Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome

Abstract

Background: Anguilla japonica (Japanese eel) is currently one of the most important research subjects in eastern Asia aquaculture. Enigmatic life cycle of the organism makes study of artificial reproduction extremely limited. Henceforth genomic and transcriptomic resources of eels are urgently needed to help solving the problems surrounding this organism across multiple fields. We hereby provide a reconstructed transcriptome from deep sequencing of juvenile (glass eels) whole body samples. The provided expressed sequence tags were used to annotate the currently available draft genome sequence. Homologous information derived from the annotation result was applied to improve the group of scaffolds into available linkage groups.

Results: With the transcriptome sequence data combined with publicly available expressed sequence tags evidences, 18,121 genes were structurally and functionally annotated on the draft genome. Among them, 3,921 genes were located in the 19 linkage groups. 137 scaffolds covering 13 million bases were grouped into the linkage groups in additional to the original partial linkage groups, increasing the linkage group coverage from 13 to 14%.

Conclusions: This annotation provide information of the coding regions of the genes supported by transcriptome based evidence. The derived homologous evidences pave the way for phylogenetic analysis of important genetic traits and the improvement of the genome assembly.

Fig. 1

Overview of the Genome Annotation Process. The overall flowchart of the genome annotation of Anguilla Japonica is showed in this graph. De Novo assembly of the transcriptome was treated as EST evidences, combined with other previously published information, aligned onto the draft genome. The annotation process was performed through MAKER

Fig. 2

Homolog Linkage Map of Anguilla Japonica (Linkage Groups 1 to 6). The graph shows genetic linkage maps on 6 of the 19 linkage groups. With the homologs synteny information derived from the functional annotation, we successfully allocated 137 scaffolds (13 Mb) into the established linkage group. This graph illustrates the relative position of the scaffolds. Order of the combined scaffolds was determined by an application of topological sort to combine the linkage maps of male and female linkage. Since evidence of the distance between scaffolds is not available, only the putative order was demonstrated here. The homologs gene cluster was showed in gray color

Fig. 3

Homolog Linkage Map of Anguilla Japonica (Linkage Groups 7 to 12). The graph shows genetic linkage maps on 6 of the 19 linkage groups. With the homologs synteny information derived from the functional annotation, we successfully allocated 137 scaffolds (13 Mb) into the established linkage group. This graph illustrates the relative position of the scaffolds. Order of the combined scaffolds was determined by an application of topological sort to combine the linkage maps of male and female linkage. Since evidence of the distance between scaffolds is not available, only the putative order was demonstrated here. The homologs gene cluster was showed in gray color

Fig. 4

Homolog Linkage Map of Anguilla Japonica (Linkage Groups 13 to 16). The graph shows genetic linkage maps on 4 of the 19 linkage groups. With the homologs synteny information derived from the functional annotation, we successfully allocated 137 scaffolds (13 Mb) into the established linkage group. This graph illustrates the relative position of the scaffolds. Order of the combined scaffolds was determined by an application of topological sort to combine the linkage maps of male and female linkage. Since evidence of the distance between scaffolds is not available, only the putative order was demonstrated here. The homologs gene cluster was showed in gray color

Fig. 5

Homolog Linkage Map of Anguilla Japonica (Linkage Groups 17 to 19). The graph shows genetic linkage maps on 3 of the 19 linkage groups. With the homologs synteny information derived from the functional annotation, we successfully allocated 137 scaffolds (13 Mb) into the established linkage group. This graph illustrates the relative position of the scaffolds. Order of the combined scaffolds was determined by an application of topological sort to combine the linkage maps of male and female linkage. Since evidence of the distance between scaffolds is not available, only the putative order was demonstrated here. The homologs gene cluster was showed in gray color

Fig. 6

Phylogenetic Tree of Thyroid Hormone Receptor Interactor (TRIP) Family Homologs. This graph illustrated the thyroid hormone receptors homologs of Anguilla Japonica. From the separate color subtree of TRIP4, TRIP11, TRIP12 and TRIP13 genes homologs, we can see that the different homologs of same gene family are distributed into different subtree

Fig. 7

Phylogenetic Trees of Thyroid Hormone Receptor Interactor (TRIP) Subfamilies. In this graph, each circular tree represents the corresponding color subtrees illustrated in Fig. 6. a The blue circular tree represent the TRIP11 subtree, with 2 Anguilla Japonica homologs marked in red dots. b The yellow circular tree represent the TRIP4 subtree, with 1 Anguilla Japonica homologs marked in red dot. c The red circular tree represent the TRIP13 subtree, with 1 Anguilla Japonica homologs marked in red dot. d The green circular tree represent the TRIP12 subtree, with 7 Anguilla Japonica homologs marked in red dots. Through the analysis we found that the thyroid hormone receptor interactor family genes of Japanese eel are homologous to Asian arowana, Northern Pike, Rainbow trout, Marbled rockcod, Atlantic herring and Spotted gar

Fig. 8

Phylogenetic Tree of Nuclear Receptor Subfamily 2. This graph illustrated the nuclear receptors homologs of Anguilla Japonica. From the separate color circular subtree of NR2F2, NR2F6, NR2C1, NR2C2, NR2E1 and NR2E3 genes homologs, we can see that the different homologs of same gene family are distributed into different subtree

Fig. 9

Phylogenetic Trees of Nuclear Receptor Subfamily 2 Groups. In this graph, each circular tree represents the corresponding color subtrees illustrated in Fig. 8. a The green circular tree represent the NR2E3 subtree, with 3 Anguilla Japonica homologs marked in red dots. b The brown circular tree represent the NR2E1 subtree, with 1 Anguilla Japonica homolog marked in red dot. c The purple circular tree represent the NR2C1 subtree, with 2 Anguilla Japonica homologs marked in red dots. d The gray circular tree represent the NR2C2 subtree, with 1 Anguilla Japonica homolog marked in red dot. e The yellow circular tree represent the NR2F2 subtree, with 3 Anguilla Japonica homologs marked in red dots. f The blue circular tree represent the NR2F6 subtree, with 2 Anguilla Japonica homologs marked in red dots. Through the analysis we found that the thyroid hormone receptor interactor family genes of Japanese eel are homologous to Asian arowana, Northern Pike, Rainbow trout, Marbled rockcod, Atlantic herring and Spotted gar

Fig. 10

Phylogenetic Tree and Linkage Location of LYST Homologs. In this graph, we found a lysosomal trafficking regulator LYST cluster (in red box) in linkage group 10 (LG10). The gene was close related to the homolog of Asian arowana. There are 4 other Anguilla Japonica homologs of LYST marked on the circular tree

Fig. 11

Overview of the Genetic Linkage Map Building Process. a We utilized the following phylogenetic tree. While provided with 7190 scaffolds with homologous genes on them, scaffolding method identified 525 links and assembled scaffolds respectively. These scaffolds were then mapped into male and female linkage maps provided by the Kai et al. study. b The scaffolds mapped into male and female linkage groups were then sorted into single group. As illustrated in the graph, scaffolds marked with same colors provide the evidences for the general order of them on the chromosome. The order can then be sorted through topological sort algorithm