Dataset Information

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.

ABSTRACT: Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.

SUBMITTER: Makova KD

PROVIDER: S-EPMC10705393 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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Publications

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.

Makova Kateryna D KD Pickett Brandon D BD Harris Robert S RS Hartley Gabrielle A GA Cechova Monika M Pal Karol K Nurk Sergey S Yoo DongAhn D Li Qiuhui Q Hebbar Prajna P McGrath Barbara C BC Antonacci Francesca F Aubel Margaux M Biddanda Arjun A Borchers Matthew M Bomberg Erich E Bouffard Gerard G GG Brooks Shelise Y SY Carbone Lucia L Carrel Laura L Carroll Andrew A Chang Pi-Chuan PC Chin Chen-Shan CS Cook Daniel E DE Craig Sarah J C SJC de Gennaro Luciana L Diekhans Mark M Dutra Amalia A Garcia Gage H GH Grady Patrick G S PGS Green Richard E RE Haddad Diana D Hallast Pille P Harvey William T WT Hickey Glenn G Hillis David A DA Hoyt Savannah J SJ Jeong Hyeonsoo H Kamali Kaivan K Kosakovsky Pond Sergei L SL LaPolice Troy M TM Lee Charles C Lewis Alexandra P AP Loh Yong-Hwee E YE Masterson Patrick P McCoy Rajiv C RC Medvedev Paul P Miga Karen H KH Munson Katherine M KM Pak Evgenia E Paten Benedict B Pinto Brendan J BJ Potapova Tamara T Rhie Arang A Rocha Joana L JL Ryabov Fedor F Ryder Oliver A OA Sacco Samuel S Shafin Kishwar K Shepelev Valery A VA Slon Viviane V Solar Steven J SJ Storer Jessica M JM Sudmant Peter H PH Sweetalana Sweeten Alex A Tassia Michael G MG Thibaud-Nissen Françoise F Ventura Mario M Wilson Melissa A MA Young Alice C AC Zeng Huiqing H Zhang Xinru X Szpiech Zachary A ZA Huber Christian D CD Gerton Jennifer L JL Yi Soojin V SV Schatz Michael C MC Alexandrov Ivan A IA Koren Sergey S O'Neill Rachel J RJ Eichler Evan E Phillippy Adam M AM

bioRxiv : the preprint server for biology 20231201

Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosom ...[more]

PMID: 38077089

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Project description:The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach. A total of 1,855 open reading frames (ORFs) have been identified that appear to encode polypeptides, 844 (46%) of which have been assigned putative functions based on their similarities to database sequences with assigned functions. A total of 514 (28%) of the ORF-encoded polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no homology to sequences in public databases. Comparisons with Eucarya-, Bacteria-, and Archaea-specific databases reveal that 1,013 of the putative gene products (54%) are most similar to polypeptide sequences described previously for other organisms in the domain Archaea. Comparisons with the Methanococcus jannaschii genome data underline the extensive divergence that has occurred between these two methanogens; only 352 (19%) of M. thermoautotrophicum ORFs encode sequences that are >50% identical to M. jannaschii polypeptides, and there is little conservation in the relative locations of orthologous genes. When the M. thermoautotrophicum ORFs are compared to sequences from only the eucaryal and bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) are more similar to eucaryal sequences. The bacterial domain-like gene products include the majority of those predicted to be involved in cofactor and small molecule biosyntheses, intermediary metabolism, transport, nitrogen fixation, regulatory functions, and interactions with the environment. Most proteins predicted to be involved in DNA metabolism, transcription, and translation are more similar to eucaryal sequences. Gene structure and organization have features that are typical of the Bacteria, including genes that encode polypeptides closely related to eucaryal proteins. There are 24 polypeptides that could form two-component sensor kinase-response regulator systems and homologs of the bacterial Hsp70-response proteins DnaK and DnaJ, which are notably absent in M. jannaschii. DNA replication initiation and chromosome packaging in M. thermoautotrophicum are predicted to have eucaryal features, based on the presence of two Cdc6 homologs and three histones; however, the presence of an ftsZ gene indicates a bacterial type of cell division initiation. The DNA polymerases include an X-family repair type and an unusual archaeal B type formed by two separate polypeptides. The DNA-dependent RNA polymerase (RNAP) subunits A', A", B', B" and H are encoded in a typical archaeal RNAP operon, although a second A' subunit-encoding gene is present at a remote location. There are two rRNA operons, and 39 tRNA genes are dispersed around the genome, although most of these occur in clusters. Three of the tRNA genes have introns, including the tRNAPro (GGG) gene, which contains a second intron at an unprecedented location. There is no selenocysteinyl-tRNA gene nor evidence for classically organized IS elements, prophages, or plasmids. The genome contains one intein and two extended repeats (3.6 and 8.6 kb) that are members of a family with 18 representatives in the M. jannaschii genome.

Dataset Information

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.

Publications

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.

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