Supplementary Information

Supplementary Information for

The Marmoset Genome Sequencing and Analysis Consortium

The common marmoset genome provides insight into primate biology and evolution. Nature Genetics 46, 850 (2014)

Tables

Supplementary Tables Includes:

Table 10: Duplications. Number of Mb. of all , inter- and intra-chromosomal duplications per chromosome.
Table 15: Expanded Families. Number of Mb. of all , inter- and intra-chromosomal duplications per chromosome.
Table 16: Contracted Families. Contracted gene families.
Table 17: Validated Expansions. Manually validated gene family expansions in marmoset duplicated regions.
Table 22: Marmoset miRNAs. List of all MiRNAs in Marmoset, grouped as in Supplementary Table 20.
Table 23: Summary. Data for Supplementary Tables 20, 21.
Table 24: Marmoset_caljac3. Mapping positions of marmoset MiRNAs.
Table 25: Human_blast. Blast results for marmoset MiRNAs mapped to Human hg18.
Table 26: Chimp_blast. Blast results for marmoset MiRNAs mapped to Chimp.
Table 27: Rhesus_blast. Blast results for marmoset MiRNAs mapped to Rhesus.
Table 28: Orangutan_blast. Blast results for marmoset MiRNAs mapped to Orangutan.
Table 31: Placenta. Human MiRNA, Gene ID, Go terms.
Table 32: Pregnancy. Human MiRNA, Gene ID, Go terms.
Table 33. Known miRNAs. Gene ID, MiRNA family ID, Species ID, MSA positions, UTR positions, Group number, Site type, etc.
Table 34: Let7. Data for Let-7 miRNA targets.
Table 35: ChrX. Data for Chr. X miRNA targets.
Table 36: Chr22. Data for Chr. 22 miRNA targets.
Table 37: Gene Counts. Gene count data for MiRNAs.
Table 38: Positive Selection. Selected genes under positive selection.
Table 39: Targeted Sequencing. Genes and genomic coordinates for targeted resequencing.
Table 40: Phylogenetic Panel. Source animals used for the phylogenetic panel.

Text and Figures

Supplementary Information Includes:

Table of Contents
I.  Supplementary Figures 1-13..................................................................................    2
II.  Supplementary Tables 1-41..................................................................................    14
III.  Supplementary Note........................................................................................    23
1.  New World monkey (NWM) phylogeny............................................................................    23
2.  Assembly Quality Assessment.................................................................................    23
3.  Marmoset Karyotype..........................................................................................    24

II.  Supplementary Tables 1-41..................................................................................    14
III.  Supplementary Note........................................................................................    23
1.  New World monkey (NWM) phylogeny............................................................................    23
2.  Assembly Quality Assessment.................................................................................    23
3.  Marmoset Karyotype..........................................................................................    24

II.  Supplementary Tables 1-41..................................................................................    14
III.  Supplementary Note........................................................................................    23
1.  New World monkey (NWM) phylogeny............................................................................    23
2.  Assembly Quality Assessment.................................................................................    23
3.  Marmoset Karyotype..........................................................................................    24

II.  Supplementary Tables 1-41..................................................................................    14
III.  Supplementary Note........................................................................................    23
1.  New World monkey (NWM) phylogeny............................................................................    23
2.  Assembly Quality Assessment.................................................................................    23
3.  Marmoset Karyotype..........................................................................................    24

II.  Supplementary Tables 1-41..................................................................................    14
III.  Supplementary Note........................................................................................    23
1.  New World monkey (NWM) phylogeny............................................................................    23
2.  Assembly Quality Assessment.................................................................................    23
3.  Marmoset Karyotype..........................................................................................    24
4.  Chimerism of reads and assembly.............................................................................    24
4.2 Estimation of chimerism in blood samples based upon SNP analysis    ........................................    26
5. Segmental duplication analyses...............................................................................    28
5.1 Duplications on the marmoset genome as a quality control check    ..........................................    28
5.2 Comparison with great-ape evolution of segmental duplications    ...........................................    29
6. Sequence elements constrained in anthropoid primates.........................................................    32
7.  Gene and feature annotation.................................................................................    33
7.1 Mobile elements    .........................................................................................    33
7.2 Ensembl annotation    ......................................................................................    34
7.3 Functional RNAs – miRNAs, siRNAs    ........................................................................    34
7.4 Functional RNAs – miRNA targets    .........................................................................    37
8.  Orthologs and positive selection............................................................................    39
8.1 Gene family expansions/contractions compared to other primates    ..........................................    39
8.2 Positively selected genes in marmoset and other primates    ................................................    43
9.  Specific gene family studies................................................................................    44
9.1 Genes involved in growth pathways and twinning    ..........................................................    44
9.2 Protease Genes    ..........................................................................................    47
9.3 PRDM9/PRDM7    .............................................................................................    50
9.4 HLA, KIR and immunogenetics    .............................................................................    50
URLs    ........................................................................................................    51
References    ..................................................................................................    51