---
title: "Quantitative Biology new submissions"
description: "Today's new preprints in Quantitative Biology (q-bio) on CCCURJ, the open-access archive of research by California Community College students."
url: "https://cccurj.org/list/q-bio/new"
license: "CC BY 4.0"
---

# Quantitative Biology

## New submissions

Showing new listings for Monday, 19 October 2026

Total of 10 entries | [New submissions](https://cccurj.org/list/q-bio/new#new)

### New submissions (showing 10 of 10 entries)

**[\[1\]](https://cccurj.org/list/q-bio/new#item1) [CCCURJ:2610.00014](https://cccurj.org/abs/2610.00014) [[pdf](https://cccurj.org/pdf/2610.00014)]**

[Research in progress](https://cccurj.org/help/artifacts#research-in-progress) Guide reselection expands canonical PAM candidates in an HGD editing resource for alkaptonuria

[William Zane Duncan](https://cccurj.org/search#William_Zane_Duncan), [Annie de Paula Bento](https://cccurj.org/search#Annie_de_Paula_Bento), [Laura Nadia Cabrera](https://cccurj.org/search#Laura_Nadia_Cabrera), [Quoc Huy Hoang](https://cccurj.org/search#Quoc_Huy_Hoang), [Maddison Lila Kahn](https://cccurj.org/search#Maddison_Lila_Kahn), [Zhuolang Li](https://cccurj.org/search#Zhuolang_Li), [Raj Mathur](https://cccurj.org/search#Raj_Mathur), [Malaika Theresa Mekkattuparamban](https://cccurj.org/search#Malaika_Theresa_Mekkattuparamban), [Cristian Emanuel Vasquez](https://cccurj.org/search#Cristian_Emanuel_Vasquez), [Yuritzia Alexandra Zaragoza](https://cccurj.org/search#Yuritzia_Alexandra_Zaragoza), [Giorgio Lagna](https://cccurj.org/search#Giorgio_Lagna)

Comments: 20 pages. Republished from a Research Square preprint (posted September 22, 2026) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN); Quantitative Methods (q-bio.QM)

Rare monogenic diseases offer defined molecular targets, but sequence-level editing options require explicit selection and verification. Using artificial intelligence assisted analysis and public tools within a community-college research cohort, we assembled an editing resource for the homogentisate 1,2-dioxygenase gene (HGD) in alkaptonuria. The inventory contained 278 variants and represented 268 of 271 eligible records in a defined ClinVar census. We compared filtering fixed prime-editing designs with re-selection requiring canonical NGG protospacer-adjacent motifs at both guide targets. Re-selection preserved 93 compatible configurations and added 140, all using a second nick without predicted edited-allele discrimination (PE3), while retaining 92 predicted allele-discriminating configurations (PE3b). Under a shared genomic count screen including NGG, NAG and NGA sites, 70 preserved and 79 added configurations remained. With an unchanged base-editing arm, combined representation increased from 110 to 188 variants, or 106 to 180 of 271 eligible ClinVar records. Preserving fixed configurations makes nonnegative gain structural; a 33-setting threshold grid quantified additional representation, with gains of 2–121. Conservative base-window exclusions and a prime-only control retained the increase. Sequence reconstruction and independent PrimeDesign comparisons checked component conventions. The result identifies nicking-guide selection as a source of additional canonical candidates and motivates planned tests of editing activity, product purity and restoration of HGD function.

**[\[2\]](https://cccurj.org/list/q-bio/new#item2) [CCCURJ:2610.00013](https://cccurj.org/abs/2610.00013) [[pdf](https://cccurj.org/pdf/2610.00013)]**

[Research note](https://cccurj.org/help/artifacts#research-note) Complete chloroplast genome of the federally endangered Menzies' wallflower Erysimum menziesii (Brassicaceae, Anthophyta) from California, USA

[Alondra G Aguilar](https://cccurj.org/search#Alondra_G_Aguilar), [Pilar Arreguin](https://cccurj.org/search#Pilar_Arreguin), [Isabel Bejar](https://cccurj.org/search#Isabel_Bejar), [Alejandra Castro](https://cccurj.org/search#Alejandra_Castro), [Millo D Chavarria](https://cccurj.org/search#Millo_D_Chavarria), [Oscar Chavez](https://cccurj.org/search#Oscar_Chavez), [Jacqueline Cruz-Martinez](https://cccurj.org/search#Jacqueline_Cruz-Martinez), [Ruby J De la Cruz-Ortiz](https://cccurj.org/search#Ruby_J_De_la_Cruz-Ortiz), [Paloma L Degrandis-Figueroa](https://cccurj.org/search#Paloma_L_Degrandis-Figueroa), [Kaleigh Gonzalez](https://cccurj.org/search#Kaleigh_Gonzalez), [Mayra E Gutierrez-Vargas](https://cccurj.org/search#Mayra_E_Gutierrez-Vargas), [Mason Hill](https://cccurj.org/search#Mason_Hill), [Jeffery R Hughey](https://cccurj.org/search#Jeffery_R_Hughey), [Cameron M Jones](https://cccurj.org/search#Cameron_M_Jones), [Kayla Kennamore](https://cccurj.org/search#Kayla_Kennamore), [Vanessa Lopez](https://cccurj.org/search#Vanessa_Lopez), [Madry M Nelson](https://cccurj.org/search#Madry_M_Nelson), [Itzel Lopez Magana](https://cccurj.org/search#Itzel_Lopez_Magana), [Jasmine Magana-Zavala](https://cccurj.org/search#Jasmine_Magana-Zavala), [Brianna S Martinez](https://cccurj.org/search#Brianna_S_Martinez), [Vanessa Mendez Gutierrez](https://cccurj.org/search#Vanessa_Mendez_Gutierrez), [Brayan Mendoza](https://cccurj.org/search#Brayan_Mendoza), [Jorge E Morales](https://cccurj.org/search#Jorge_E_Morales), [Sarahi Ochoa](https://cccurj.org/search#Sarahi_Ochoa), [Rosalie Perea-Lopez](https://cccurj.org/search#Rosalie_Perea-Lopez), [Judith Perez-Rizo](https://cccurj.org/search#Judith_Perez-Rizo), [Dalyla Quiroz-Contreras](https://cccurj.org/search#Dalyla_Quiroz-Contreras), [Emily C Ramirez](https://cccurj.org/search#Emily_C_Ramirez), [Fidel Ramirez](https://cccurj.org/search#Fidel_Ramirez), [Izes Ramirez](https://cccurj.org/search#Izes_Ramirez), [Tatiana Rozin](https://cccurj.org/search#Tatiana_Rozin), [Maria G Salazar](https://cccurj.org/search#Maria_G_Salazar), [Paulina Saldana-Landeros](https://cccurj.org/search#Paulina_Saldana-Landeros), [Joel Sosa](https://cccurj.org/search#Joel_Sosa), [Joana Vega-Valencia](https://cccurj.org/search#Joana_Vega-Valencia), [Andrea Villanueva](https://cccurj.org/search#Andrea_Villanueva), [Ruby Villicana](https://cccurj.org/search#Ruby_Villicana), [Janet Zambrano](https://cccurj.org/search#Janet_Zambrano)

Comments: 4 pages. Republished from Microbiology Resource Announcements 15(3):e0129825 (2026) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)

We present the complete chloroplast genome of the federally endangered plant species Erysimum menziesii from Pacific Grove, California, USA. The chloroplast genome is circular, AT skewed (63.4%), and 154,668 bp in length. The genome is quadripartite in structure and contains 85 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes.

**[\[3\]](https://cccurj.org/list/q-bio/new#item3) [CCCURJ:2610.00012](https://cccurj.org/abs/2610.00012) [[pdf](https://cccurj.org/pdf/2610.00012)]**

[Research note](https://cccurj.org/help/artifacts#research-note) Complete mitochondrial genome of the introduced Indian walking stick Carausius morosus (Lonchodidae, Insecta) from California

[Aiden Clarke](https://cccurj.org/search#Aiden_Clarke), [Alice Trujillo](https://cccurj.org/search#Alice_Trujillo), [Andres Mandujano](https://cccurj.org/search#Andres_Mandujano), [Angelica G Fernandez](https://cccurj.org/search#Angelica_G_Fernandez), [Aniyah Chambers](https://cccurj.org/search#Aniyah_Chambers), [Areli Ruiz Nunez](https://cccurj.org/search#Areli_Ruiz_Nunez), [Audri Contreras](https://cccurj.org/search#Audri_Contreras), [Benny Cuevas](https://cccurj.org/search#Benny_Cuevas), [Caitlin Collins](https://cccurj.org/search#Caitlin_Collins), [Christian B Trujillo](https://cccurj.org/search#Christian_B_Trujillo), [Claudia L Dominguez-Trejo](https://cccurj.org/search#Claudia_L_Dominguez-Trejo), [Danilo E Bustamante](https://cccurj.org/search#Danilo_E_Bustamante), [Eduardo Pantoja-Garcia](https://cccurj.org/search#Eduardo_Pantoja-Garcia), [Elizabeth Anguiano](https://cccurj.org/search#Elizabeth_Anguiano), [Emily D Alcaraz](https://cccurj.org/search#Emily_D_Alcaraz), [Felipe Rodriguez](https://cccurj.org/search#Felipe_Rodriguez), [Flavio C Mora](https://cccurj.org/search#Flavio_C_Mora), [Froylan Tinoco Rivera](https://cccurj.org/search#Froylan_Tinoco_Rivera), [Gladys Cabrera Luis](https://cccurj.org/search#Gladys_Cabrera_Luis), [Hailey B Nava](https://cccurj.org/search#Hailey_B_Nava), [Henry N Huynh](https://cccurj.org/search#Henry_N_Huynh), [Javier C Diaz](https://cccurj.org/search#Javier_C_Diaz), [Jeffery R Hughey](https://cccurj.org/search#Jeffery_R_Hughey), [Jenny Do](https://cccurj.org/search#Jenny_Do), [Jeriel S Sevilla](https://cccurj.org/search#Jeriel_S_Sevilla), [Jessica C Llaja](https://cccurj.org/search#Jessica_C_Llaja), [Jessica Lopez](https://cccurj.org/search#Jessica_Lopez), [Jesus Rosas](https://cccurj.org/search#Jesus_Rosas), [Jhordy Perez](https://cccurj.org/search#Jhordy_Perez), [Johann E Oyola](https://cccurj.org/search#Johann_E_Oyola), [Jois V Carrion](https://cccurj.org/search#Jois_V_Carrion), [Joni J Black](https://cccurj.org/search#Joni_J_Black), [Jorge F Chavez](https://cccurj.org/search#Jorge_F_Chavez), [José I Barboza](https://cccurj.org/search#José_I_Barboza), [Juan Pablo Rodriguez Cortes](https://cccurj.org/search#Juan_Pablo_Rodriguez_Cortes), [Konnor L Barrett](https://cccurj.org/search#Konnor_L_Barrett), [Lacey E Prescott](https://cccurj.org/search#Lacey_E_Prescott), [Layla Alvarez](https://cccurj.org/search#Layla_Alvarez), [Lizbet Merino Juarez](https://cccurj.org/search#Lizbet_Merino_Juarez), [Maria J Velasquez-Moreno](https://cccurj.org/search#Maria_J_Velasquez-Moreno), [Mariah I Marquez-Gonzalez](https://cccurj.org/search#Mariah_I_Marquez-Gonzalez), [Mariana Aguirre Linares](https://cccurj.org/search#Mariana_Aguirre_Linares), [Maricela Chavez-Huigo](https://cccurj.org/search#Maricela_Chavez-Huigo), [Martha S Calderon](https://cccurj.org/search#Martha_S_Calderon), [Mateo Brambila](https://cccurj.org/search#Mateo_Brambila), [Maximiliano Villa](https://cccurj.org/search#Maximiliano_Villa), [Mia J Windham](https://cccurj.org/search#Mia_J_Windham), [Michael Perez](https://cccurj.org/search#Michael_Perez), [Natalie Trujillo](https://cccurj.org/search#Natalie_Trujillo), [Pearl Chenevert](https://cccurj.org/search#Pearl_Chenevert), [Phoebe Lewis](https://cccurj.org/search#Phoebe_Lewis), [Pilar Guiop](https://cccurj.org/search#Pilar_Guiop), [Reema Y Mubarz](https://cccurj.org/search#Reema_Y_Mubarz), [Roberto Garcia Velazquez](https://cccurj.org/search#Roberto_Garcia_Velazquez), [Rosmery Y Ayala-Tocto](https://cccurj.org/search#Rosmery_Y_Ayala-Tocto), [Samantha Santos](https://cccurj.org/search#Samantha_Santos), [Samia L J Fernandez-Güimac](https://cccurj.org/search#Samia_L_J_Fernandez-Güimac), [Sandra R Zalasar](https://cccurj.org/search#Sandra_R_Zalasar), [Smith E Aguilar-Trauco](https://cccurj.org/search#Smith_E_Aguilar-Trauco), [Soledad Duran](https://cccurj.org/search#Soledad_Duran), [Stephanie Solis](https://cccurj.org/search#Stephanie_Solis), [Steven L Meza](https://cccurj.org/search#Steven_L_Meza), [Taym Al-Zuhairi](https://cccurj.org/search#Taym_Al-Zuhairi), [Victor M Padilla](https://cccurj.org/search#Victor_M_Padilla), [Yadhira M Olano](https://cccurj.org/search#Yadhira_M_Olano), [Yareli Alfaro Maldonado](https://cccurj.org/search#Yareli_Alfaro_Maldonado), [Hartnell College Genomics Group](https://cccurj.org/search#Hartnell_College_Genomics_Group)

Comments: 4 pages. Republished from Microbiology Resource Announcements 13(7):e0032124 (2024) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)

We present the complete mitochondrial genome of Carausius morosus from Salinas, CA. The mitochondrial genome of C. morosus is circular, AT rich (78.1%), and 16,671 bp in length. It consists of 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes and is identical in gene content to Carausius sp.

**[\[4\]](https://cccurj.org/list/q-bio/new#item4) [CCCURJ:2610.00011](https://cccurj.org/abs/2610.00011) [[pdf](https://cccurj.org/pdf/2610.00011)]**

[Research note](https://cccurj.org/help/artifacts#research-note) Complete Chloroplast Genome Sequence of the Western Poison Oak, Toxicodendron diversilobum (Anacardiaceae), from California

[Laura I Huitron Vazquez](https://cccurj.org/search#Laura_I_Huitron_Vazquez), [Perla E Aviles](https://cccurj.org/search#Perla_E_Aviles), [Samantha A Bailon](https://cccurj.org/search#Samantha_A_Bailon), [Abner G Cabanillas](https://cccurj.org/search#Abner_G_Cabanillas), [Andrea Fernandez](https://cccurj.org/search#Andrea_Fernandez), [Juan I Galarza](https://cccurj.org/search#Juan_I_Galarza), [Brianna Guerrero](https://cccurj.org/search#Brianna_Guerrero), [Araceli B Hernandez](https://cccurj.org/search#Araceli_B_Hernandez), [Daniel Hernandez](https://cccurj.org/search#Daniel_Hernandez), [Khegan Jarrett](https://cccurj.org/search#Khegan_Jarrett), [Tong Li](https://cccurj.org/search#Tong_Li), [Francisco J Maravillo](https://cccurj.org/search#Francisco_J_Maravillo), [Magdalena Moreno](https://cccurj.org/search#Magdalena_Moreno), [Azalea Perez](https://cccurj.org/search#Azalea_Perez), [Nathan A Rosales](https://cccurj.org/search#Nathan_A_Rosales), [Hunter F Ruegg](https://cccurj.org/search#Hunter_F_Ruegg), [Joel Valdez](https://cccurj.org/search#Joel_Valdez), [Kyla Mae Bravo](https://cccurj.org/search#Kyla_Mae_Bravo), [Vidal L Chávez](https://cccurj.org/search#Vidal_L_Chávez), [Daisy I Diaz](https://cccurj.org/search#Daisy_I_Diaz), [Daniela Enriquez](https://cccurj.org/search#Daniela_Enriquez), [Edgar L Martinez](https://cccurj.org/search#Edgar_L_Martinez), [Jesus Mendoza Padilla](https://cccurj.org/search#Jesus_Mendoza_Padilla), [Jose Meza](https://cccurj.org/search#Jose_Meza), [Scott V Nelson](https://cccurj.org/search#Scott_V_Nelson), [Crystal Quintero-Ahumada](https://cccurj.org/search#Crystal_Quintero-Ahumada), [Adriene Mariah Ramirez](https://cccurj.org/search#Adriene_Mariah_Ramirez), [Jeffery R Hughey](https://cccurj.org/search#Jeffery_R_Hughey)

Comments: 3 pages. Republished from Microbiology Resource Announcements 12(3):e0127922 (2023) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN)

Here, we present the complete chloroplast genome sequence of Toxicodendron diversilobum, western poison oak, from Pacific Grove, California. The genome is 159,543 bp in length, contains 133 genes, and has a high level of gene synteny to other species of Toxicodendron.

**[\[5\]](https://cccurj.org/list/q-bio/new#item5) [CCCURJ:2610.00010](https://cccurj.org/abs/2610.00010) [[pdf](https://cccurj.org/pdf/2610.00010)]**

[Literature review](https://cccurj.org/help/artifacts#literature-review) Meta-Analysis of the Expansion in the Field of Structural Biology of ABC Transporters

[Soomi Kim](https://cccurj.org/search#Soomi_Kim), [Teena Bajaj](https://cccurj.org/search#Teena_Bajaj), [Cole Chabon](https://cccurj.org/search#Cole_Chabon), [Eric Tablante](https://cccurj.org/search#Eric_Tablante), [Tatyana Kulchinskaya](https://cccurj.org/search#Tatyana_Kulchinskaya), [Tae Seok Moon](https://cccurj.org/search#Tae_Seok_Moon), [Ruchika Bajaj](https://cccurj.org/search#Ruchika_Bajaj)

Comments: 12 pages. Republished from BioDesign Research 2022:9806979 (2022) under CC BY 4.0; not submitted to CCCURJ

Subjects: Biomolecules (q-bio.BM)

ABC transporters are molecular machines which power the solute transport using ATP hydrolysis. The structural biology of ABC transporters has been exploding for the last few years, and this study explores timelines and trends for various attributes such as structural tools, resolution, fold, sources, and group leaders. This study also evidences the significance of mammalian expression systems, advancements in structural biology tools, and the developing interest of group leaders across the world in the remarkably progressing field. The field started in 2002 and bloomed in 2016, and COVID years were really productive to the field. Specifically, the study explores 337 structures of 58 unique ABC transporters deposited in the PDB database from which P-glycoprotein has the largest number of structures. Approximately, 62% of total structures are determined at the resolution of 3-4 Å and 53% of structures belong to fold IV type. With progressive advancements in the field, the field is shifting from prokaryotic to eukaryotic sources and X-ray crystallography to cryoelectron microscopy. In the nutshell, this study uniquely provides the detailed snapshot of the field of structural biology of ABC transporters with real-time data.

**[\[6\]](https://cccurj.org/list/q-bio/new#item6) [CCCURJ:2610.00009](https://cccurj.org/abs/2610.00009) [[pdf](https://cccurj.org/pdf/2610.00009)]**

[Research note](https://cccurj.org/help/artifacts#research-note) The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA

[Hartnell College Genomics Group](https://cccurj.org/search#Hartnell_College_Genomics_Group), [Ivan D Agudelo](https://cccurj.org/search#Ivan_D_Agudelo), [Griselda Aldaco](https://cccurj.org/search#Griselda_Aldaco), [Angel Brito-Pizano](https://cccurj.org/search#Angel_Brito-Pizano), [Kimberly G Chavez](https://cccurj.org/search#Kimberly_G_Chavez), [Karina G Cortina](https://cccurj.org/search#Karina_G_Cortina), [Jorge Flores](https://cccurj.org/search#Jorge_Flores), [Alejandro Fuentes](https://cccurj.org/search#Alejandro_Fuentes), [Adam N Garcia](https://cccurj.org/search#Adam_N_Garcia), [Alejandro Garcia](https://cccurj.org/search#Alejandro_Garcia), [Daniel Gonzalez-Martinez](https://cccurj.org/search#Daniel_Gonzalez-Martinez), [Jennifer Hernandez Ramos](https://cccurj.org/search#Jennifer_Hernandez_Ramos), [Jeffery R Hughey](https://cccurj.org/search#Jeffery_R_Hughey), [Fernando R Katada](https://cccurj.org/search#Fernando_R_Katada), [Felix A Leon](https://cccurj.org/search#Felix_A_Leon), [Maleny P Lopez](https://cccurj.org/search#Maleny_P_Lopez), [Sandra Z Lopez](https://cccurj.org/search#Sandra_Z_Lopez), [Aileen G Mendoza](https://cccurj.org/search#Aileen_G_Mendoza), [Maritta Molina](https://cccurj.org/search#Maritta_Molina), [Asmahan Muhrram](https://cccurj.org/search#Asmahan_Muhrram), [Daisy Ortiz-Matias](https://cccurj.org/search#Daisy_Ortiz-Matias), [Tonantzin E Ortiz](https://cccurj.org/search#Tonantzin_E_Ortiz), [Alicia Pacheco](https://cccurj.org/search#Alicia_Pacheco), [Nandini Patel](https://cccurj.org/search#Nandini_Patel), [Paz M Ramirez](https://cccurj.org/search#Paz_M_Ramirez), [Jennifer L Scaramuzzino](https://cccurj.org/search#Jennifer_L_Scaramuzzino), [Alexandria Soto](https://cccurj.org/search#Alexandria_Soto), [Richard A Stabler](https://cccurj.org/search#Richard_A_Stabler), [Jessica M Vidauri](https://cccurj.org/search#Jessica_M_Vidauri), [Jose Villicana](https://cccurj.org/search#Jose_Villicana), [James A Yhip](https://cccurj.org/search#James_A_Yhip)

Comments: 3 pages. Republished from Mitochondrial DNA Part B 7(1):283–285 (2022) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)

Amorpha californica var. napensis Jeps. 1925, the Napa false indigo, is a threatened shrub endemic to northern California. Here the complete chloroplast genome of topotype material of var. napensis was assembled and characterized to contribute to the bioinformatics, systematics, and conservation of this variety. The chloroplast genome (GenBank accession OK274088) is 158,294 base pairs (bp) in length, encodes 130 genes including 85 protein-coding, 37 tRNA, 8 rRNA, and shows a high-level of gene synteny to other Papilionoideae. Phylogenetic analysis fully resolved var. napensis in a clade with A. fruticosa L. and A. roemeriana Scheele, sister to the Dalbergieae. The newly sequenced chloroplast genome shows that the genetic differences between var. napensis and Amorpha californica Nutt. var. californica are greater than the variation observed between var. napensis and many other Amorpha spp. sequences deposited in GenBank. These data suggest that var. napensis should be elevated to full species rank.

**[\[7\]](https://cccurj.org/list/q-bio/new#item7) [CCCURJ:2610.00008](https://cccurj.org/abs/2610.00008) [[pdf](https://cccurj.org/pdf/2610.00008)]**

[Research article](https://cccurj.org/help/artifacts#research-article) Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia

[Savanah Senn](https://cccurj.org/search#Savanah_Senn), [Kelly Pangell](https://cccurj.org/search#Kelly_Pangell), [Adrianna L Bowerman](https://cccurj.org/search#Adrianna_L_Bowerman)

Comments: 16 pages. Republished from Biotech 11(1):1 (2022) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10-5), Bradyhizobium (p = 1 × 10-8), and Paenibacillus (p = 1.46 × 10-6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10-3) and permease genes (p \< 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.

**[\[8\]](https://cccurj.org/list/q-bio/new#item8) [CCCURJ:2610.00007](https://cccurj.org/abs/2610.00007) [[pdf](https://cccurj.org/pdf/2610.00007)]**

[Research note](https://cccurj.org/help/artifacts#research-note) The complete mitochondrial genome of the strawberry aphid Chaetosiphon fragaefolii Cockerell, 1901 (Hemiptera: Aphididae) from California, USA

[Miguel Acosta](https://cccurj.org/search#Miguel_Acosta), [Diana Alcantar](https://cccurj.org/search#Diana_Alcantar), [Ivan Alier-Reyes](https://cccurj.org/search#Ivan_Alier-Reyes), [Carlos Alvarez](https://cccurj.org/search#Carlos_Alvarez), [Crystal B Arroyo](https://cccurj.org/search#Crystal_B_Arroyo), [David Calderon](https://cccurj.org/search#David_Calderon), [David Cardenas](https://cccurj.org/search#David_Cardenas), [Alejandro R Castro](https://cccurj.org/search#Alejandro_R_Castro), [Janelle K Companion](https://cccurj.org/search#Janelle_K_Companion), [Cristian Constante](https://cccurj.org/search#Cristian_Constante), [Evelyn S Diaz Telles](https://cccurj.org/search#Evelyn_S_Diaz_Telles), [Gabriel Fletes](https://cccurj.org/search#Gabriel_Fletes), [Fatima C Gama](https://cccurj.org/search#Fatima_C_Gama), [Celia Garcia Perez](https://cccurj.org/search#Celia_Garcia_Perez), [Abigail Garcia](https://cccurj.org/search#Abigail_Garcia), [Bailey Garcia](https://cccurj.org/search#Bailey_Garcia), [Brandon S Gutierrez](https://cccurj.org/search#Brandon_S_Gutierrez), [Karina L Guzman](https://cccurj.org/search#Karina_L_Guzman), [Cecilia Hernandez](https://cccurj.org/search#Cecilia_Hernandez), [Jeffery R Hughey](https://cccurj.org/search#Jeffery_R_Hughey), [Monica Ibarra Flores](https://cccurj.org/search#Monica_Ibarra_Flores), [Adilene I Jacobo](https://cccurj.org/search#Adilene_I_Jacobo), [Brianna Lopez](https://cccurj.org/search#Brianna_Lopez), [Norma C Lopez-De Leon](https://cccurj.org/search#Norma_C_Lopez-De_Leon), [Jaden D Martinez](https://cccurj.org/search#Jaden_D_Martinez), [Nayelli Mendoza](https://cccurj.org/search#Nayelli_Mendoza), [Kimberly Perez](https://cccurj.org/search#Kimberly_Perez), [Lucio J Perez](https://cccurj.org/search#Lucio_J_Perez), [Milagros Perez-Moreno](https://cccurj.org/search#Milagros_Perez-Moreno), [Caitlin D Pineda](https://cccurj.org/search#Caitlin_D_Pineda), [Elizabeth Pinedo](https://cccurj.org/search#Elizabeth_Pinedo), [Julissa G Portillo](https://cccurj.org/search#Julissa_G_Portillo), [Anais Rico](https://cccurj.org/search#Anais_Rico), [Laura V Ruiz](https://cccurj.org/search#Laura_V_Ruiz), [Genevie M Serrano](https://cccurj.org/search#Genevie_M_Serrano), [Kalia M Sheldon](https://cccurj.org/search#Kalia_M_Sheldon), [Hiroki Terada](https://cccurj.org/search#Hiroki_Terada), [Victoria A Trujillo](https://cccurj.org/search#Victoria_A_Trujillo), [Clarissa Vazquez-Ramos](https://cccurj.org/search#Clarissa_Vazquez-Ramos), [Frank Wang](https://cccurj.org/search#Frank_Wang), [Dawn Flora](https://cccurj.org/search#Dawn_Flora), [Felipe G Zavala](https://cccurj.org/search#Felipe_G_Zavala), [Hartnell College Genomics Group](https://cccurj.org/search#Hartnell_College_Genomics_Group)

Comments: 3 pages. Republished from Mitochondrial DNA Part B 6(8):2373–2375 (2021) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)

The aphid Chaetosiphon fragaefolii Cockerell, 1901 is an agricultural pest and known vector of strawberry viruses. To better understand its biology and systematics, we performed a genomic analysis on C. fragaefolii collected from Quinalt strawberry plants from Pacific Grove, Monterey county, California, USA using Oxford Nanopore and Illumina sequencing. The resulting data were used to assemble the aphids complete mitogenome. The mitogenome of C. fragaefolii is 16,108 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank accession number LC590896). The mitogenome is similar in content and organization to other Aphididae. Phylogenetic analysis of the C. fragaefolii mitogenome resolved it in a fully supported clade in the tribe Macrosiphini. Analysis of the cox1 barcode sequence of C. fragaefolii from California found exact and nearly identical sequences to C. fragaefolii and Chaetosiphon thomasi Hille Ris Lambers, 1953, suggesting the two species are conspecific.

**[\[9\]](https://cccurj.org/list/q-bio/new#item9) [CCCURJ:2610.00006](https://cccurj.org/abs/2610.00006) [[pdf](https://cccurj.org/pdf/2610.00006)]**

[Research note](https://cccurj.org/help/artifacts#research-note) The complete mitochondrial and plastid genomes of the invasive marine red alga Caulacanthus okamurae (Caulacanthaceae, Rhodophyta) from Moss Landing, California, USA

[Hartnell College Genomics Group](https://cccurj.org/search#Hartnell_College_Genomics_Group), [Alejandro Aguilar](https://cccurj.org/search#Alejandro_Aguilar), [Tania J Ahumada](https://cccurj.org/search#Tania_J_Ahumada), [Noemi Amezcua Moreno](https://cccurj.org/search#Noemi_Amezcua_Moreno), [Jacob Bohn](https://cccurj.org/search#Jacob_Bohn), [Danilo E Bustamante](https://cccurj.org/search#Danilo_E_Bustamante), [Martha S Calderon](https://cccurj.org/search#Martha_S_Calderon), [Edgar Cardoso](https://cccurj.org/search#Edgar_Cardoso), [Rocio Carranza](https://cccurj.org/search#Rocio_Carranza), [Maria Castillo](https://cccurj.org/search#Maria_Castillo), [Elizabeth Cazares](https://cccurj.org/search#Elizabeth_Cazares), [Emmanuel Cazares](https://cccurj.org/search#Emmanuel_Cazares), [Janelle K Companion](https://cccurj.org/search#Janelle_K_Companion), [Jeanette Cruz](https://cccurj.org/search#Jeanette_Cruz), [Neovid Cuevas](https://cccurj.org/search#Neovid_Cuevas), [Lizbeth De La Torre](https://cccurj.org/search#Lizbeth_De_La_Torre), [Daniel P Dietz](https://cccurj.org/search#Daniel_P_Dietz), [Kathleen M Fernando](https://cccurj.org/search#Kathleen_M_Fernando), [Bryan Garcia](https://cccurj.org/search#Bryan_Garcia), [Pamela Gomez](https://cccurj.org/search#Pamela_Gomez), [Bianca Gonzales-Miramontes](https://cccurj.org/search#Bianca_Gonzales-Miramontes), [Yuviana Hernandez](https://cccurj.org/search#Yuviana_Hernandez), [Kayla Huaracha](https://cccurj.org/search#Kayla_Huaracha), [Jeffery R Hughey](https://cccurj.org/search#Jeffery_R_Hughey), [Gabriela Lazaro](https://cccurj.org/search#Gabriela_Lazaro), [Feifei Zhai Lorenzo](https://cccurj.org/search#Feifei_Zhai_Lorenzo), [Diana Medrano](https://cccurj.org/search#Diana_Medrano), [Ailen Mendoza](https://cccurj.org/search#Ailen_Mendoza), [Daniel Mendoza](https://cccurj.org/search#Daniel_Mendoza), [Adam Mohssin](https://cccurj.org/search#Adam_Mohssin), [Jeanette Orozco Medina](https://cccurj.org/search#Jeanette_Orozco_Medina), [Aislinn Pacheco](https://cccurj.org/search#Aislinn_Pacheco), [Gustavo Palacios Ruvalcaba](https://cccurj.org/search#Gustavo_Palacios_Ruvalcaba), [Jankiben Patel](https://cccurj.org/search#Jankiben_Patel), [Jatin Patel](https://cccurj.org/search#Jatin_Patel), [Samantha Patino](https://cccurj.org/search#Samantha_Patino), [Karina Perez-Alfaro](https://cccurj.org/search#Karina_Perez-Alfaro), [Alejandra N Ponce](https://cccurj.org/search#Alejandra_N_Ponce), [Jasmine G Poso](https://cccurj.org/search#Jasmine_G_Poso), [Gabriel Ramirez](https://cccurj.org/search#Gabriel_Ramirez), [Hector A Ramirez](https://cccurj.org/search#Hector_A_Ramirez), [Nathalie Resendiz](https://cccurj.org/search#Nathalie_Resendiz), [Rachelle Reyno](https://cccurj.org/search#Rachelle_Reyno), [Diego Rodriguez](https://cccurj.org/search#Diego_Rodriguez), [Ian A Russell](https://cccurj.org/search#Ian_A_Russell), [Paola Saenz-Verdugo](https://cccurj.org/search#Paola_Saenz-Verdugo), [Angel S Carmona](https://cccurj.org/search#Angel_S_Carmona), [Fabian Sanchez](https://cccurj.org/search#Fabian_Sanchez), [Sabrina X Sheffer](https://cccurj.org/search#Sabrina_X_Sheffer), [Carmen Solorio](https://cccurj.org/search#Carmen_Solorio), [Alejandra Soto Trujillo](https://cccurj.org/search#Alejandra_Soto_Trujillo), [Geraldine S Vasaya](https://cccurj.org/search#Geraldine_S_Vasaya), [Victoria Velasquez Lopez](https://cccurj.org/search#Victoria_Velasquez_Lopez)

Comments: 3 pages. Republished from Mitochondrial DNA Part B 5(3):2067–2069 (2020) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)

Caulacanthus okamurae is an invasive red alga that forms extensive mats in sheltered marine habitats around the world. To determine its genomic structure and genetic relationship to native and other non-native populations of C. okamurae, high-throughput sequencing analysis was performed on an introduced specimen from Bennett Slough, Moss Landing, California, USA. Assembly of 23,146,595 filtered 150 bp paired-end Illumina sequencing reads yielded its complete mitogenome (GenBank accession MT193839) and plastid genome (GenBank accession MT193838). The mitogenome is 25,995 bp in length and contains 50 genes. The plastid genome is 173,516 bp and contains 234 genes. Comparison of the organellar chromosomes to other Gigartinales revealed a high-level of gene synteny. BLAST analysis of marker sequences (rbcL, cox1, cox2) of C. okamurae from Moss Landing identified four identical DNA sequences: one from a specimen from a native population of C. okamurae from South Korea and three from specimens representing invasive populations from France, Spain, and the USA. These genetic results confirm the presence of C. okamurae in central California, USA, and represent the first complete mitogenome and plastid genome from the Caulacanthaceae.

**[\[10\]](https://cccurj.org/list/q-bio/new#item10) [CCCURJ:2610.00005](https://cccurj.org/abs/2610.00005) [[pdf](https://cccurj.org/pdf/2610.00005)]**

[Research note](https://cccurj.org/help/artifacts#research-note) The complete mitogenome of the invasive Japanese mud snail Batillaria attramentaria (Gastropoda: Batillariidae) from Elkhorn Slough, California, USA

[Hartnell College Genomics Group](https://cccurj.org/search#Hartnell_College_Genomics_Group), [Paulina Andrade](https://cccurj.org/search#Paulina_Andrade), [Lisbeth Arreola](https://cccurj.org/search#Lisbeth_Arreola), [Melissa Belnas](https://cccurj.org/search#Melissa_Belnas), [Estefania Bland](https://cccurj.org/search#Estefania_Bland), [Araceli Castillo](https://cccurj.org/search#Araceli_Castillo), [Omar Cisneros](https://cccurj.org/search#Omar_Cisneros), [Valentin Contreras](https://cccurj.org/search#Valentin_Contreras), [Celeste Diaz](https://cccurj.org/search#Celeste_Diaz), [Kevin T Do](https://cccurj.org/search#Kevin_T_Do), [Carlos Donate](https://cccurj.org/search#Carlos_Donate), [Estevan Espinoza](https://cccurj.org/search#Estevan_Espinoza), [Nathan Frater](https://cccurj.org/search#Nathan_Frater), [Garry G Gabriel](https://cccurj.org/search#Garry_G_Gabriel), [Eric A Gomez](https://cccurj.org/search#Eric_A_Gomez), [Gino F Gonzalez](https://cccurj.org/search#Gino_F_Gonzalez), [Myrka Gonzalez](https://cccurj.org/search#Myrka_Gonzalez), [Paola Guido](https://cccurj.org/search#Paola_Guido), [Dylan Guidotti](https://cccurj.org/search#Dylan_Guidotti), [Mishell Guzman Espinoza](https://cccurj.org/search#Mishell_Guzman_Espinoza), [Ivan Haro](https://cccurj.org/search#Ivan_Haro), [Javier Hernandez Lopez](https://cccurj.org/search#Javier_Hernandez_Lopez), [Caden E Hernandez](https://cccurj.org/search#Caden_E_Hernandez), [Karina Hernandez](https://cccurj.org/search#Karina_Hernandez), [Jazmin A Hernandez-Salazar](https://cccurj.org/search#Jazmin_A_Hernandez-Salazar), [Jeffery R Hughey](https://cccurj.org/search#Jeffery_R_Hughey), [Héctor Jácome-Sáenz](https://cccurj.org/search#Héctor_Jácome-Sáenz), [Luis A Jimenez](https://cccurj.org/search#Luis_A_Jimenez), [Eli R Kallison](https://cccurj.org/search#Eli_R_Kallison), [Mylisa S King](https://cccurj.org/search#Mylisa_S_King), [Luis J Lazaro](https://cccurj.org/search#Luis_J_Lazaro), [Feifei Zhai Lorenzo](https://cccurj.org/search#Feifei_Zhai_Lorenzo), [Isaac Madrigal](https://cccurj.org/search#Isaac_Madrigal), [Savannah Madruga](https://cccurj.org/search#Savannah_Madruga), [Adrian J Maldonado](https://cccurj.org/search#Adrian_J_Maldonado), [Alexander M Medina](https://cccurj.org/search#Alexander_M_Medina), [Marcela Mendez-Molina](https://cccurj.org/search#Marcela_Mendez-Molina), [Ali Mendez](https://cccurj.org/search#Ali_Mendez), [David Murillo Martinez](https://cccurj.org/search#David_Murillo_Martinez), [David Orozco](https://cccurj.org/search#David_Orozco), [Juan Orozco](https://cccurj.org/search#Juan_Orozco), [Ulises Ortiz](https://cccurj.org/search#Ulises_Ortiz), [Jennifer M Pantoja](https://cccurj.org/search#Jennifer_M_Pantoja), [Alejandra N Ponce](https://cccurj.org/search#Alejandra_N_Ponce), [Angel R Ramirez](https://cccurj.org/search#Angel_R_Ramirez), [Israel Rangel](https://cccurj.org/search#Israel_Rangel), [Eliza Rojas](https://cccurj.org/search#Eliza_Rojas), [Adriana Roque](https://cccurj.org/search#Adriana_Roque), [Beatriz Rosas](https://cccurj.org/search#Beatriz_Rosas), [Colt Rubbo](https://cccurj.org/search#Colt_Rubbo), [Justin A Saldana](https://cccurj.org/search#Justin_A_Saldana), [Elian Sanchez](https://cccurj.org/search#Elian_Sanchez), [Alicia Steinhardt](https://cccurj.org/search#Alicia_Steinhardt), [Maria O Taveras Dina](https://cccurj.org/search#Maria_O_Taveras_Dina), [Judith Torres](https://cccurj.org/search#Judith_Torres), [Silvestre Valdez-Mata](https://cccurj.org/search#Silvestre_Valdez-Mata), [Valeria Vargas](https://cccurj.org/search#Valeria_Vargas), [Paola Vazquez](https://cccurj.org/search#Paola_Vazquez), [Michelle M Vazquez](https://cccurj.org/search#Michelle_M_Vazquez), [Irene Vidales](https://cccurj.org/search#Irene_Vidales), [Frances L Wong](https://cccurj.org/search#Frances_L_Wong), [Christian S Zagal](https://cccurj.org/search#Christian_S_Zagal), [Santiago Zamora](https://cccurj.org/search#Santiago_Zamora), [Jesus Zepeda Amador](https://cccurj.org/search#Jesus_Zepeda_Amador)

Comments: 2 pages. Republished from Mitochondrial DNA Part B 4(2):4031–4032 (2019) under CC BY 4.0; not submitted to CCCURJ

Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)

Genomic analysis of the invasive marine snail Batillaria attramentaria from Elkhorn Slough, Moss Landing, California, USA using 150 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,095 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank Accession MN557850). Gene content and organization of B. attramentaria are identical to the Turritellidae and Pachychilidae. The phylogenetic analysis of B. attramentaria resolves it in a fully supported clade with these same two families in the superfamily Cerithioidea. Nucleotide BLAST searches of the Elkhorn Slough cox1 gene of B. attramentaria yielded identical sequences from invasive populations from California and British Columbia, and native populations from northeastern and central Japan. These data show that mitogenome sequencing is a useful tool for studying the classification and phylogenetic history Cerithioidea.

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