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Aleksandra Greshnova, Karol Pál, Juan Francisco Iturralde Martinez, Stefan Canzar, Kateryna D Makova
Y chromosomes of great apes harbor A mpliconic G enes (YAGs)-multi-copy gene families ( BPY2 , CDY , DAZ , HSFY , PRY , RBMY , TSPY , VCY , and XKRY ) that encode proteins important for spermatogenesis. Previous work assembled YAG transcripts based on their targeted sequencing but not using reference genome assemblies, potentially resulting in an incomplete transcript repertoire. Here we used the recently produced gapless telomere-to-telomere (T2T) Y chromosome assemblies of great ape species (bonobo, chimpanzee, human, gorilla, Bornean orangutan, and Sumatran orangutan) and analyzed RNA data from whole-testis samples for the same species...
April 3, 2024: bioRxiv
#2
JOURNAL ARTICLE
Yafei Mao, William T Harvey, David Porubsky, Katherine M Munson, Kendra Hoekzema, Alexandra P Lewis, Peter A Audano, Allison Rozanski, Xiangyu Yang, Shilong Zhang, DongAhn Yoo, David S Gordon, Tyler Fair, Xiaoxi Wei, Glennis A Logsdon, Marina Haukness, Philip C Dishuck, Hyeonsoo Jeong, Ricardo Del Rosario, Vanessa L Bauer, Will T Fattor, Gregory K Wilkerson, Yuxiang Mao, Yongyong Shi, Qiang Sun, Qing Lu, Benedict Paten, Trygve E Bakken, Alex A Pollen, Guoping Feng, Sara L Sawyer, Wesley C Warren, Lucia Carbone, Evan E Eichler
We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e...
February 23, 2024: Cell
#3
REVIEW
Robert A Foley, Marta Mirazón Lahr
We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor...
January 31, 2024: Trends in Ecology & Evolution
#4
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bomberg, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara Potapova, Arang Rhie, Joana L Rocha, Fedor Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, Sweetalana, Alex Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan Eichler, Adam M Phillippy
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...
December 1, 2023: bioRxiv
#5
JOURNAL ARTICLE
Marta Tomaszkiewicz, Kristoffer Sahlin, Paul Medvedev, Kateryna D Makova
Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes, however, the diversity of splicing variants remains unexplored. Here we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan)...
November 15, 2023: Genome Biology and Evolution
#6
JOURNAL ARTICLE
M I Zarudnaya, A L Potyahaylo, I M Kolomiets, L G Gorb
We investigated in silico the secondary structure of the region encompassing DIS, SD and Psi hairpins in HIV-1 genomes of rare groups N, O and P, HIV-2 genomes and SIV genomes from chimpanzees, gorillas and monkeys. We found that the structure of this region in SIVcpzptt genomes of the 1st and the 2nd clusters is similar to that in HIV-1 genomes of groups M and N, respectively. Further, the structure of the region encompassing DIS, SD and Psi hairpins is similar in HIV-1 genomes of groups O and P and SIVgor genomes...
August 11, 2023: Virus Research
#7
JOURNAL ARTICLE
Harvinder Pawar, Aigerim Rymbekova, Sebastian Cuadros-Espinoza, Xin Huang, Marc de Manuel, Tom van der Valk, Irene Lobon, Marina Alvarez-Estape, Marc Haber, Olga Dolgova, Sojung Han, Paula Esteller-Cucala, David Juan, Qasim Ayub, Ruben Bautista, Joanna L Kelley, Omar E Cornejo, Oscar Lao, Aida M Andrés, Katerina Guschanski, Benard Ssebide, Mike Cranfield, Chris Tyler-Smith, Yali Xue, Javier Prado-Martinez, Tomas Marques-Bonet, Martin Kuhlwilm
Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions...
July 27, 2023: Nature Ecology & Evolution
#8
JOURNAL ARTICLE
Feiyang Zhao, Yubin Yan, Yaxi Wang, Yuan Liu, Ruolin Yang
BACKGROUND: As a significant process of post-transcriptional gene expression regulation in eukaryotic cells, alternative splicing (AS) of exons greatly contributes to the complexity of the transcriptome and indirectly enriches the protein repertoires. A large number of studies have focused on the splicing inclusion of alternative exons and have revealed the roles of AS in organ development and maturation. Notably, AS takes place through a change in the relative abundance of the transcript isoforms produced by a single gene, meaning that exons can have complex splicing patterns...
April 12, 2023: BMC Genomics
#9
Marta Tomaszkiewicz, Kristoffer Sahlin, Paul Medvedev, Kateryna D Makova
Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been recently studied in great apes, however, the diversity of splicing variants remains unexplored. Here we deciphered the sequences of polyadenylated transcripts of all nine YAG families ( BPY2 , CDY , DAZ , HSFY , PRY , RBMY , TSPY , VCY , and XKRY ) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan)...
March 18, 2023: bioRxiv
#10
Yafei Mao, William T Harvey, David Porubsky, Katherine M Munson, Kendra Hoekzema, Alexandra P Lewis, Peter A Audano, Allison Rozanski, Xiangyu Yang, Shilong Zhang, David S Gordon, Xiaoxi Wei, Glennis A Logsdon, Marina Haukness, Philip C Dishuck, Hyeonsoo Jeong, Ricardo Del Rosario, Vanessa L Bauer, Will T Fattor, Gregory K Wilkerson, Qing Lu, Benedict Paten, Guoping Feng, Sara L Sawyer, Wesley C Warren, Lucia Carbone, Evan E Eichler
To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences...
March 7, 2023: bioRxiv
#11
JOURNAL ARTICLE
Samantha R Queeno, Peter J Reiser, Caley M Orr, Terence D Capellini, Kirstin N Sterner, Matthew C O'Neill
Humans are unique among terrestrial mammals in our manner of walking and running, reflecting 7 to 8 Ma of musculoskeletal evolution since diverging with the genus Pan. One component of this is a shift in our skeletal muscle biology towards a predominance of myosin heavy chain (MyHC) I isoforms (i.e. slow fibers) across our pelvis and lower limbs, which distinguishes us from chimpanzees. Here, new MyHC data from 35 pelvis and hind limb muscles of a Western gorilla (Gorilla gorilla) are presented. These data are combined with a similar chimpanzee dataset to assess the MyHC I content of humans in comparison to African apes (chimpanzees and gorillas) and other terrestrial mammals...
March 15, 2023: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
#12
JOURNAL ARTICLE
Rafael González-Álvarez, Irám Pablo Rodríguez-Sánchez, Hugo A Barrera-Saldaña
The growth hormone (GH) locus has experienced a dramatic evolution in primates, becoming multigenic and diverse in anthropoids. Despite sequence information from a vast number of primate species, it has remained unclear how the multigene family was favored. We compared the structure and composition of apes' GH loci as a prerequisite to understanding their origin and possible evolutionary role. These thorough analyses of the GH loci of the chimpanzee, gorilla, and orangutan were done by resorting to previously sequenced bacterial artificial chromosomes (BACs) harboring them, as well as to their respective genome projects data available in GenBank...
January 17, 2023: Genes
#13
JOURNAL ARTICLE
Mengying Liu, Lei Jia, Xing Guo, Xiuli Zhai, Hanping Li, Yongjian Liu, Jingwan Han, Bohan Zhang, Xiaolin Wang, Tianyi Li, Yanglan Wang, Jingyun Li, Changyuan Yu, Lin Li
Human endogenous retroviruses (HERVs) can be vertically transmitted in a Mendelian fashion, are stably maintained in the human genome, and are estimated to constitute approximately 8% of the genome. HERVs affect human physiology and pathology via their provirus-encoded protein or long terminal repeat (LTR) element effect. Characterization of the genomic distribution is an essential step to understanding the relationships between endogenous retrovirus expression and diseases. However, the poor characterization of HML-8 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome...
January 19, 2023: AIDS Research and Human Retroviruses
#14
JOURNAL ARTICLE
Masoud Arabfard, Mahmood Salesi, Yazdan Hassani Nourian, Iman Arabipour, AliMohammad Ali Maddi, Kaveh Kavousi, Mina Ohadi
BACKGROUND: While of predominant abundance across vertebrate genomes and significant biological implications, the relevance of short tandem repeats (STRs) (also known as microsatellites) to speciation remains largely elusive and attributed to random coincidence for the most part. Here we collected data on the whole-genome abundance of mono-, di-, and trinucleotide STRs in nine species, encompassing rodents and primates, including rat, mouse, olive baboon, gelada, macaque, gorilla, chimpanzee, bonobo, and human...
November 3, 2022: BMC genomic data
#15
JOURNAL ARTICLE
Matko Glunčić, Ines Vlahović, Marija Rosandić, Vladimir Paar
Previously it was found that the neuroblastoma breakpoint family ( NBPF ) gene repeat units of ∼1.6 kb have an important role in human brain evolution and function. The higher order organization of these repeat units has been discovered by both methods, the higher order repeat (HOR)-searching method and the HLS searching method. Using the HOR searching method with global repeat map algorithm, here we identified the tandemly organized NBPF HORs in the human and nonhuman primate NCBI reference genomes. We identified 50 tandemly organized canonical 3mer NBPF HOR copies (Olduvai triplets), but none in nonhuman primates chimpanzee, gorilla, orangutan, and Rhesus macaque...
January 2023: Life Science Alliance
#16
JOURNAL ARTICLE
Selas T F Bots, Vera Kemp, Iris J C Dautzenberg, Rob C Hoeben
The adenoviruses (AdVs) isolated from humans are taxonomically grouped in seven different species in the Mastadenovirus genus (HAdV-A through G). AdVs isolated from apes are often included in one of the human AdV species. Here we describe the sequence analyses of ten new AdVs that are related to the HAdV-C species and that were isolated from healthy western lowland gorillas, bonobos, chimpanzees, and orangutans kept in Dutch zoos. We analyzed these viruses and compared their genome sequences to those of human- and ape-derived AdV sequences in the NCBI GenBank database...
August 30, 2022: International Journal of Molecular Sciences
#17
JOURNAL ARTICLE
Ariko Miyake, Minh Ha Ngo, Shelly Wulandari, Masayuki Shimojima, So Nakagawa, Junna Kawasaki, Kazuo Nishigaki
Host genetic resistance to viral infection controls the pathogenicity and epidemic dynamics of infectious diseases. Refrex-1 is a restriction factor against feline leukemia virus subgroup D (FeLV-D) and an endogenous retrovirus (ERV) in domestic cats (ERV-DC). Refrex-1 is encoded by a subset of ERV-DC loci with truncated envelope genes and secreted from cells as a soluble protein. Here, we identified the copper transporter CTR1 as the entry receptor for FeLV-D and genotype I ERV-DCs. We also identified CTR1 as a receptor for primate ERVs from crab-eating macaques and rhesus macaques, which were found in a search of intact envelope genes capable of forming infectious viruses...
June 28, 2022: Proceedings of the National Academy of Sciences of the United States of America
#18
JOURNAL ARTICLE
Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors.
Konstantin Popadin, Konstantin Gunbin, Leonid Peshkin, Sofia Annis, Zoe Fleischmann, Melissa Franco, Yevgenya Kraytsberg, Natalya Markuzon, Rebecca R Ackermann, Konstantin Khrapko
The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA ("NUMTs"). NUMTs are considered "mtDNA fossils" as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4...
May 1, 2022: Genes
#19
JOURNAL ARTICLE
Annette Damert
Segmental duplications (SDs) constitute a considerable fraction of primate genomes. They contribute to genetic variation and provide raw material for evolution. Groups of SDs are characterized by the presence of shared core duplicons. One of these core duplicons, low copy repeat (lcr)16a, has been shown to be particularly active in the propagation of interspersed SDs in primates. The underlying mechanisms are, however, only partially understood. Alu short interspersed elements (SINEs) are frequently found at breakpoints and have been implicated in the expansion of SDs...
May 3, 2022: Molecular Biology and Evolution
#20
JOURNAL ARTICLE
Jiaqi Wu, Takahiro Yonezawa, Hirohisa Kishino
It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution...
April 17, 2022: Genes
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