Additional file 3. Text file of multiple alignment of mammalian GTF2IRD2/2A to predicted GTF2IRD2/2A sequences in vertebrates

Additional file 3. Text file of multiple alignment of mammalian GTF2IRD2/2A to predicted GTF2IRD2/2A sequences in vertebrates

Sophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). However, there is little genomic information available for S. flavescens, which has greatly hindered the breeding of S. flavescens and characterisation of bioactive compounds. Therefore, in this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs). We also annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues. We also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome provides valuable resources for conservation, genetic research and breeding of S. flavescens.

Sophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). However, there is little genomic information available for S. flavescens, which has greatly hindered the breeding of S. flavescens and characterisation of bioactive compounds. Therefore, in this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs). We also annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues. We also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome provides valuable resources for conservation, genetic research and breeding of S. flavescens.

Sophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). However, there is little genomic information available for S. flavescens, which has greatly hindered the breeding of S. flavescens and characterisation of bioactive compounds. Therefore, in this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs). We also annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues. We also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome provides valuable resources for conservation, genetic research and breeding of S. flavescens.

Abstract Transposable elements (TEs) are self replicating genetic sequences and are often described as important “drivers of evolution”. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions will be neutral or harmful, therefore host genomes have evolved machinery to supress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonise new genomes, and since new hosts may not be able to shut them down, these TEs may proliferate rapidly. Here we describe HTT of the Harbinger-Snek DNA transposon into sea kraits (Laticauda), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids ~15-25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8-12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat. Dataset The deposited dataset contains scripts used in analysis, GFFs of the Laticauda genome gene annotations produced using Liftoff, repeat sequences of all Harbinger-Snek variants and Harbinger-Snek-like TEs, repeat library used in RepeatMasker repeat annotation, repeat annotation of Laticauda, Notechis and Pseudonaja genomes, screenshots of IGV showing RNASeq reads mapped to gene exons and UTRs containing Harbinger-Snek insertions, and all phylogenetic trees and the sequence data used in generating them.

Abstract Transposable elements (TEs) are self replicating genetic sequences and are often described as important “drivers of evolution”. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions will be neutral or harmful, therefore host genomes have evolved machinery to supress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonise new genomes, and since new hosts may not be able to shut them down, these TEs may proliferate rapidly. Here we describe HTT of the Harbinger-Snek DNA transposon into sea kraits (Laticauda), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids ~15-25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8-12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat. Dataset The deposited dataset contains scripts used in analysis, GFFs of the Laticauda genome gene annotations produced using Liftoff, repeat sequences of all Harbinger-Snek variants and Harbinger-Snek-like TEs, repeat library used in RepeatMasker repeat annotation, repeat annotation of Laticauda, Notechis and Pseudonaja genomes, screenshots of IGV showing RNASeq reads mapped to gene exons and UTRs containing Harbinger-Snek insertions, and all phylogenetic trees and the sequence data used in generating them.

Table 1 - Laticauda colubrina and Laticauda laticaudata genes with Harbinger-Snek insertions into or overlapping open reading frames, and any noticeable effects on insertion noted from transcript data. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using BEDTools [54]. Transcripts mapped to the genome assembly using STAR [44] and viewed in IGV [45]. Table 2 - Biological processes with an over/under-representation of Harbinger-Snek insertions into Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 3 - Molecular functions with an over/under-representation of Harbinger-Snek insertions into Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 4 - Biological processes with an over/under-representation of Harbinger-Snek insertions into potential regulatory regions of Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 5 - Molecular functions with an over/under-representation of Harbinger-Snek insertions into potential regulatory regions of Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 6 - Latin species names and versions of all public genomes used. All were downloaded from RefSeq [41] when available, else from GenBank [55].

Table 1 - Laticauda colubrina and Laticauda laticaudata genes with Harbinger-Snek insertions into or overlapping open reading frames, and any noticeable effects on insertion noted from transcript data. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using BEDTools [54]. Transcripts mapped to the genome assembly using STAR [44] and viewed in IGV [45]. Table 2 - Biological processes with an over/under-representation of Harbinger-Snek insertions into Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 3 - Molecular functions with an over/under-representation of Harbinger-Snek insertions into Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 4 - Biological processes with an over/under-representation of Harbinger-Snek insertions into potential regulatory regions of Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 5 - Molecular functions with an over/under-representation of Harbinger-Snek insertions into potential regulatory regions of Laticauda colubrina genes. Representation test performed using PANTHER [43]. Gene coordinates predicted with Liftoff [40] using the RefSeq Notechis scutatus assembly and gene annotation as reference. Repeat annotation performed with RepeatMasker [39] using a custom repeat library (see Methods). Intersect performed using plyranges [42]. Table 6 - Latin species names and versions of all public genomes used. All were downloaded from RefSeq [41] when available, else from GenBank [55].

These repeat consensus sequences are part of the genome analysis of the Tuatara genome.