Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer
Abstract
:1. Introduction
2. Materials and Methods
2.1. Re-Analyzing Phylogenetic Relationships of GH6-Containing Proteins of Tunicates, Fungi, Other Eukaryotes, and Bacteria
2.2. Sequence Comparison
3. Results
3.1. Tunicate CesA-GH6 Domains and Tunicate GH6-1 Genes Represent Two Independent Monophyletic Groups
3.2. The Origin of Tunicate GH6 Domains Is Hard to Deduce
3.3. Many Tunicate GH6-1 Proteins Maintain the Probable Active Site, in Contrast to Tunicate CesA Proteins
3.4. Splice Site Conservation in Tunicate CesA Genes or GH6-1 Genes
3.5. Genomic Locations of Tunicate CesA Genes and GH6-1 Genes are Separated
4. Discussion
4.1. Two GH6-Containing Genes Exist in Tunicate Genomes
4.2. Lineage-Specific Gene Content Change Along with Sequence Signature Conservation
4.3. Shared Splice Sites Indicate the Ancient History of Tunicate GH6 Genes
4.4. Future Perspective
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species | Domain Content | Short Name of the Gene Used in this Manuscript * | Source Database | Accession/ID of Gene, Transcript, or Protein | Note |
---|---|---|---|---|---|
Ciona intestinalis type A (C. robusta) | GH6 | CinGH6-1 | GenBank | XM_002119543.4/XP_002119579.1 | |
CesA+GH6 | CinCesA | GenBank | NM_001047983.1/BAD10864.1 | As reported in [10] | |
Ciona savignyi | GH6 | CsaGH6-1 | GenBank (Transcriptome) | GGEI01013363.1 | |
CesA+GH6 | CsaCesA | GenBank | AY504665.1/AAR89623.1 | As reported in [11] | |
Salpa thompsoni | GH6 | SthGH6-1a | GenBank (Transcriptome) | GFCC01117283.1 | Possible lineage-specific duplication |
GH6 | SthGH6-1b | GenBank (Transcriptome) | GFCC01119318.1 | No possible catalytic Asp; possible lineage-specific duplication. | |
CesA+GH6 | SthCesA | GenBank (Transcriptome) | GFCC01072613.1 | ||
Molgula occidentalis | GH6 | MoxGH6-1 | Aniseed database | Moocci.CG.ELv1_2.S285391.g07021.01.t | |
CesA+GH6 | MoxCesAa | Aniseed database | Moocci.CG.ELv1_2.S469068.g15915.01.t | Short GH6 part | |
GH6 | (MoxCesAbGH6) | Aniseed database | Moocci.CG.ELv1_2.S469068.g15914.01.t | Very short | |
GH6 | MoxCesAcGH6 | Aniseed database | Moocci.CG.ELv1_2.S469068.g15913.01.t | ||
Molgula oculata | GH6 | MocGH6-1 | Aniseed database | Moocul.CG.ELv1_2.S112948.g12660.01.t | |
CesA+GH6 | MocCesAa | Aniseed database | Moocul.CG.ELv1_2.S71617.g04842.01.t | Rhodopsin-like GPCR domain at upstream part | |
GH6 | MocCesAbGH6 | Aniseed database | Moocul.CG.ELv1_2.S69739.g04625.01.t | ||
Botryllus schlosseri | GH6 | BscGH6-1 | Botryllus schlosseri Genome Project | g9326 | |
GH6 | (BscGH6-1b) | Botryllus schlosseri Genome Project | g61144 | Short, similar to BscGH6-1 | |
GH6 | BscCesAaGH6 | Botryllus schlosseri Genome Project | g44331 | Similar to BscCesAbGH6 (89.6% identity in the matching 222 AA region) | |
GH6 | BscCesAbGH6 | Botryllus schlosseri Genome Project | g45080 | Similar to BscCesAaGH6 | |
Botrylloides leachii | GH6 | BleGH6-1 | Aniseed database | Boleac.CG.SB_v3.S133.g02304.01.t | |
CesA+GH6 | BleCesA | Aniseed database | Boleac.CG.SB_v3.S157.g03251.01.t | ||
Oikopleura dioica | GH6 | OdiGH6-1 | OikoBase/GenBank | GSOIDT00010490001/CBY09680.1 | |
GH6 | (OdiGH6-1b) | OikoBase/GenBank | GSOIDT00021901001/CBY33927.1 | 98% identical to OdiGH6 | |
CesA+GH6 | OdiCesA2 | GenBank | AB543593.1/BAJ65326.1 | As reported in [12,13] | |
CesA+GH6 | OdiCesA1 | GenBank | AB543594.1/BAJ65327.1 | As reported in [12,13] |
Taxa | GH6 presence? | |||
---|---|---|---|---|
Bacteria | Present | |||
Archaea | Not yet observed | |||
Eukaryota | Opisthokonta | Metazoa | tunicates | Present |
Metazoa, except tunicate | No? Contamination? *1 | |||
Fungi | Present | |||
Opisthokonta, except Metazoa and fungi | Not yet observed | |||
Viridiplantae | No? Contamination? *2 | |||
SAR-Stramenopiles | Present | |||
SAR-Alveolate | Present | |||
SAR-Rhizaria | Not yet observed | |||
Haptista | Present | |||
Rhodophyta | Present | |||
Other eukaryotes | Not yet observed |
Splice site name | ||||
---|---|---|---|---|
Cin217 | Cin256 | Cin316 | ||
Protein | Introns within coding region | Splice site residue & frame | ||
CinGH6-1 | 3 | V217, +2 | G256, +1 | K316, +3 |
CsaGH6-1 | 3 | V223, +2 | G262, +1 | K322, +3 |
SthGH6-1a | 6 | E229, +2 | G268, +1 | P328, +3 |
SthGH6-1b | 5 | K230, +2 | G269, +1 | K329, +3 |
MoxGH6-1 | 3 | R222, +2 | G260, +1 | A320, +3 |
MocGH6-1 | 2 | n.s.*1 (R222) | G260, +1 | A320, +3 |
BscGH6-1 | 5 | K335, +2 | G373, +1 | A433, +3 |
BleGH6-1 | 4 | K229, +2 | n.s.*2 (G285) | A345, +3 |
OdiGH6-1 | 6 | n.s.*1 (N244) | n.s.*2 (G282) | n.s.*1 (K343) |
OdiCesA1*3 | 8 | n.s.*1 (R1001) | n.s.*2 (G1040) | R1100*3, frame +2 |
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Li, K.-L.; Nakashima, K.; Inoue, J.; Satoh, N. Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer. Genes 2020, 11, 937. https://doi.org/10.3390/genes11080937
Li K-L, Nakashima K, Inoue J, Satoh N. Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer. Genes. 2020; 11(8):937. https://doi.org/10.3390/genes11080937
Chicago/Turabian StyleLi, Kun-Lung, Keisuke Nakashima, Jun Inoue, and Noriyuki Satoh. 2020. "Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer" Genes 11, no. 8: 937. https://doi.org/10.3390/genes11080937
APA StyleLi, K.-L., Nakashima, K., Inoue, J., & Satoh, N. (2020). Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer. Genes, 11(8), 937. https://doi.org/10.3390/genes11080937