Comparison of shrimp linkage map studies.

<p>Comparison of shrimp linkage map studies.</p

Comparison of map intervals and number of SNPs between male and female maps.

<p>¹ LG, linkage group.</p

The Development of a High Density Linkage Map for Black Tiger Shrimp (<i>Penaeus monodon</i>) Based on cSNPs

<div><p>Transcriptome sequencing using Illumina RNA-seq was performed on populations of black tiger shrimp from India. Samples were collected from (i) four landing centres around the east coastline (EC) of India, (ii) survivors of a severe WSSV infection during pond culture (SUR) and (iii) the Andaman Islands (AI) in the Bay of Bengal. Equal quantities of purified total RNA from homogenates of hepatopancreas, muscle, nervous tissue, intestinal tract, heart, gonad, gills, pleopod and lymphoid organs were combined to create AI, EC and SUR pools for RNA sequencing. <i>De novo</i> transcriptome assembly resulted in 136,223 contigs (minimum size 100 base pairs, bp) with a total length 61 Mb, an average length of 446 bp and an average coverage of 163× across all pools. Approximately 16% of contigs were annotated with BLAST hit information and gene ontology annotations. A total of 473,620 putative SNPs/indels were identified. An Illumina iSelect genotyping array containing 6,000 SNPs was developed and used to genotype 1024 offspring belonging to seven full-sibling families. A total of 3959 SNPs were mapped to 44 linkage groups. The linkage groups consisted of between 16–129 and 13–130 markers, of length between 139–10.8 and 109.1–10.5 cM and with intervals averaging between 1.2 and 0.9 cM for the female and male maps respectively. The female map was 28% longer than the male map (4060 and 2917 cM respectively) with a 1.6 higher recombination rate observed for female compared to male meioses. This approach has substantially increased expressed sequence and DNA marker resources for tiger shrimp and is a useful resource for QTL mapping and association studies for evolutionarily and commercially important traits.</p></div

Single nucleotide polymorphism detection statistics (includes insertions/deletions).

<p>¹ Minimum count of non-reference alleles.</p

Proportion of gene ontology terms related to (A) process, (B) function and (C) category, for transcripts containing linkage mapped SNPs.

<p>Proportion of gene ontology terms related to (A) process, (B) function and (C) category, for transcripts containing linkage mapped SNPs.</p

Summary of results from Illumina GAII sequencing performed on cDNA pools.

<p>Results are shown before and after adaptor, poly-A trimming and quality filtering. <i>De novo</i> transcriptome assembly was performed using the combined dataset (All). Results of the ‘mapping assemblies’ for the detection of SNPs are also shown. <i>De novo</i> contig assembly statistics are also shown in parentheses for more stringent settings (minimum contig size of 200 bp).</p><p>¹ AI, EC and SUR represent sequence results for individual RNA pools made of samples from the Andaman Island landing centre, East Coast landing centres (Chennai, Vishakhapatnam and Tuticorin) and surviving animals from a WSSV outbreak on a farm in Bapatla respectively.</p

Individuals, locations and tissues sampled for RNA-seq.

<p>Individuals, locations and tissues sampled for RNA-seq.</p

Map showing areas from which <i>P. monodon</i> were sampled.

<p><i>AI</i>, <i>CH</i>, <i>TU</i> and <i>VI</i> represent catch areas covered by landing centres in the Andaman Islands, Chennai, Tuticorin and Vishakhapatnam respectively. <i>BA</i> represents the Bapatla location where shrimp that survived a severe WSSV infection were sampled. Approximate degrees of latitude and longitude are shown.</p

Scaffolding using optical map, genetic map and synteny with closely related fish genomes produced chromosome-level assembly of the Asian seabass genome.

<p>(A) Comparison of <i>L</i>. <i>calcarifer</i> to two closely related fish species (<i>G</i>. <i>aculeatus</i>, and <i>D</i>. <i>labrax</i>) at the genome-wide level. Colours used for depicting assembled chromosomes are random for each of the three genomes. Different colours in a single <i>L</i>. <i>calcarifer</i> linkage group are used to represent the inter-chromosomal rearrangements. Black arcs show collinear blocks that are intra-chromosomally rearranged between the species. (B) Genome assembly (middle panel) shown anchored to two (LG15 and LG18) of the twenty four <i>L</i>. <i>calcarifer</i> linkage groups while the right panel represents the scaffolded assembly (regions in grey depict the additional contigs brought together by scaffolding).</p

Survey of the <i>L</i>. <i>calcarifer</i> genome assembly identified long stretches of TRs lacking in the short read-based assembly and a continuous assembled telomeric region identified at the end of LG3.

<p>(A) Stretches of TRs were virtually missing from the <i>L</i>. <i>calcarifer</i> short read assembly (SRA) generated using 80X Illumina reads scaffolded with ~11,000 BAC ends (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005954#pgen.1005954.s016" target="_blank">S1 Table</a>) whereas the long read assembly (LRA) had a good representation of TRs (upper panel) and the different repeats were more fragmented in the SRA <i>vis-à-vis</i> the LRA (lower panel). (B) Arrangement of telomere monomer sequence (TTAGGG) on a single assembled contig, (unitig_1659; ~0.5 Mb) placed at the terminal end of LG3 (region indicated in orange). Every occurrence of the monomer is indicated by green bars. A highly dense region of (TTAGGG)n was observed between 455.5–466.9 kb, containing the monomer repeated in tandem 1,655 times. The region upstream to this dense region had short dispersed stretches of (TTAGGG)n and contained eight predicted genes (indicated by blue boxes).</p