Genome Research 11 (10):1784-1795. To drive canine comparative genomics forward, we generated a high-quality canine reference assembly using a combination of Pacific Biosciences (PacBio) long read sequencing, 10x Genomics Chromium Linked Reads (henceforth called 10x) and HiC proximity ligation. R 12). Mapping accuracy was increased by only using reads with a quality value above 15. S Fischer This contrasts with 4% variation in mitochondrial sequences between gray wolves and their nearest wild relative, the coyote ( Canis latrans ). Applebaum P Candidate SVs were further refined and categorised (DEL deletion, CNV copy number variant, INV inversion) by comparing the layout of reads and barcodes around the breakpoints. EL Vet. A novel gene was defined if it (1) had at least 80% of the gene body identified from the filled CanFam3.1 gaps; (2) was not a pseudogene; (3) had not been annotated in the unplaced scaffolds of CanFam3.1; and (4) did not have the duplicated/homologous fragment in another region of the genome. Chromosome 1 is the largest human chromosome, spanning about 249 million DNA building blocks (base pairs) and representing approximately 8 percent of the total DNA in cells. These mutations lead to variant forms of a gene, called alleles, which can change the function of the gene. The genome of a dog contains approximately 2.4 billion nucleotides. Importation of canine tissues was approved by Jordbruksverket (6.7.18-14513/17). By analyzing DNA samples from over 200 dog breeds . and S.M. Gffread70 was used to re-group transcripts into genes, retaining only one transcript per unique CDS region. Canfam_GSD: de novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience 9,giaa027 (2020). Total RNA from a further 24 tissues (including 15 brain regions; Supplementary Table2) was extracted using a standard TRIzol protocol (Invitrogen) and used for nanopore cDNA and Illumina miRNA-sequencing. Molin, A.-M., Berglund, J., Webster, M. T. & Lindblad-Toh, K. Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. Some powerful genes have been identified that can start the process themselves, often with a simple mutation. These genes have diverse functions ranging from embryonic stem cell co-activator (UTF1) to osmoregulation (SCT). A fruit fly, for example, has four pairs of chromosomes, while a rice plant has 12 and a dog, 39. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. End pairs that mapped to both assemblies were compared and defined as concordant when they aligned in forward and reverse direction with a distance <500kb. High molecular weight (HMW) DNA was extracted from blood with MagAttract HMW DNA Kit (Qiagen). CpG islands were detected with the cpg_lh script from UCSC utilities (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/), a modified method from Gardiner-Garden64. Intersection with existing SV catalogues based on either SNP or aCGH arrays28,29,30 showed between 12.6 and 39.0% agreement, but these numbers are likely a reflection of within project breed and detection technology. Genome 13, 380387 (2002). The only genetic elements of the region are the long noncoding RNA (lncRNA) AL353753.1 gene with an unknown function and pseudogene FAM71BP1. the formatoin of chromosome groups at opposite ends of cell. Price. Circulating exosomes suppress the induction of regulatory T cells via let-7i in multiple sclerosis. A novel canine reference genome resolves genomic architecture and uncovers transcript complexity, https://doi.org/10.1038/s42003-021-01698-x. Lolley The latter map is estimated to cover 2073 cM. These arms are held together at the center by the centromere. Genome Biol. Exp. The tips of the chromosome are capped by sections of DNA called telomeres. GridSS79 and Manta80 are assembly-based callers which have been reported to have a good performance in different studies81,82. CAS Sampson Stringtie2 was further used to merge transcripts from the individual assemblies of long and short reads. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. Radiation treatment is used as a "local therapy," directed at killing cells within the tumor site itself. Detection and replication in Boxer. Sign up for the Nature Briefing: Translational Research newsletter top stories in biotechnology, drug discovery and pharma. The bases are paired in fixed units of adenine-thymine (A-T) and guanine-cytosine (G-C). PubMed Central EA Kent, W. J. BLAT-the BLAST-like alignment tool. Many of these variants were embedded in genes that may be important for morphology or associated with disease. Mol. Contiguous sequence was also reported for both the T cell receptor alpha (TRA) and T cell receptor beta (TRB) loci on chr 8 and 16, respectively (Supplementary Fig. One allele comes from the father, and one comes from . Plasmid DNA was extracted using QIAprep Spin Miniprep Kit (Qiagen), PCR products and plasmids sequenced using the Mix2Seq service (Eurofins Genomics) and analysed using CodonCode Aligner v6.0.2 (CodonCode). BMC Genomics 13, 324 (2012). Bowtie alignments of unique sequences were used for MiRDeep271 analysis and compared to known dog and human miRNAs (miRBase) in order to identify the position of both known and novel miRNAs. Further, 7725 were defined as long noncoding genes. The availability of a large number of markers will allow the evolutionary relationships between the breeds to be investigated in more detail and should allow breed histories to be established on a more scientific basis than is currently possible. Updated on January 22, 2020. Small Anim. Juneja SM NeuroImage 63, 16811694 (2012). Different dog breeds developed from small founder populations lollowed by carefully controlled breeding. Assembly and Analysis of Unmapped Genome Sequence Reads Reveal Novel Sequence and Variation in Dogs, Characterisation and functional predictions of canine long non-coding RNAs, Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology, Jasmine and Iris: population-scale structural variant comparison and analysis, Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing, Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools, A curated dataset of modern and ancient high-coverage shotgun human genomes, Towards a reference genome that captures global genetic diversity, Highly accurate long-read HiFi sequencing data for five complex genomes, http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/, https://github.com/PapenfussLab/StructuralVariantAnnotation, http://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=canFam4, https://doi.org/10.1101/2020.07.31.231761, https://www.skk.se/sv/Agria-SKK-Forskningsfond/, Description of Additional Supplementary Files, http://creativecommons.org/licenses/by/4.0/, De-novo and genome-wide meta-analyses identify a risk haplotype for congenital sensorineural deafness in Dalmatian dogs, Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis, Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome, Sign up for Nature Briefing: Translational Research. Four DELs and four CNVs which overlapped protein-coding genes that were polymorphic within the 10x dataset (>3/27 individuals) were selected (Supplementary Data2). R 2a). Genes 10, 433 (2019). PLoS ONE 9, e112963 (2014). 50, 15741583 (2018). SVs were further merged across individuals into a nonredundant SVs set. Chader Walker, B. J. et al. These settings improved mapping both to genes with long introns and to short exons. The ancient types of dog include examples closely resembling the modern day greyhound, mastiff, Pekingese, and spitz breeds. 27, 20502060 (2017). G Sequencing technology reveals more secrets of canine genes much faster than ever before. Roy . At the time of this writing, no accurate estimates of the genetic length of the dog genome exist, although the physical sizes of most canine chromosomes have been estimated by comparison of their flow karyotype peaks with human chromosome 4 ( Langford and others 1996 ). B) Each chromosome is replicated into two chromatids during the S phase of interphase. b Comparison of GC content (50bp window) between GSD_1.0 and CanFam3.1. Article Most of these cells contain a nucleus. Parfitt CL . The majority of the established synteny groups are correlated with linkage groups so that as more of the linkage groups become fixed to chromosomes, gross comparative gene organization in the dog will rapidly become defined. 2006). These chr 9 insertions are missing from GSD_1.0, but allelic depth analysis revealed that most 10x dogs (26/27) carry between 2 and 6 chr 9 copies (Fig. Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. JM Med. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. PS In dogs this is often at an advanced stage since they are unable to tell someone they do not feel well. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now . BEDTools was used to intersect exons, miRNA and ATAC-seq peaks mapped above with filled CanFam3.1 gaps. In sexually reproducing organisms, the number of chromosomes in the body (somatic) cells typically is diploid (2n; a pair of each chromosome), twice the haploid (1n) number found in the sex cells, or gametes. G 8b, c). Genome Res. Schelling Pertea, G. & Pertea, M. GFF Utilities: GffRead and GffCompare. A standard karyotype for chromosomes 1 through 21 has recently been established ( Switonski and others 1996). Science 360,eaar6343 (2018). Versatile and open software for comparing large genomes. Further scaffolding using 94 of 10x and 48 of HiC linked reads resulted in 39 single-scaffold chromosomes (total 2.35Gb) and 2159 unplaced scaffolds (total 128.5Mb; Fig. BMC Genomics 21, 307 (2020). As the camouflaged regions detected in one individual could have been assigned as dark in others, we excluded those dark dogs before we calculated the fraction of camouflaged bases for each window. The annotation consisted of 159 thousand transcripts in 29,583 genes; of which 20,654 had an open reading frame (ORF) of at least 100 amino acids and 19,691 genes had a significant BLAST hit against proteins in Swissprot or ENSEMBL. SNPs and indels were called from short reads aligned to the polished assembly (FreeBayes60 v1.1.0). Acland GC content (%) was assessed in 50bp windows (NUC from BEDTools63 v2.29.2). Anim. Fournier Megquier, K. et al. These calculations included primer specific efficiencies and used the average Ct from all control samples for initial delta Ct normalisation. Preprint at bioRxiv https://doi.org/10.1101/254797 (2018). CAS Ultimately, the researchers analyzed DNA from more than 3,000 dogs from 143 breeds to pinpoint a specific . CAS Throughout a lifetime, the DNA within the cells of a dog's body is capable of undergoing spontaneous genetic changes. June 11, 2022 . E Holmes TP . Puck A chromosome is formed when DNA wraps around a protein know as a histone. A microsatellite marker linked to the disease locus has recently been characterized, enabling identification of affected and carrier animals in pedigrees containing at least I member with confirmed Copper toxicosis ( Yuzbasiyan-Gurkan and others 1996 ). CS Hurwitz 8, 14061 (2017). Each chromosome has two short arms called p arms and two long arms called q arms. Two libraries were run on two separate SMRT cells using the Sequel system, and yielded ~500,000 reads each with mean read lengths of 2452 and 451bp. & Bassham, S. Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny. One pair of genes determines the animal's sex, and the remaining ones affect everything else that makes the dog unique. PubMed Central Cao Dryja Humans, for instance, have 46 chromosomes in a typical body cell (somatic cell), while dogs have 78 ^1 1. Genetic mapping in the dog is a rapidly developing science. 2008; Parker et al. Compared to proteins extracted from CanFam3.1, our new GSD1.0 annotation has a higher number of genes with BLAST hits and the number of genes with a full-length match has increased by 11% (Supplementary Fig. Mellersh Figure 3: Nondisjunction results in daughter cells with unusual chromosome numbers. Two main dog leucocyte antigen (DLA) regions on chr 12 (Fig. English, A. C. et al. The diagrams below show stages of mitosis. . 40, 3752 (2012). Gastroenterology 151, 945960.e6 (2016). Chromosomes have thousands of genes with DNA-encoded traits, and each gene has allele pairs. Girman Nicholas, T. J. et al. There were a few genes that stood out as consistently different . This may sound like a simple gardening experiment, but from pea plants to dogs to humans, genetics is complex. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted overCanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. 467, 1928 (2019). In order to locate nucleotide sequences responsible for traits of interest, researchers have to comb through approximately 3 billion base pairs, the length of the canine genome. Mischka was assessed to be representative of the population via expected inbreeding value (F=0.037) and multiple dimensional scaling genetic distance measures (PLINK v1.9) and selected for the genome assembly. Bosma Most of these cells contain a nucleus. The reduction in chromosome number was caused by the head-to-head fusion of two ancestral chromosomes to form human chromosome 2 (HSA2) and may have contributed to the reproductive barrier with Great Apes. Shi, Y. et al. Pharmacogenetics 14, 769773 (2004). Genet. D Penso-Dolfin, L. et al. Biol. Wang, L., Wang, S. & Li, W. RSeQC: quality control of RNA-seq experiments. PubMed This brings the canine reference genome quality in line with other key mammalian species, e.g. The breakpoint region on chromosome 9 has several areas of high homology with the breakpoint region on chromosome 15 that may have served as a substrate for the balanced-reciprocal-translocation event. From the three callers above, only high-quality SV calls marked as PASS in vcfs were kept for analysis. In the last decade, scientists working at more than 100 laboratories worldwide have made significant progress in painting a detailed picture of the complex relationships between physical traits, behavior and disease in purebred dogs . Crandall C Mitochondrial DNA sequences have also been used to examine the evolution of the Canidae and the origins of the domestic dog ( Wayne 1993 ). Dolf Bioinformatics 43, 11.10.111.10.33 (2013). Bedlington terriers suffer from copper toxicosis, in which dietary copper accumulates in the liver to toxic levels, a condition similar to Wilson's disease in humans. Ferguson Assembled transcripts were processed with TAMA tools68 for ORF detection and BLAST parsing to identify coding regions based on hits against a database of curated proteins from Uniprot_Swissprot and proteins from the latest ENSEMBL dog annotation (v100, Great Dane assembly). MG Thus chromosomes as a whole play an important role in inheritance. Approval was obtained from dog owners before collecting the biological samples at veterinary clinics. Polymorphic expression of CYP1A2 leading to interindividual variability in metabolism of a novel benzodiazepine receptor partial inverse agonist in dogs. E We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Int. Loss of cadherin related family member 5 (CDHR5) expression in clear cell renal cell carcinoma is a prognostic marker of disease progression. Phased diploid genome assembly with single-molecule real-time sequencing. Length of DNA. To date, treatment for most diseases are undertaken retrospectively, once the disease is diagnosed. EA . The types of canine variants implicated in disease range from single-nucleotide polymorphisms (SNPs) (e.g. HMW DNA was extracted from the blood of 27 additional dogs (19 breeds), and Chromium library preparation and sequencing completed as per Genome sequencing. Mappability was assessed with Iso-Seq data using only PacBio CCS reads supported by >10 subreads (483,702 reads). ML VJ In any given asexually reproducing species, the chromosome number is always the same. c Sequence comparison of DLA on chr 12 between CanFam3.1 and GSD_1.0. S USA 106, 27942799 (2009). Loechel Notably, eight genes with expression across multiple tissues were completely absent or represented by pseudogenes in CanFam3.1 but were now available for interrogation (PSMA4, CDHR5, SCT, PAOX, UTF1, EFNA2, GPX4 and SLC25A22). Brewer If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. PacBio iso-seq alignments were combined with alignments of nanopore full-length cDNA reads for assembly with Stringtie2 with options -L -c 3 -s 10 -f 0.05 to suppress low-coverage transcript models from internal priming and partially spliced mRNAs. The dog family Canidae is thought to have diverged from other carnivore families 50 to 60 million years ago. This characteristic applies to both animal and plant cells. . Domestic dogs have lived alongside humans for at least 10,000 years1,2, and during this time, they have adapted to a shared environment and diet, while being selectively bred for traits such as morphology3 and behaviour4. Genetic mapping in the dog will produce results of veterinary importance and, through comparative genetics, will provide data of medical and biological interest. c The duplication was validated in the 10x sequenced individuals using ddPCR. BAC sequences were mapped as paired reads (BWA58 mem default setting), to GSD_1.0 and CanFam3.1. All living organisms, including humans, use this four-letter code. When the genetic basis for an interesting disorder has been established, it is relatively easy to generate large pedigrees segregating the disease due to the large litter size and short generation intervals of the dog. volume4, Articlenumber:185 (2021) PubMed Central Mischka was genotyped with the CanineHD BeadChip (Illumina) and compared to a population of 260 German Shepherds from a previous study49. Durand, N. C. et al. Francisco In addition, a limited number of microsatellites isolated from cosmid libraries have been assigned to chromosomes by FISH mapping (for example, Fischer and others 1996 ; Dolf and others 1997 ). Berson Dark regions comprised 5.8, 5.7 and 6.4Mb, respectively, while camouflaged regions comprised 15.9, 6.4 and 1.0Mb (Fig. Fate Chem. Gene predictions and non-dog refSeq alignments were used to identify potentially missed genes that did not overlap with our annotation, yielding an additional 874 protein-coding genes with BLAST evidence. Google Scholar. Vandesompele, J. et al. Courtesy of the NHGRI Intramural Publication Support Office. Henthorn Both fall under the umbrella of National Genomics Infrastructure (NGI) Sweden and Science for Life Laboratory, Sweden and themselves are supported by RFI/VR and the Swedish Research Council and the Knut and Alice Wallenberg Foundation respectively. Like many species of animals and plants, humans are diploid ( 2n ), meaning that most of their chromosomes come in matched sets known as homologous pairs. Gordon, D. et al. Aside from being our loyal pets, they can serve as model organisms for scientific studies because of their . 11a): a gene linked to brown colour in dogs32 and melanoma in humans33,34. 1). Chromosomes seem to be thread-like in appearance and are located inside the nucleus of an animal and plant cells. Preprint at https://arxiv.org/abs/1207.3907 (2012). We searched for and merged the genomic windows that reached the threshold from each dog. 20, 97 (2019). lifepoint health . Friedrich, J. et al. We identified and manually adjusted contigs placed in either the wrong order or orientation (chr 6, 14, 17, 26 and X), and joined separated contigs from the same chromosome (chr 8 and 18). By submitting a comment you agree to abide by our Terms and Community Guidelines. Oliver, J. Question 13. 2011). Curzon Through the combination of sequencing technologies, PacBio (~100X) long read, 10x and HiC proximity ligation, we have generated a contiguous, chromosome length scaffolded GSD_1.0 canine reference genome. Cluster 2 included largely mastiff-type dogs with big, boxy heads and large, sturdy bodies. 1773: Chromosome 3: CM000003. An improved microRNA annotation of the canine genome. 3c). All tissue samples were amplified with PBC096 barcoding for 810 cycles with both LongAmp (female samples, 62C annealing; NEB) and PrimeSTAR GXL (both sexes, 64C annealing; Takara Bio), with a 10minutes extension time. MS Aguirre Pittler Google Scholar. Acrocentric Chromosome (Actual Shape is difficult to observe) . The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Some have long fur and others have short fur. Researchers have identified over 360 genetic disorders that occur in both humans and dogs, with approximately 46% of those occurring in only one or a few breeds. Dogs therefore have potential as animal models for gene therapy experiments, and although dogs have some disadvantages as experimental animals, they may be suitable intermediate-sized models with their greater lifespan allowing longer term studies than are possible in mice. answer choices. Scaffolding correctness was evaluated by aligning scaffold sequences onto the high-density canine linkage map15. Werner Dovetail Genomics prepared three HiC libraries which were sequenced on an Illumina HiSeq X (2150bp paired-end reads; 121.47Gb data, Supplementary Table8). In addition, the q-arms of 21 autosomes now begin with centromeric repeats, and 17 autosomes end in telomeric repeats (Fig. Association between polymorphisms in the SOX9 region and canine disorder of sex development (78,XX; SRY-negative) revisited in a multibreed case-control study. 02/18/2011. 1a). A lower cutoff was applied in low-coverage samples to select a maximum of 60Mb (Supplementary Data3). Both detected SVs using evidence from split and paired reads, and also assembled the sequences of breakpoints to accurately estimate these positions. These two chromosomal re-orientations were further supported by published recombination rate patterns and fluorescence in situ hybridization experiments15. every chromosome is either X or Y: girls have two X's and boys have an X and a Y chromosome. MM G3-Genes Genom. Genome Biol. EP Lee Oxford University Press is a department of the University of Oxford. A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Silver, M. et al. Refinement of the dog map will facilitate the identification of candidate genes for these complex disorders in human and other species through comparative mapping. Matthew Binns, Ph.D., Nigel Holmes, Ph.D., and Matthew Breen, Ph.D., are with the Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, United Kingdom. If the organism has two different alleles, this is referred to as heterozygous. Ostrander Holmes If a single cell accumulates enough mutations or acquires variation in a critical gene the cell may begin to divide and grow uncontrollably. 30, 12061213 (2002). dog chromosome 1 functionwhat are scissors used for in a first aid kit. Protoc. W Y The vast majority of pedigree dog breeds have been selectively bred over the last 200 years, although the origin of many of the breeds is uncertain. Chromosomes were first discovered by Strasburger in 1815 and the term 'chromosome' was first used by Waldeyer in 1888. Savolainen Polymorphisms in this gene have previously been associated with psychiatric and neurological disorders (bipolar disorder35 and Alzheimers disease36), and response to associated drug therapies of schizophrenia37 in humans. We live in an age that is exploding with knowledge and information. Tragically, many dogs with such . Protein Cell 10, 143148 (2019). Once scientists have sequenced a gene, you might think that their job is done, but it is not that simple. 19, 13481357 (2017). Chromosomes are located within the nucleus of our cells. Blanton These chromosomes are tightly packed inside the nucleus of a cell and are made of DNA molecules. Chromosome Meaning and Discovery. This protein is made from a master set of genetic instructions in two genes . Centromeric regions were defined based on satellite repeat67 (CarSat1/Carsat2/SAT1_CF) content in 5kb windows. Recently, markers linked to canine progressive rod-cone degeneration ( prcd ) have been mapped to a region of dog chromosome 9 showing conserved synteny with human chromosome 17q, the mapped location of retinitis pigmentosa RP17 ( Acland and others 1998 ). PBjelly from PBSuite55 v15.8.24 was used with PacBio subreads to close 648 gaps. GJ Langston GM A dog's body contains trillions of cells. Chromosome 3 spans about 198 million base pairs (the building blocks of DNA) and represents approximately 6.5 percent of the total DNA in cells. It can be argued that the domestic dog ( Canis familiaris ) demonstrates the power of selective breeding more than any other domesticated species. O.W. Lilue, J. et al. DF Fate Chem. Several genes have been physically mapped by fluorescence in situ hybridization (FISH 1 ) analysis and are shown in Table 1 . Each species has a set number of chromosomes arranged in pairs within each cell, but the number of chromosomes can differ between species. K RK RL Bioinformatics 25, 17541760 (2009). For the other closed gaps, we extracted the filled sequences from GSD_1.0 and calculated GC and repeat content. 5). Each chromosome is made of protein and a single molecule of deoxyribonucleic acid (DNA). Vila Oncotarget 8, 7507675086 (2017). Chromosomal conditions are also thought to be rarer in dogs. Acland Results from such work will be particularly useful in identifying positional candidate genes once markers linked to disease traits have been located. a missense variation in SOD1 leading to degenerative myelopathy5) through complex genomic rearrangements (e.g. Reads were base called with the high accuracy model in guppy (v3.6 for direct cDNA and v3.3 for amplified samples). S Study Resources. Berglund, J. et al. Langston Genetics 184, 595605 (2010). Comparative genomic structure of human, dog, and cat MHC: HLA, DLA, and FLA. J. Hered. & Birol, I. ARCS: scaffolding genome drafts with linked reads. The dog also presents a special opportunity for studying the genetic basis of morphological and behavioral traits. Felsburg Dogs, which are under the species Canis lupus familiaris, are known to have a total of 78 chromosomes (2n). PubMedGoogle Scholar. Syst. The reference base was replaced with the variant allele at 149,264 positions where 10x sequencing depth was at least 30 and the variant allele ratio was >90% using FastaAlternateReferenceMaker from GATK61 v4.1.1.0.
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