Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master's Course
Copyright © 2020 Prost et al..
Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master's course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master's course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2020 |
|---|---|
| Erschienen: |
2020 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:10 |
|---|---|
| Enthalten in: |
G3 (Bethesda, Md.) - 10(2020), 7 vom: 07. Juli, Seite 2179-2183 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Prost, Stefan [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Betta splendens |
|---|
| Anmerkungen: |
Date Completed 21.06.2021 Date Revised 21.06.2021 published: Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1534/g3.120.401205 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM309682878 |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM309682878 | ||
| 003 | DE-627 | ||
| 005 | 20231226201419.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231225s2020 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1534/g3.120.401205 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1032.xml |
| 035 | |a (DE-627)NLM309682878 | ||
| 035 | |a (NLM)32385046 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Prost, Stefan |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master's Course |
| 264 | 1 | |c 2020 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 21.06.2021 | ||
| 500 | |a Date Revised 21.06.2021 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2020 Prost et al. | ||
| 520 | |a Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master's course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master's course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Betta splendens | |
| 650 | 4 | |a chromosome-level genome assembly | |
| 650 | 4 | |a master’s course | |
| 700 | 1 | |a Petersen, Malte |e verfasserin |4 aut | |
| 700 | 1 | |a Grethlein, Martin |e verfasserin |4 aut | |
| 700 | 1 | |a Hahn, Sarah Joy |e verfasserin |4 aut | |
| 700 | 1 | |a Kuschik-Maczollek, Nina |e verfasserin |4 aut | |
| 700 | 1 | |a Olesiuk, Martyna Ewa |e verfasserin |4 aut | |
| 700 | 1 | |a Reschke, Jan-Olaf |e verfasserin |4 aut | |
| 700 | 1 | |a Schmey, Tamara Elke |e verfasserin |4 aut | |
| 700 | 1 | |a Zimmer, Caroline |e verfasserin |4 aut | |
| 700 | 1 | |a Gupta, Deepak K |e verfasserin |4 aut | |
| 700 | 1 | |a Schell, Tilman |e verfasserin |4 aut | |
| 700 | 1 | |a Coimbra, Raphael |e verfasserin |4 aut | |
| 700 | 1 | |a De Raad, Jordi |e verfasserin |4 aut | |
| 700 | 1 | |a Lammers, Fritjof |e verfasserin |4 aut | |
| 700 | 1 | |a Winter, Sven |e verfasserin |4 aut | |
| 700 | 1 | |a Janke, Axel |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t G3 (Bethesda, Md.) |d 2011 |g 10(2020), 7 vom: 07. Juli, Seite 2179-2183 |w (DE-627)NLM215888499 |x 2160-1836 |7 nnns |
| 773 | 1 | 8 | |g volume:10 |g year:2020 |g number:7 |g day:07 |g month:07 |g pages:2179-2183 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1534/g3.120.401205 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 10 |j 2020 |e 7 |b 07 |c 07 |h 2179-2183 | ||