Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii)
The economically important Southern bluefin tuna (Thunnus maccoyii) is a world-famous fast-swimming fish, but its genomic information is limited. Here, we performed whole genome sequencing and assembled a draft genome for Southern bluefin tuna, aiming to generate useful genetic data for comparative...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-11-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1020017/full |
| _version_ | 1811334929897750528 |
|---|---|
| author | Xiaomeng Zhao Xiaomeng Zhao Yu Huang Chao Bian Xinxin You Xinxin You Xinhui Zhang Xinhui Zhang Xinhui Zhang Jieming Chen Min Wang Cancan Hu Yun Xu Yun Xu Yun Xu Junmin Xu Junmin Xu Junmin Xu Qiong Shi Qiong Shi Qiong Shi |
| author_facet | Xiaomeng Zhao Xiaomeng Zhao Yu Huang Chao Bian Xinxin You Xinxin You Xinhui Zhang Xinhui Zhang Xinhui Zhang Jieming Chen Min Wang Cancan Hu Yun Xu Yun Xu Yun Xu Junmin Xu Junmin Xu Junmin Xu Qiong Shi Qiong Shi Qiong Shi |
| author_sort | Xiaomeng Zhao |
| collection | DOAJ |
| description | The economically important Southern bluefin tuna (Thunnus maccoyii) is a world-famous fast-swimming fish, but its genomic information is limited. Here, we performed whole genome sequencing and assembled a draft genome for Southern bluefin tuna, aiming to generate useful genetic data for comparative functional prediction. The final genome assembly is 806.54 Mb, with scaffold and contig N50 values of 3.31 Mb and 67.38 kb, respectively. Genome completeness was evaluated to be 95.8%. The assembled genome contained 23,403 protein-coding genes and 236.1 Mb of repeat sequences (accounting for 29.27% of the entire assembly). Comparative genomics analyses of this fast-swimming tuna revealed that it had more than twice as many hemoglobin genes (18) as other relatively slow-moving fishes (such as seahorse, sunfish, and tongue sole). These hemoglobin genes are mainly localized in two big clusters (termed as “MNˮ and “LAˮ respectively), which is consistent with other reported fishes. However, Thr39 of beta-hemoglobin in the MN cluster, conserved in other fishes, was mutated as cysteine in tunas including the Southern bluefin tuna. Since hemoglobins are reported to transport oxygen efficiently for aerobic respiration, our genomic data suggest that both high copy numbers of hemoglobin genes and an adjusted function of the beta-hemoglobin may support the fast-swimming activity of tunas. In summary, we produced a primary genome assembly and predicted hemoglobin-related roles for the fast-swimming Southern bluefin tuna. |
| first_indexed | 2024-04-13T17:16:35Z |
| format | Article |
| id | doaj.art-856d52d3b9654bedad746b076d93094d |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T17:16:35Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-856d52d3b9654bedad746b076d93094d2022-12-22T02:38:07ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-11-011310.3389/fgene.2022.10200171020017Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii)Xiaomeng Zhao0Xiaomeng Zhao1Yu Huang2Chao Bian3Xinxin You4Xinxin You5Xinhui Zhang6Xinhui Zhang7Xinhui Zhang8Jieming Chen9Min Wang10Cancan Hu11Yun Xu12Yun Xu13Yun Xu14Junmin Xu15Junmin Xu16Junmin Xu17Qiong Shi18Qiong Shi19Qiong Shi20College of Life Sciences, University of Chinese Academy of Sciences, Beijing, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaAquatic Breeding Center, BGI Marine, Shenzhen, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaAquatic Breeding Center, BGI Marine, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaBGI Zhenjiang Institute of Hydrobiology, Zhenjiang, ChinaAquatic Breeding Center, BGI Marine, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaAquatic Breeding Center, BGI Marine, Shenzhen, ChinaBGI Zhenjiang Institute of Hydrobiology, Zhenjiang, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaAquatic Breeding Center, BGI Marine, Shenzhen, ChinaBGI Zhenjiang Institute of Hydrobiology, Zhenjiang, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaAquatic Breeding Center, BGI Marine, Shenzhen, ChinaThe economically important Southern bluefin tuna (Thunnus maccoyii) is a world-famous fast-swimming fish, but its genomic information is limited. Here, we performed whole genome sequencing and assembled a draft genome for Southern bluefin tuna, aiming to generate useful genetic data for comparative functional prediction. The final genome assembly is 806.54 Mb, with scaffold and contig N50 values of 3.31 Mb and 67.38 kb, respectively. Genome completeness was evaluated to be 95.8%. The assembled genome contained 23,403 protein-coding genes and 236.1 Mb of repeat sequences (accounting for 29.27% of the entire assembly). Comparative genomics analyses of this fast-swimming tuna revealed that it had more than twice as many hemoglobin genes (18) as other relatively slow-moving fishes (such as seahorse, sunfish, and tongue sole). These hemoglobin genes are mainly localized in two big clusters (termed as “MNˮ and “LAˮ respectively), which is consistent with other reported fishes. However, Thr39 of beta-hemoglobin in the MN cluster, conserved in other fishes, was mutated as cysteine in tunas including the Southern bluefin tuna. Since hemoglobins are reported to transport oxygen efficiently for aerobic respiration, our genomic data suggest that both high copy numbers of hemoglobin genes and an adjusted function of the beta-hemoglobin may support the fast-swimming activity of tunas. In summary, we produced a primary genome assembly and predicted hemoglobin-related roles for the fast-swimming Southern bluefin tuna.https://www.frontiersin.org/articles/10.3389/fgene.2022.1020017/fullsouthern bluefin tuna (Thunnus maccoyii)genome sequencingassemblyhemoglobinevolution |
| spellingShingle | Xiaomeng Zhao Xiaomeng Zhao Yu Huang Chao Bian Xinxin You Xinxin You Xinhui Zhang Xinhui Zhang Xinhui Zhang Jieming Chen Min Wang Cancan Hu Yun Xu Yun Xu Yun Xu Junmin Xu Junmin Xu Junmin Xu Qiong Shi Qiong Shi Qiong Shi Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii) Frontiers in Genetics southern bluefin tuna (Thunnus maccoyii) genome sequencing assembly hemoglobin evolution |
| title | Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii) |
| title_full | Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii) |
| title_fullStr | Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii) |
| title_full_unstemmed | Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii) |
| title_short | Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii) |
| title_sort | whole genome sequencing of the fast swimming southern bluefin tuna thunnus maccoyii |
| topic | southern bluefin tuna (Thunnus maccoyii) genome sequencing assembly hemoglobin evolution |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1020017/full |
| work_keys_str_mv | AT xiaomengzhao wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT xiaomengzhao wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT yuhuang wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT chaobian wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT xinxinyou wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT xinxinyou wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT xinhuizhang wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT xinhuizhang wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT xinhuizhang wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT jiemingchen wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT minwang wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT cancanhu wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT yunxu wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT yunxu wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT yunxu wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT junminxu wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT junminxu wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT junminxu wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT qiongshi wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT qiongshi wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii AT qiongshi wholegenomesequencingofthefastswimmingsouthernbluefintunathunnusmaccoyii |