Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae

Sampling and sequencing Whole genome shotgun short read sequencing data of 48 individuals covering all four giraffe species and seven subspecies from Coimbra et al. (2021) was used for TE analysis using MELT (Gardner et al. 2017). The northern giraffe (G. camelopardalis) is represented by 15 individuals, including its three subspecies: the Nubian (G. c. camelopardalis), the Kordofan (G. c. antiquorum), and the West African giraffe (G. c. peralta). The reticulated giraffe (G. reticulata) is represented by ten individuals. The Masai giraffe sensu lato (G. tippelskirchi) is represented by 12 individuals, including its two subspecies: the Luangwa (G. t. thornicrofti) and the Masai giraffe sensu stricto (G. t. tippelskirchi). Finally, the southern giraffe (G. giraffa) is represented by 11 individuals from its two subspecies: the Angolan (G. g. angolensis) and the South African giraffe (G. g. giraffa). The read FASTQ files are available on SRA from the Coimbra et al. (2021) publication BioProject PRJNA635165. Quality control of short-reads: FastQC version 0.11.7 (www.bioinformatics.babraham.ac.uk/projects/fastqc/) Trimmomatic version 0.38 with options ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10’, ‘SLIDINGWINDOW:4:20’, and ‘MINLEN:40’ Mapping: Reference genome: Kordofan giraffe (accession: ASM1828223v1) BWA-MEM version 0.7.17-r1188 BAM sorting with Samtools version 1.9 Marked duplicates with MarkDuplicates tool from Picard version 2.18.21 The mapped BAM files from the 48 giraffe individuals have a mean coverage of 19.5X (7-31X) and a mean insert size of 310 bp (247-515 bp). TE annotation in genome assemblies of Kordofan giraffe, okapi and cattle: RepeatMasker with curated giraffe-specific repeat library Annotation tracks and consensus sequences for LINE1v3 and RTEv3 used to create MEI files for MELT (see below) TE insertion calling and analysis: MELT (Gardner et al. 2017); helper scripts available at Gitlab repository Filtering and downstream analysis: RMarkdown document and all parameters and auxiliary files also available at Gitlab repository