including 56,188 transcripts were identified compared with the reference genome”
Claim · model-written summary
Compared with the reference genome, 56,188 new faba bean transcripts were identified
- Taxon
- faba beanVicia fabat0
- Outcome
- transcriptse4
- Value
- 56,188e4
- Comparator
- reference genomee4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e4“Moreover, a total of 38,850 new genes including 56,188 transcripts were identified compared with the reference genome”
Claim · model-written summary
The integrated faba bean transcriptome sequence contains 103,267 transcripts
- Taxon
- faba beanVicia fabat0
- Outcome
- transcriptome sequencee5
- Value
- 103,267 transcriptse5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e5“a comprehensive and complete faba bean transcriptome sequence of 103,267 transcripts derived from 54,753 uni-genes was formed”
Claim · model-written summary
The integrated faba bean transcriptome is derived from 54,753 uni-genes
- Taxon
- faba beanVicia fabat0
- Outcome
- uni-genese5
- Value
- 54,753 uni-genese5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“faba bean”
e5“a comprehensive and complete faba bean transcriptome sequence of 103,267 transcripts derived from 54,753 uni-genes was formed”